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* Cancer Research UK Receptor Structure Group, The Division of Structural Biology, and
Cancer Research UK Tumor Immunology Group, The Weatherall Institute of Molecular Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom;
Department of Rheumatology and Clinical Immunology, University of Berne, Berne, Switzerland;
School of Biosciences, The University of Birmingham, Birmingham, United Kingdom; and
¶ Medical Research Council Laboratory of Molecular Biology, Medical Research Council Centre, Cambridge, United Kingdom
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Abstract |
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 Top Abstract IntroductionMaterials and MethodsResultsDiscussionReferences |
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Introduction |
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TopAbstractIntroductionMaterials and MethodsResultsDiscussionReferences |
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Binding studies and structural studies have led to the definition of a general molecular mechanism for lipid Ag presentation by CD1 molecules. The crystal structure of mouse (m)CD1d1 suggested that CD1 molecules accommodate hydrophobic acyl chains in a hydrophobic binding groove (2). Functional studies supporting this view were conducted using a series of analogues of glucose monomycolate (GMM)5 presented by CD1b molecules varying in glycosylation, hydroxylation, and lipid length (3, 4). The combination of these structural and functional studies suggested that the alkyl components of the Ags bind within a hydrophobic groove in the CD1 protein, the hydrophilic glycan moiety protrudes from the binding groove, making contacts with the TCR (5).
This model for lipid Ag presentation has been recently confirmed by the crystal structures of human CD1b (6) and CD1a (7) in complex with specific glycolipids. In addition, the structure of CD1b suggested that, unlike other CD1 molecules, this molecule has a unique binding groove architecture characterized by a series of channels capable of accommodating a very broad range of acyl chain length.
Refolding of denatured CD1b molecules in the presence of ganglioside GM2 and phosphatidylinositol (PI) was obtained using a protocol based on the inclusion of single acyl chain detergents in the refolding to prevent CD1b precipitation (6). The three-dimensional structure of CD1b molecules refolded using this protocol showed the presence of detergent moieties occupying the channels that were not filled by the lipid ligands. To test the hypothesis that longer acyl chain lipids (such as mycolates and GMM) occupy the full set of interlinked channels, the crystal structure of CD1b-GMM complex, refolded in the absence of detergent, was determined.
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Materials and Methods |
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TopAbstractIntroductionMaterials and MethodsResultsDiscussionReferences |
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The extracellular 
1-3 domains of human CD1b (residues 1–283) and 
2-microglobulin (2m) were synthesized separately using a prokaryotic expression system (pET; Novagen, Madison, WI) (6). Both recombinant proteins were purified from Escherichia coli inclusion bodies and solubilized in 6 M guanidine-HCl solution containing 10 mM DTT. GMM was purified from Nocardia farcinica as previously described (8), solubilized at 200 µg/ml in 150 mM NaCl and 0.5% Tween 20 solution, and sonicated. CD1b and 2m proteins were refolded with the GMM by oxidative refolding chromatography using a protocol previously described (9, 10). The concentrated refolding mix was purified by size-exclusion chromatography using a HiLoad 26/60 Superdex-75 (Amersham Pharmacia, Piscataway, NJ). Crystallization conditions were screened using purified monomeric CD1b-GMM glycolipid complexes (7.5 mg/ml in 20 mM Tris-Cl (pH 6.5), 25 mM NaCl, and 2 mM EDTA). Nanoliter-scale crystallization experiments were set up using a Cartesian Technologies Microsys MIC4000 (Genomic Technologies, Huntingdon, U.K.) (11, 12). Conditions yielding crystals in nanoliter-scale sitting drops (100 nl of protein plus 100 nl of reservoir solution) were subsequently scaled up and optimized by hand pipetting. Optimally diffracting crystals were grown at 20°C from 2-µl sitting drops, using a 1:1 protein to precipitant (100 mM Na citrate (pH 5.6), 0.20–1.25 M ammonium sulfate, and 0.20–0.75 M Li2SO4) ratio and 5–15 mM urea as an additive in the drops.
Structure determination and analysis
Crystals were flash frozen at 100 K in mother liquor containing 20–25% glycerol. X-ray diffraction data were collected at beam lines 14.2 (Synchrotron Radiation Source (SRS), Daresbury, U.K.) and ID-14 EH4 (European Synchrotron Radiation Facility (ESRF), Grenoble, France) with 0.98- and 1.01-Å radiation, respectively, recorded on Area Detector Systems Corporation (Poway, CA) Quantum 4 charge-coupled device detectors. The data were processed using DENZO, SCALEPACK (13), and TRUNCATE (CCP4 suite). Processing statistics are given in Table I. The crystals belong to spacegroup P3121 with diffraction to 3.8 Å at SRS 14.2 (with unit cell dimensions, a = b = 97.5 Å, c = 115.2 Å) and to 3.1 Å at ID-14 EH4 (with unit cell dimensions, a = b = 97.0 Å, c = 114.8 Å). The crystallographic asymmetric unit contains one molecule of CD1b-GMM with a solvent content of 67%.
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An initial Fo-Fc map was calculated using the molecular replacement solution (unliganded) after rigid-body, positional, and B-factor refinement. At a contour level of 2.0 
, tubular electron density was clearly visible in the A', T', F', and C' channels. The density spanning A'-T'-F' was continuous with the exception of missing density at three points in the T' channel giving gaps of 
0.5, 2.3, and 2.5 Å. Density was also visible for some hydroxyl groups of the sugar head group.
Between each further refinement round, the model was manually checked and glycolipid atoms built in using O (16), with reference to 2Fo-Fc and Fo-Fc electron density maps generated using phase information calculated from the models. Glycolipid parameter and topology files for CNS were generated using PRODRG (17). Water molecules were automatically picked using CNS and manually verified. Protein stereochemistry was validated using PROCHECK (18). Statistics for the refined structure are shown in Table I.
Atomic interactions between glycolipid and protein were calculated using LIGPLOT (19). Volume calculations for cavities within the protein were calculated using VOLUMES (R. M. Esnouf, unpublished program). Variant glycolipids were modeled into the CD1b binding groove and energy minimized in CNS. The CD1b-GMM specific TCR, LDN5 (3), was built using sequence information from the IMGT database (20) and modeled using SWISS-MODEL (21). Superimposition of coordinates for comparative analyses was conducted using SHP (22). Sequence alignments were performed using the MULTALIN web interface (23), and the output was formatted using ESPRIPT (24). Hydrophobicity calculations were performed via the PROTSCALE web interface (25) using the Eisenberg method (26). Figures were produced using BOBSCRIPT (27) and RASTER3D (28).
Mass-spectrometric analysis of GMM
GMM extracted from N. farcinica was analyzed by mass spectrometry as previously described (29). The mass of the GMM bound in the CD1b-GMM crystal structure was analyzed using the following protocols. Drops containing crystals were removed by pipette from crystallization trays and dissolved in 6 M guanidium-HCl to denature the protein and dislodge the GMM from the CD1b binding groove. This treatment also cleaved off the sugar group in the GMM to afford free mycolic acids. Separation of mycolic acids from the protein was conducted by organic extraction using chloroform/methanol. The organic phase containing the liberated mycolic acid was dried under a nitrogen stream, and the resulting pellet was dissolved in chloroform/methanol. This sample was analyzed by electrospray mass spectroscopy. Measurements were conducted in positive-ion mode and performed on a triple quadrupole LCT instrument (Micromass, Altrincham, U.K.) fitted with an atmospheric pressure electrospray source. Samples were directly injected (10 µl) using a Rheodyne injector (Rheodyne, Bensheim, Germany) with methanol as the mobile phase. The machine was run at a flow rate of 200 µl/min with the cone voltage at 35 V and the spraying needle voltage set at 3 kV. The scan rate was 1 s for the mass range from 200 to 2000 Da.
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Results |
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TopAbstractIntroductionMaterials and MethodsResultsDiscussionReferences |
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The structure of CD1b-GMM was determined by molecular replacement (see Materials and Methods) and refined at 3.1-Å resolution (Table I). The final model contains CD1b residues 3–282 (extracellular 1-3 domains), 2m residues 1–100, and one GMM molecule (Fig. 1, A and B).
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3 domain with respect to the 12 domain differs by 5.5° between the CD1b-GMM and CD1b-PI structures. This hinge-like effect results from a conformational flexibility of the linker region (between the 2 and 3 domains) centered on residues 175–184 (Fig. 1A). A similar point of flexion has been noted between the 12 and 3 domains of classical MHC class I molecules (30). The electron density for the glycolipid
The Ag-binding groove of CD1b is a network of hydrophobic channels in the core of the 12 domain (Fig. 1C). Three channels, denoted as A', C', and F', connect directly to the surface, and a fourth channel, the tunnel T', runs through the core below the 1 and 2 helices. A', T', and F' are sequentially connected, whereas C' also connects to T' and leads from the TCR recognition surface to a portal in the side of the molecule beneath the 2 helix (Fig. 1A) (6).
Electron density maps calculated using phase information from the final model show clear density for GMM. At a level of 2.5 on a simulated annealing Fo-Fc omit map calculated after omitting the GMM, the density is continuous for the sugar head group, -chain, and meromycolate chain (Fig. 1B). The meromycolate chain completely occupies the A', T', and F' channels, and protrudes out of the F' channel into the TCR recognition surface. Additional, weaker electron density is visible extending beyond the TCR binding surface to the same height as the sugar head group of the GMM. This suggests the presence of a longer meromycolate chain bound at a partial occupancy; however, this minor species is not included in the final model (see next section).
The -chain occupies the C' channel and stops well short of the portal. There was no electron density visible at any stage of model building beyond what is seen in the final model. The electron density for the protein shows the C' channel portal in an open state.
Mass-spectrometric analysis of GMM
GMM purified from the bacterium N. farcinica comprises a range of species with molecular mass spanning from 930.0 to 1040.1 Da (C50-GMM-C58-GMM; Fig. 1E). Recovery of GMM from CD1b-GMM crystals using organic solvents proved unsuccessful. However, under basic denaturation conditions as revealed by mass spectrometry, four peaks could be accounted for as free mycolic acids liberated from bound GMM species in the CD1b-GMM crystals (Fig. 1F). These correspond to mycolic acids containing a total of 51, 53, 55, or 57 carbon atoms in the meromycolate chain plus the -chain (denoted as C54, C56, C58, and C60, respectively) counting the total number of carbons up to the ester group bridging the glucose moiety, i.e., including the , , and carboxylate atoms.
The refined structure for CD1b-GMM contains the largest of the GMM species detected, with 8 carbon atoms in the -chain and 49 carbons atoms in the meromycolate chain (i.e., the C60 species; Fig. 1D). As described above, weaker electron density seen protruding further out of the F' channel could possibly be due to an even larger species of GMM bound at low occupancy. Atoms were not modeled into this density because the presence of such species was not confirmed by mass spectrometry and the x-ray data were of limited resolution. The mass spectrum of the lipid sample directly after extraction from N. farcinica shows the predominant species to be a C54-GMM (Fig. 1E), whereas the C58-GMM is the predominant species in the crystallization drops (F). This would suggest that the process of refolding has enriched the fraction of CD1b-GMM complexes containing larger-species GMM.
Comparison with CD1b-PI/GM2 structures
The CD1b-GMM structure was compared with the CD1b-PI/GM2 structures to analyze binding groove architectures, glycolipid positions, and protein-glycolipid interactions. In both the CD1b-PI and GM2 structures, the relatively short lipid acyl chains occupy the C' and A' channels, whereas the F' and T' channels are occupied by detergent molecules (6). An analysis of the CD1b-PI and GM2 structures when combined with the mutagenesis analysis by Niazi et al. (31) on residues affecting glycolipid Ag presentation led to the hypothesis that the meromycolate chain of a GMM ligand would occupy the network of A', T', and F' channels (6). The current structural analysis confirms that the meromycolate chain of GMM is bound in the CD1b groove traversing from the A' (via T') to the F' channel, whereas the -chain occupies the C' channel.
Comparison of side-chain conformations between the CD1b-GMM and CD1b-PI structures generally reveals relatively minor conformational changes for residues lining the channels (root-mean-square deviation (RMSD) values of <0.50 Å between equivalent side-chain atoms). However, side-chain conformations for the residues lining the connecting regions between the F'-T' channels and for residues at the bottom of the A' channel are significantly different in the two structures (RMSD values of 0.50–1.50 Å).
The volume in the channel around each acyl carbon atom was calculated for the CD1b-glycolipid structures (effectively sectioning the channel using atom coordinates as grid points). In terms of volume (Fig. 2), the most significant differences between CD1b-GMM and CD1b-PI/GM2 are in the connecting regions between the A'-T' and T'-F' channels (i.e., corresponding to the regions with high RMSD for the comparison of side chains) (Fig. 2, A and B). The connecting regions between these channels are curved or bent, with A'-T' taking a hairpin shape. The differences in channel volume can be attributed to the fact that, in the CD1b-GMM structure, the acyl chain is continuous and tracks smoothly around the curve, whereas in CD1b-PI/GM2, the acyl chain termini and detergent termini occupy these regions and point into the outer wall of the bend. Residues forming the wall of the channels have altered conformations to accommodate these termini. The key role of the residues at the A'-T' junction in presenting long acyl chain ligands has been previously highlighted by mutagenesis data (31).
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Mycobacterial mycolic acids that bear substitutions along the meromycolate chain have been identified (Fig. 3) (32). These substitutions can be cyclopropyl, methyl, methoxy, or keto groups, and occur at variable positions on the chain. To investigate how CD1b could accommodate such structures, the CD1b-GMM crystal structure was used as a template for the modeling of these lipids into the binding groove. Lipids were inserted into the binding groove, and the complexes were energy minimized with the protein backbone harmonically restrained. The substituent groups in the resultant models were positioned at a wide range of points in the A' channel, A'-T' junction, or T' tunnel. Two representative examples are illustrated in Fig. 3. Analysis of the model structures revealed no stereochemical clashes. The CD1b binding groove is capable of accommodating these groups with only minor changes to side-chain conformations (for example, Fig. 3). Volume calculations on the channels reveal that there is no significant change in the total volume of the binding groove; however, volume calculations along sections of the binding groove show that there are local changes in volume. The substituent groups are accommodated by slight increases (typically 5–10%) in the channel volume at these points. Because these increases are achieved by changes in side-chain conformations, they tend to be counterbalanced by subtle decreases in volume extending through neighboring regions. These model-based results imply a degree of flexibility in the CD1b binding groove, consistent with this molecule’s ability to bind lipids containing substituent groups at a wide range of positions. The current structural data provide no evidence of any mechanism whereby differences in such substituent groups could influence TCR recognition as reported by Grant et al. (33).
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In an attempt to generate additional insights into the similarities and differences in the binding groove architectures of the CD1 molecules, the sequences of CD1a, CD1b, CD1c, CD1d, and mCD1d1 were analyzed in terms of hydrophobicity (Fig. 4A). The analysis reveals a particularly complex pattern of hydrophobicity in CD1b, and in Fig. 4B, specific regions/patches of hydrophobicity are related to distinct structural features in the binding groove. Of the other family members, CD1c shows the most similarity to CD1b in the hydrophobicity analysis. However, certain features (e.g., patch 7; Fig. 4) that map to the T' channel are unique to CD1b. It has previously been predicted that the substitution of G98 by a valine in CD1a and CD1c would abolish the continuous T' tunnel (Fig. 4E) (6). This has now been confirmed for CD1a by the determination of its crystal structure in complex with sulfatide (7). The CD1a structure also reinforces the conclusion that the A' region is the section of the binding groove that shows most similarity between group 1 family members. The presence of CD1b-like A' channel and A'-T' junction in the CD1a binding groove can be related to the conservation of hydrophobic patches 1, 4, 13, and 14 (Fig. 4). Because CD1c exhibits a similar pattern in its primary structure, it is likely that it too has a CD1b-like A' channel. This conservation of A' structure is consistent with the shared ability of CD1a, CD1b, and CD1c to bind sulfatide (34); however, Zajonc et al. (7) note that variations in the detailed architecture in this region are important in modulating the ligand-binding characteristics of CD1a vs the other CD1s.
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Lipid head group positions and TCR recognition
To gain insight into how TCRs bind to the CD1b-GMM complex, CD1b-GMM and a model of a cognate TCR, LDN5 (Ref. 3 and Materials and Methods), were superimposed onto all available crystal structures of MHC-TCR complexes. Due to the elevated position of the glycolipid head group of GMM and the structure of the 2 helix (which at its midpoint forms a more prominent apex, unlike that of the 2 helix in MHC class I or II molecules; Fig. 1A), there are steric clashes with the backbone of the TCR in all resultant model complexes. Detailed conclusions must therefore await the structure determination of a CD1-TCR complex. However, these docking experiments imply that the complementarity-determining region 3 loops of a TCR would sample parts of the lipid.
In addition to the structure of the glycolipid head group, its position is likely to be an important determinant for recognition by TCR. Site-directed mutagenesis experiments have identified several residues in CD1b that appear to be required for TCR recognition (35). These residues fall into two groups in the context of the structure, the first group being R79, E80, and D83 on the 1 helix, and the second group being T165 and T157 on the 2 helix (35) (Fig. 5A). Both groups of residues may contribute to TCR recognition directly by making contacts with the complementarity-determining region loops of the TCR; however, they may also contribute by stabilizing a specific orientation of the glycolipid head group by hydrogen bonding. Indeed the CD1b-GM2, PI, and GMM crystal structures show that residues from both clusters (specifically R79 and T157) can make hydrogen bonds to the glycolipid headgroups (6) (Fig. 5, B–D). Mutagenesis of other CD1b residues affects Ag-presenting function to a lesser degree (35), and in the crystal structures, these do not make any direct interactions with the glycolipid (Fig. 5A). In common with the CD1a structure (7), the CD1b-GMM structure reveals a portion of acyl tail protruding from the F' pocket. This is an additional component of the glycolipid that may potentially contribute to TCR recognition.
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Discussion |
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TopAbstractIntroductionMaterials and MethodsResultsDiscussionReferences |
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-chain of 8 carbons only partially occupies the C' channel in CD1b-GMM. The previously reported structure for CD1b-PI indicates that a GMM with a longer -chain will extend further into this channel (6). The full capacity of this channel is 16 carbon atoms; any additional -chain carbon atoms may exit the binding groove via the portal under the 2 helix. The crystal structure of CD1b-GMM provides the first detailed information on the presentation of a natural bacterial glycolipid Ag. Recent functional studies have confirmed the ability of CD1b molecules to present full-length GMM to T cells (T.-Y. Cheng and B. Moody, unpublished data). Further insights into T cell recognition of CD1b-glycolipid complexes await the determination of CD1b-glycolipid-TCR complex structures.
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Acknowledgments |
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Footnotes |
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2 The atomic coordinates of the CD1b-GMM structure have been deposited in the Protein Data Bank (http://www.rcsb.org; PDB ID code 1UQS).
3 T.B. and D.S. contributed equally to this work.
4 Address correspondence and reprint requests to Dr. Vincenzo Cerundolo, Cancer Research UK Tumor Immunology Group, The Weatherall Institute of Molecular Medicine, Nuffield Department of Medicine, University of Oxford, Oxford OX3 9DS, U.K. E-mail address: vincenzo.cerundolo{at}imm.ox.ac.uk; or Dr. E. Yvonne Jones, Cancer Research UK Receptor Structure Group, The Division of Structural Biology, The Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Headington, Oxford OX3 7BN, U.K. E-mail address: yvonne{at}strubi.ox.ac.uk
5 Abbreviations used in this paper: GMM, glucose monomycolate; PI, phosphatidylinositol; 2m, 2-microglobulin; RMSD, root-mean-square deviation; m, mouse.
Received for publication September 5, 2003. Accepted for publication November 25, 2003.
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References |
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TopAbstractIntroductionMaterials and MethodsResultsDiscussionReferences |
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