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- PDB-7koz: CD1a-36:2 SM binary complex -

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Basic information

Entry
Database: PDB / ID: 7koz
TitleCD1a-36:2 SM binary complex
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • T-cell surface glycoprotein CD1a
KeywordsIMMUNE SYSTEM / CD1 / antigen presentation / lipid
Function / homology
Function and homology information


endogenous lipid antigen binding / exogenous lipid antigen binding / antigen processing and presentation, endogenous lipid antigen via MHC class Ib / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / lipopeptide binding / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / Nef mediated downregulation of MHC class I complex cell surface expression ...endogenous lipid antigen binding / exogenous lipid antigen binding / antigen processing and presentation, endogenous lipid antigen via MHC class Ib / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / lipopeptide binding / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / positive regulation of protein binding / ER-Phagosome pathway / iron ion transport / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / adaptive immune response / learning or memory / endosome membrane / immune response / membrane raft / Amyloid fiber formation / lysosomal membrane / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane / cytosol
Similarity search - Function
MHC-I family domain / Beta-2-Microglobulin / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...MHC-I family domain / Beta-2-Microglobulin / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Chem-WU7 / T-cell surface glycoprotein CD1a / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsWegrecki, M. / Le Nours, J. / Rossjohn, J.
CitationJournal: J.Exp.Med. / Year: 2021
Title: CD1a selectively captures endogenous cellular lipids that broadly block T cell response.
Authors: Cotton, R.N. / Wegrecki, M. / Cheng, T.Y. / Chen, Y.L. / Veerapen, N. / Le Nours, J. / Orgill, D.P. / Pomahac, B. / Talbot, S.G. / Willis, R. / Altman, J.D. / de Jong, A. / Van Rhijn, I. / ...Authors: Cotton, R.N. / Wegrecki, M. / Cheng, T.Y. / Chen, Y.L. / Veerapen, N. / Le Nours, J. / Orgill, D.P. / Pomahac, B. / Talbot, S.G. / Willis, R. / Altman, J.D. / de Jong, A. / Van Rhijn, I. / Clark, R.A. / Besra, G.S. / Ogg, G. / Rossjohn, J. / Moody, D.B.
History
DepositionNov 10, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: T-cell surface glycoprotein CD1a
B: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0948
Polymers44,8942
Non-polymers1,2006
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint8 kcal/mol
Surface area19420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.188, 90.034, 105.083
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein T-cell surface glycoprotein CD1a / T-cell surface antigen T6/Leu-6 / hTa1 thymocyte antigen


Mass: 32464.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD1A / Production host: Homo sapiens (human) / References: UniProt: P06126
#2: Protein Beta-2-microglobulin / Beta-2 microglobulin


Mass: 12429.966 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Homo sapiens (human) / References: UniProt: P61769

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Sugars , 1 types, 1 molecules

#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 93 molecules

#3: Chemical ChemComp-WU7 / (4S,7S,17Z)-4-hydroxy-7-[(1S,2E)-1-hydroxyhexadec-2-en-1-yl]-N,N,N-trimethyl-4,9-dioxo-3,5-dioxa-8-aza-4lambda~5~-phosphahexacos-17-en-1-aminium / N-oleoylsphingosine-1-phosphocholine / C18:1 Sphingomyelin


Mass: 730.073 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H82N2O6P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20-25% PEG 1500, 0.1M MMT pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.25→45.38 Å / Num. obs: 19734 / % possible obs: 100 % / Redundancy: 13.1 % / Biso Wilson estimate: 38.47 Å2 / CC1/2: 0.998 / Net I/σ(I): 12.4
Reflection shellResolution: 2.25→2.32 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 1771 / CC1/2: 0.78

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NUX

6nux


Resolution: 2.25→45.38 Å / SU ML: 0.272 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.1258
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2465 930 4.73 %
Rwork0.21 18744 -
obs0.2118 19674 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.69 Å2
Refinement stepCycle: LAST / Resolution: 2.25→45.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3061 0 80 88 3229
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00223232
X-RAY DIFFRACTIONf_angle_d0.89434379
X-RAY DIFFRACTIONf_chiral_restr0.102451
X-RAY DIFFRACTIONf_plane_restr0.0035559
X-RAY DIFFRACTIONf_dihedral_angle_d18.89921167
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.370.30141220.27782627X-RAY DIFFRACTION99.89
2.37-2.520.28231500.26632603X-RAY DIFFRACTION99.96
2.52-2.710.32481280.24532630X-RAY DIFFRACTION99.93
2.71-2.980.25121370.23022660X-RAY DIFFRACTION100
2.98-3.420.23121260.20442670X-RAY DIFFRACTION100
3.42-4.30.22091100.18332732X-RAY DIFFRACTION100
4.3-45.380.23481570.19682822X-RAY DIFFRACTION99.97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.93642500588-1.073197068832.784337741253.48235034642-0.4313328743147.750229231730.3294493578780.360021934548-0.933266123751-0.674855212643-0.03539623183940.2712806389090.56458379474-1.23732629984-0.3422941330670.363853508827-0.04405830573730.02666931982410.667840925389-0.1604763017740.57442117280518.884654754830.394511582836.4556073263
24.742018088560.0451244591620.0843249878463.952454471860.2431257233467.077823024840.1820200000520.686141884316-0.508368996517-0.522808822124-0.0684820990485-0.1466018537910.454162341157-0.0787411740037-0.1194916571290.3722078509890.009102140315380.05395059067710.390493883355-0.1451766414690.44584415799233.128030677530.393163212433.3027028125
35.38203933791-0.07944109035630.2837358588155.174413003810.5847990786164.077209577790.06995874439830.005744056444330.5281720268810.05959541899520.0148400338525-0.104816742775-0.0571343098954-0.0669265166421-0.09192340442170.1298632356790.004747052922640.02961261240950.1774906954620.03781687274280.2792073556179.4900970579261.443024344349.0625544833
42.00372012832-6.07494825439-2.04115472268.548302024050.3403010673885.738978404090.0357324473136-0.05372233574010.253039599129-0.1804820738790.140350591659-0.9170105132640.02494003917431.06890875692-0.1503973011940.367670061391-0.0706626030745-0.05069048042930.426168682025-0.08002299770170.37031341064821.452851528544.172891099655.3361482897
52.00794457947.26990952234-8.030725914938.95126899043-8.291487202852.00637095473-0.1736979110960.5937781313040.8737736710440.7912412150490.3882877171721.56680172378-0.445257895919-1.46361491201-0.1828345391620.3152951629150.07234896600450.0742107690110.5145708713380.01467460900680.440089424616-2.3996444376650.633726630853.8725330348
68.06741835935-3.1437893241-0.8917505944613.69976525597-0.01864076902613.134571114980.115068675579-0.123131608604-0.08852521583850.2641768912910.1115910086880.1737299693880.2632219458140.208952538909-0.2496519291760.2793311152250.0194295768014-0.05339606090450.200206588338-0.05778538285080.25048973800311.717897909243.450765484152.4686723247
71.99786749943-7.931899238881.975167837935.422422101024.156185913197.00423745938-0.942329497413-1.323645247-2.027906234660.9220420028450.5249737890430.3885236819350.7711567560950.548319113370.5553895779050.4556931096680.0296446925223-0.02080635464720.1994488010110.0491025045460.41666559551617.274187300535.455906510557.3772629741
82.00146957564-3.790750285141.353043951272.000126872226.827551939572.00403152438-0.955749443452-0.975191596-1.829543058141.76398355145-0.1054541048181.023915524282.1508798109-0.6916269574431.029642458850.701673454381-0.02552944408520.2074439143640.5566948380260.01122387066060.6489835955944.9940485185435.950778401864.285756478
92.001595279698.94430589132.000051507072.00209852158-6.997118147912.00167654811-0.3764536351630.232716901903-1.22348050572-0.5416565716920.76951458871.172897857531.91252097915-1.96708928936-0.3972886716720.556707156337-0.0883448345836-0.05415111834460.4276787796360.1863311537430.6801571200686.8396891575233.279787791352.5845658336
102.02871947556-0.648290906123-4.491714850852.509841734730.3186919036163.33991759945-0.2840177762370.283637025943-0.5105264198470.09758407325710.2340972202030.0985336768550.178664110529-0.09944976417630.05952163921690.296582366210.00179876942626-0.006163111479090.26251358904-0.0148487854120.30326780881516.667882738439.696864339748.1943280386
112.001032866024.589676731370.3306273240792.003206376071.549700527192.00312327677-0.056366388805-2.40539521659-0.08417920751431.53321019137-0.4821957008421.38134355409-0.988628295795-2.275965314640.5444295539490.6977842727950.05116258705060.08766804718750.990101183352-0.04864573207490.720540905933-1.6538530343646.158528189365.1323831265
127.92723346842-5.96801474313-0.1236259846957.31985505112-0.3588928860823.76408641398-0.531949761658-2.16892051348-0.4247573929361.403384696370.780061161581-0.3237631926740.2485755867270.310219152817-0.2286023363410.6227873386430.0229204385132-0.1211279790560.5802813767060.0872216159580.35494455599817.960616929739.838161714663.2426349877
136.78389905956-6.46093643149-6.610231260386.167187427596.29838581966.437155713780.372410220053-0.6977157147150.4975253818840.680953134707-0.343050478830.575638502934-0.612700936957-0.436834353181-0.04556843774550.761757416886-0.1421997235670.2130523148330.65459121855-0.2205758416760.69836448891.4358504216455.94370221565.3019618002
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 59 )
2X-RAY DIFFRACTION2chain 'A' and (resid 60 through 174 )
3X-RAY DIFFRACTION3chain 'A' and (resid 175 through 285 )
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 12 )
5X-RAY DIFFRACTION5chain 'B' and (resid 13 through 20 )
6X-RAY DIFFRACTION6chain 'B' and (resid 21 through 31 )
7X-RAY DIFFRACTION7chain 'B' and (resid 32 through 42 )
8X-RAY DIFFRACTION8chain 'B' and (resid 43 through 47 )
9X-RAY DIFFRACTION9chain 'B' and (resid 48 through 52 )
10X-RAY DIFFRACTION10chain 'B' and (resid 53 through 72 )
11X-RAY DIFFRACTION11chain 'B' and (resid 73 through 78 )
12X-RAY DIFFRACTION12chain 'B' and (resid 79 through 95 )
13X-RAY DIFFRACTION13chain 'B' and (resid 96 through 105 )

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