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- PDB-7kp0: CD1a-42:1 SM binary complex -

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Basic information

Entry
Database: PDB / ID: 7kp0
TitleCD1a-42:1 SM binary complex
Components
  • Beta-2-microglobulin
  • T-cell surface glycoprotein CD1a
KeywordsIMMUNE SYSTEM / CD1 / antigen presentation / lipid
Function / homology
Function and homology information


exogenous lipid antigen binding / antigen processing and presentation, endogenous lipid antigen via MHC class Ib / lipopeptide binding / endogenous lipid antigen binding / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport ...exogenous lipid antigen binding / antigen processing and presentation, endogenous lipid antigen via MHC class Ib / lipopeptide binding / endogenous lipid antigen binding / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / adaptive immune response / intracellular iron ion homeostasis / learning or memory / endosome membrane / immune response / membrane raft / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / lysosomal membrane / external side of plasma membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / 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 ...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-WUA / T-cell surface glycoprotein CD1a / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)45,8355
Polymers44,8942
Non-polymers9403
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-1 kcal/mol
Surface area19830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.469, 90.918, 107.351
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

#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


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
#3: Chemical ChemComp-WUA / (4R,7S)-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~-phosphadotriacontan-1-aminium / N-lignoceroylsphingosine-1-phosphocholine / C24 Sphingomyelin


Mass: 816.249 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C47H96N2O6P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.31 Å3/Da / Density % sol: 46.71 %
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: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.4→46.22 Å / Num. obs: 16921 / % possible obs: 99.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 40.87 Å2 / CC1/2: 0.998 / Net I/σ(I): 13.2
Reflection shellResolution: 2.4→2.49 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1749 / CC1/2: 0.731

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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: 2.4→41.86 Å / SU ML: 0.3024 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.7866
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2644 893 5.29 %
Rwork0.1897 15973 -
obs0.1937 16866 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.17 Å2
Refinement stepCycle: LAST / Resolution: 2.4→41.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3062 0 64 116 3242
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00743226
X-RAY DIFFRACTIONf_angle_d0.98314373
X-RAY DIFFRACTIONf_chiral_restr0.0569447
X-RAY DIFFRACTIONf_plane_restr0.0053558
X-RAY DIFFRACTIONf_dihedral_angle_d18.89461168
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.550.34051570.26312575X-RAY DIFFRACTION99.49
2.55-2.750.30991410.23692623X-RAY DIFFRACTION99.68
2.75-3.020.2771420.22862632X-RAY DIFFRACTION99.78
3.02-3.460.26281520.20142634X-RAY DIFFRACTION99.82
3.46-4.360.27531450.16472688X-RAY DIFFRACTION99.89
4.36-41.860.22471560.1652821X-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)
16.62092130341-1.777328808520.4007537655083.99339723327-1.996759335097.39197166006-0.03001007930460.0442453323683-0.717821156207-0.4620195414610.146969469464-0.1716693151880.739083671396-1.18305047614-0.3110033654670.414895145727-0.148815187351-0.005237898943610.513592746099-0.08107780187890.5743895459219.070463119332.146675230336.8640248837
26.28718764537-2.520070537672.056299372883.00371469957-2.66663134292.329555703210.1187109172520.751046167166-1.61042387952-0.386660509972-0.4959418597270.6023402717450.853030041244-0.06143426302250.1669651322891.39501668366-0.2743006724640.2558824498090.862720596206-0.3872370252961.465839214525.374722387822.837899832331.7435299603
36.915438141690.346017068324-1.233176259853.428176353570.6741744574664.51372607592-0.2803471664540.462040485106-0.559656156255-0.219484561420.0306145834786-0.5579908802310.3840913577340.7942322333090.1366371560390.405050637481-0.01929388904440.1064240083980.386891982063-0.1324543333760.55553339695437.653222401432.406778398336.2379789122
42.81710779966-0.5633173762780.2317402127862.172117251210.06962852283962.577173779710.01155853372350.2419757112060.371185293534-0.01189742840720.02559640936070.004057112248060.114797938226-0.0016282246795-0.01066557722890.152032050017-0.007021033372460.0263651572080.2650058711190.07204594175250.33984523667310.649110050460.078643339447.4696072079
54.21562679316-2.02870229383-0.8195774377663.683833526290.5759522845653.187623421980.07364569141350.11437042998-0.0185837031035-0.07677550256010.03806140091650.01338583027080.09481982738410.0475588213069-0.07760861447880.217870896643-0.0102538337434-0.03121164557380.157561467431-0.01043697597740.24917541301411.881284759145.957518892754.6042174896
63.35509667049-0.859697636384-4.330645403284.615956185112.307498701626.33217588011-0.346456077425-0.619400694254-0.7771229422220.4111528441650.05225153403440.1612460397710.660103194987-0.1720978826630.3646657205330.4291668033940.0259589965245-0.006648537109470.3406276496970.07417978546010.3650073820511.753334816535.31676017958.4707133109
74.70289640084-4.11062831435-2.832729162153.91834430612.938500308762.87750180043-0.3627978245660.65991250987-0.2830971983880.1053622307360.2341097883180.003129514247750.242620347986-0.1773720179170.03577305929250.289069170528-0.000506909500662-0.01963951619720.1928259240250.04398538781960.36480285719116.96781068240.204857377148.5792472269
82.17248360733-3.510602226840.1829830767595.917481577150.7421405349764.47807605444-0.881245544925-1.48961144014-0.03160992746780.7543657926460.7703643032560.02217798441770.03672434362420.1568017916460.05321532980370.4118250497570.0550869078397-0.04259908584380.4491985946640.05142033054510.36482642003512.677483984841.885065439964.4802437164
95.34734003792-3.36458942298-4.193623829362.146226622542.818596165494.096319282120.268892251733-1.365337715460.9069633222162.12138637150.395811626859-0.0241527271075-0.837604295392-0.755050746473-0.6895074593961.022845557750.002733724203040.2236900720430.818573152128-0.196025152150.8405720626231.4657715234556.037379360965.9572135754
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 59 )
2X-RAY DIFFRACTION2chain 'A' and (resid 60 through 83 )
3X-RAY DIFFRACTION3chain 'A' and (resid 84 through 163 )
4X-RAY DIFFRACTION4chain 'A' and (resid 164 through 285 )
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 31 )
6X-RAY DIFFRACTION6chain 'B' and (resid 32 through 52 )
7X-RAY DIFFRACTION7chain 'B' and (resid 53 through 72 )
8X-RAY DIFFRACTION8chain 'B' and (resid 73 through 95 )
9X-RAY DIFFRACTION9chain 'B' and (resid 96 through 105 )

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