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- PDB-4x6e: CD1a binary complex with lysophosphatidylcholine -

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Basic information

Entry
Database: PDB / ID: 4x6e
TitleCD1a binary complex with lysophosphatidylcholine
Components
  • Beta-2-microglobulin
  • T-cell surface glycoprotein CD1a
KeywordsIMMUNE SYSTEM / CD1a / Immune complex / Lipid antigen / TCR
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 / positive regulation of receptor binding / early endosome lumen / 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 / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / 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 / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / 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 / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / endosome membrane / immune response / membrane raft / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / Golgi membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
MHC-I family domain / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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 / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-42H / D-MALATE / T-cell surface glycoprotein CD1a / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBirkinshaw, R.W. / Rossjohn, J.
CitationJournal: Nat.Immunol. / Year: 2015
Title: alpha beta T cell antigen receptor recognition of CD1a presenting self lipid ligands.
Authors: Birkinshaw, R.W. / Pellicci, D.G. / Cheng, T.Y. / Keller, A.N. / Sandoval-Romero, M. / Gras, S. / de Jong, A. / Uldrich, A.P. / Moody, D.B. / Godfrey, D.I. / Rossjohn, J.
History
DepositionDec 8, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 18, 2015Group: Database references
Revision 1.2Feb 25, 2015Group: Database references
Revision 1.3Mar 4, 2015Group: Structure summary
Revision 1.4Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / entity_src_gen / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation

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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)45,1944
Polymers44,5372
Non-polymers6572
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4020 Å2
ΔGint-11 kcal/mol
Surface area19030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.299, 90.663, 108.066
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 32178.166 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: 12358.887 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-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#4: Chemical ChemComp-42H / (4R,7R,18Z)-4,7-dihydroxy-N,N,N-trimethyl-10-oxo-3,5,9-trioxa-4-phosphaheptacos-18-en-1-aminium 4-oxide


Mass: 522.675 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H53NO7P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20 mM DL-malic acid, 40 mM MES, 40 mM tris, PEG 1500
PH range: 5-6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.09→41.8 Å / Num. obs: 24843 / % possible obs: 98.5 % / Redundancy: 4 % / Net I/σ(I): 6.3

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1onq

1onq


Resolution: 2.1→39.389 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2342 1174 4.76 %
Rwork0.1885 --
obs0.1908 24659 98.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→39.389 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2972 0 44 131 3147
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083107
X-RAY DIFFRACTIONf_angle_d1.154212
X-RAY DIFFRACTIONf_dihedral_angle_d15.9791124
X-RAY DIFFRACTIONf_chiral_restr0.056433
X-RAY DIFFRACTIONf_plane_restr0.005541
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1001-2.19560.31181300.25562824X-RAY DIFFRACTION96
2.1956-2.31140.30361490.23272884X-RAY DIFFRACTION99
2.3114-2.45620.30981370.22192911X-RAY DIFFRACTION99
2.4562-2.64580.29841410.21532932X-RAY DIFFRACTION99
2.6458-2.9120.28291480.21492907X-RAY DIFFRACTION99
2.912-3.33310.22781530.18872948X-RAY DIFFRACTION99
3.3331-4.19870.20521570.16082977X-RAY DIFFRACTION99
4.1987-39.3960.1791590.15743102X-RAY DIFFRACTION98
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)
14.93530.6982-3.13762.6817-0.79976.17050.1331-0.21580.95160.51390.131-0.0934-0.8312-0.5309-0.14310.44280.1376-0.02370.3441-0.14730.44420.7794106.016720.4237
22.5395-0.20990.72991.63772.01754.2459-0.165-0.52930.66510.22250.4389-0.7845-0.38610.7748-0.2710.32720.0301-0.09560.4312-0.22570.488637.644103.935317.5028
31.57970.4590.60852.35570.91231.59490.0321-0.3242-0.10620.1496-0.03230.0134-0.090-0.01110.1492-0.0092-00.19350.0260.136612.365379.01398.8376
43.80540.2338-0.5823.90431.44815.8018-0.05830.0333-0.4173-0.05520.1336-0.03730.319-0.2227-0.09470.1180.0184-0.01250.1220.03420.23687.047269.89180.8555
53.45624.14320.03815.3093-0.62581.94760.13210.08270.03760.03270.2028-0.34560.10520.6072-0.18820.16030.01310.04170.2744-0.10240.242721.482591.6201-1.986
66.8745-4.58376.81795.9413-4.18928.7655-0.2002-0.3729-0.4564-0.34040.06840.2826-0.0798-0.68820.23250.14390.0157-0.00350.2221-0.06020.3202-2.121384.9208-0.582
78.44644.10873.11783.54381.15742.054-0.1772-0.09540.1408-0.05880.08250.1455-0.17330.0720.09470.1755-0.0139-0.00250.114-0.03980.165611.740392.27010.8555
86.84674.2254.76664.02673.15424.0711-0.920.56120.8127-0.63810.20940.0143-0.98870.34750.62130.35470.0201-0.03260.24630.03190.231117.0275100.4337-3.9608
98.92524.81850.41757.18925.15875.3772-0.24021.53111.3205-1.1421-0.85180.7138-0.8605-0.33860.9060.36280.0813-0.17540.54920.07460.46264.9595100.0012-11.1481
106.56820.15250.3589.1303-0.89766.9531-0.43280.01650.59-0.625-0.12821.5448-1.4006-1.09810.74540.39450.1344-0.13410.3079-0.18080.5436.6991102.58070.553
118.35463.14664.52793.0681.88212.8302-0.0337-0.48240.11710.1599-0.0010.08470.0149-0.18090.0630.19280.00930.01770.1275-0.0170.157316.92995.95115.4455
125.44153.79380.76354.3031-1.27452.0782-0.1251.8934-0.9225-1.11970.36040.70510.5782-0.8151-0.12860.4802-0.0273-0.15660.5727-0.15910.5432-1.965389.3606-12.128
135.3711-2.19223.94251.79240.20286.5636-0.14140.89290.5959-0.09270.13170.0459-0.84160.21110.01480.32270.012-0.02940.30940.07370.166812.58196.2278-8.5601
140.8039-1.45060.39962.619-0.72160.19860.12991.41610.2349-1.01520.3365-0.2772-0.49240.0109-0.52320.436-0.15160.09230.55880.010.250124.640298.8786-10.4314
156.51171.0395-3.20464.1951-4.94496.456-0.23170.6696-0.7957-0.97010.1961-0.0051-0.20070.06240.04210.3629-0.0312-0.03470.4035-0.14130.22838.872186.7733-9.7321
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 85 )
2X-RAY DIFFRACTION2chain 'A' and (resid 86 through 164 )
3X-RAY DIFFRACTION3chain 'A' and (resid 165 through 242 )
4X-RAY DIFFRACTION4chain 'A' and (resid 243 through 284 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 11 )
6X-RAY DIFFRACTION6chain 'B' and (resid 12 through 19 )
7X-RAY DIFFRACTION7chain 'B' and (resid 20 through 30 )
8X-RAY DIFFRACTION8chain 'B' and (resid 31 through 41 )
9X-RAY DIFFRACTION9chain 'B' and (resid 42 through 46 )
10X-RAY DIFFRACTION10chain 'B' and (resid 47 through 51 )
11X-RAY DIFFRACTION11chain 'B' and (resid 52 through 71 )
12X-RAY DIFFRACTION12chain 'B' and (resid 72 through 77 )
13X-RAY DIFFRACTION13chain 'B' and (resid 78 through 83 )
14X-RAY DIFFRACTION14chain 'B' and (resid 84 through 90 )
15X-RAY DIFFRACTION15chain 'B' and (resid 91 through 99 )

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