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- PDB-4x6c: CD1a ternary complex with lysophosphatidylcholine and BK6 TCR -

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Basic information

Entry
Database: PDB / ID: 4x6c
TitleCD1a ternary complex with lysophosphatidylcholine and BK6 TCR
Components
  • Beta-2-microglobulin
  • T-cell surface glycoprotein CD1a
  • TCR alpha
  • TCR beta
KeywordsIMMUNE SYSTEM / CD1a / TCR / Immune complex / Lipid antigen
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 / alpha-beta T cell receptor complex / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / alpha-beta T cell activation / Generation of second messenger molecules ...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 / alpha-beta T cell receptor complex / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / alpha-beta T cell activation / Generation of second messenger molecules / PD-1 signaling / immunoglobulin complex, circulating / immunoglobulin receptor 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 / complement activation, classical pathway / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen binding / response to bacterium / 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 / Downstream TCR signaling / 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 / T cell receptor signaling pathway / iron ion transport / ER-Phagosome pathway / early endosome membrane / antibacterial humoral response / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / blood microparticle / 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
Similarity search - Function
T-cell receptor alpha chain, constant domain / MHC-I family domain / Domain of unknown function (DUF1968) / 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 ...T-cell receptor alpha chain, constant domain / MHC-I family domain / Domain of unknown function (DUF1968) / 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 / T cell receptor alpha chain constant / T cell receptor beta constant 1 / T-cell surface glycoprotein CD1a / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 1.4Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Source and taxonomy / Structure summary
Category: chem_comp / diffrn_source ...chem_comp / diffrn_source / entity / entity_src_gen / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_oper_list / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description / _entity_src_gen.pdbx_alt_source_flag / _pdbx_entity_nonpoly.name / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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
C: T-cell surface glycoprotein CD1a
D: Beta-2-microglobulin
E: TCR alpha
F: TCR beta
G: TCR alpha
H: TCR beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,97613
Polymers190,2678
Non-polymers1,7095
Water37821
1
A: T-cell surface glycoprotein CD1a
B: Beta-2-microglobulin
G: TCR alpha
H: TCR beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,0987
Polymers95,1334
Non-polymers9653
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: T-cell surface glycoprotein CD1a
D: Beta-2-microglobulin
E: TCR alpha
F: TCR beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,8776
Polymers95,1334
Non-polymers7442
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.273, 142.144, 175.752
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 4 types, 8 molecules ACBDEGFH

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


Mass: 32178.166 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD1A / Production host: Escherichia coli (E. coli) / References: UniProt: P06126
#2: Protein Beta-2-microglobulin


Mass: 12358.887 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#3: Protein TCR alpha


Mass: 22998.301 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P01848*PLUS
#4: Protein TCR beta


Mass: 27597.977 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P01850*PLUS

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Sugars , 1 types, 3 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3 / 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 , 2 types, 23 molecules

#6: 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.: 2 / Source method: obtained synthetically / Formula: C26H53NO7P
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.93 Å3/Da / Density % sol: 58.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: sodium citrate, bis-tris propane, PEG 3350 / PH range: 6.7

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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: Aug 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.8→79.59 Å / Num. obs: 55926 / % possible obs: 99.8 % / Redundancy: 5.8 % / Net I/σ(I): 10.8
Reflection shellResolution: 2.8→2.88 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 2 / Num. unique all: 4408 / % possible all: 97.5

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
iMOSFLMdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Chain A and B from 1ONQ and chain G and H from 4PJ5

1onq

4pj5


Resolution: 2.8→74.746 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2361 2647 4.75 %
Rwork0.1756 --
obs0.1785 55760 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→74.746 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12732 0 112 21 12865
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00913214
X-RAY DIFFRACTIONf_angle_d1.26917916
X-RAY DIFFRACTIONf_dihedral_angle_d14.4264777
X-RAY DIFFRACTIONf_chiral_restr0.0531888
X-RAY DIFFRACTIONf_plane_restr0.0062310
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.85090.37891230.30182772X-RAY DIFFRACTION100
2.8509-2.90580.31051380.26762741X-RAY DIFFRACTION100
2.9058-2.96510.33681310.24362787X-RAY DIFFRACTION100
2.9651-3.02960.29221210.22472751X-RAY DIFFRACTION100
3.0296-3.10.31131490.22672762X-RAY DIFFRACTION100
3.1-3.17760.30411360.22222772X-RAY DIFFRACTION100
3.1776-3.26350.28071390.22182739X-RAY DIFFRACTION100
3.2635-3.35950.28891270.19342796X-RAY DIFFRACTION100
3.3595-3.4680.27711350.18742786X-RAY DIFFRACTION100
3.468-3.59190.23951520.17842764X-RAY DIFFRACTION100
3.5919-3.73570.23741500.17362786X-RAY DIFFRACTION100
3.7357-3.90570.24321350.16672788X-RAY DIFFRACTION100
3.9057-4.11160.23841420.15662778X-RAY DIFFRACTION100
4.1116-4.36920.21881430.1442782X-RAY DIFFRACTION100
4.3692-4.70650.19281510.13142815X-RAY DIFFRACTION100
4.7065-5.180.18851490.13252803X-RAY DIFFRACTION100
5.18-5.92930.21881410.15672850X-RAY DIFFRACTION100
5.9293-7.46920.2221540.17992837X-RAY DIFFRACTION100
7.4692-74.77220.19731310.17813004X-RAY DIFFRACTION99
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)
10.79910.41390.39384.66992.68972.2826-0.0438-0.0229-0.0521-0.1942-0.16910.2577-0.129-0.17570.17750.26860.0567-0.02320.5296-0.08130.3674108.5544196.515216.3448
25.3674-1.3877-1.01627.90250.25082.6480.0077-0.00920.42950.4311-0.35151.0356-0.711-1.43950.30990.79020.26110.01690.9701-0.30620.624796.1144208.7515226.8146
31.62830.08150.53745.18553.08153.90810.12980.1376-0.402-0.3119-0.1492-0.24960.3040.0530.01840.29380.03060.04860.40820.0130.686116.9198149.6526182.3953
42.0068-0.61980.11282.66161.29142.13330.0662-0.0373-0.1904-0.02190.0186-0.18260.3305-0.1262-0.07130.2439-0.08340.03680.34190.00530.491797.8776150.2154178.8412
50.56630.21830.33553.85612.24083.34380.042-0.13610.12690.0390.09510.0993-0.4973-0.1446-0.1480.55320.03470.05180.362-0.02530.6574107.6353233.2376179.5869
63.29070.66540.34825.94940.51072.799-0.1815-0.12780.40680.02540.6342-0.9959-1.37341.3557-0.32911.1401-0.31210.1070.7421-0.33651.0442120.8029248.1142183.8993
70.96210.48870.51266.68923.93733.27030.03090.2420.06780.078-0.13750.23030.1827-0.18340.11280.169-0.03320.05120.4390.08860.435594.7269184.6801153.7663
82.95611.39181.05432.70371.02931.4873-0.00790.6246-0.1582-0.10030.1815-0.43270.11070.2169-0.12270.194-0.0040.10530.48610.04590.4324114.0983181.045156.2136
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 7 through 278)
2X-RAY DIFFRACTION2(chain 'B' and resid 1 through 98)
3X-RAY DIFFRACTION3(chain 'G' and resid 1 through 201)
4X-RAY DIFFRACTION4(chain 'H' and resid 2 through 244)
5X-RAY DIFFRACTION5(chain 'C' and resid 7 through 277)
6X-RAY DIFFRACTION6(chain 'D' and resid 1 through 98)
7X-RAY DIFFRACTION7(chain 'E' and resid 2 through 202)
8X-RAY DIFFRACTION8(chain 'F' and resid 1 through 243)

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