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- PDB-7rym: CD1a-endo-gdTCR complex -

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Basic information

Entry
Database: PDB / ID: 7rym
TitleCD1a-endo-gdTCR complex
Components
  • (T cell receptor ...) x 2
  • Beta-2-microglobulin
  • T-cell surface glycoprotein CD1a
KeywordsIMMUNE SYSTEM / CD1 / TCR / 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 / T cell receptor complex / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / alpha-beta T cell activation ...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 / 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 / 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 / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / 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 / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / 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 / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / 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 / peptide antigen binding / positive regulation of cellular senescence / 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 / positive regulation of T cell activation / sensory perception of smell / Downstream TCR signaling / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / 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 / external side of plasma membrane / Golgi membrane / lysosomal membrane / innate immune response / 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
: / : / : / T-cell receptor alpha chain, constant domain / MHC-I family domain / Domain of unknown function (DUF1968) / : / : / Immunoglobulin V-Type / Beta-2-Microglobulin ...: / : / : / T-cell receptor alpha chain, constant domain / MHC-I family domain / Domain of unknown function (DUF1968) / : / : / Immunoglobulin V-Type / Beta-2-Microglobulin / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Immunoglobulin V-set domain / MHC classes I/II-like antigen recognition protein / Immunoglobulin V-set domain / : / 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
DI(HYDROXYETHYL)ETHER / T cell receptor gamma variable 4 / T cell receptor delta variable 1 / 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: 3.2 Å
AuthorsWegrecki, M. / Le Nours, J. / Rossjohn, J.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: Nat Commun / Year: 2022
Title: Atypical sideways recognition of CD1a by autoreactive gamma delta T cell receptors.
Authors: Wegrecki, M. / Ocampo, T.A. / Gunasinghe, S.D. / von Borstel, A. / Tin, S.Y. / Reijneveld, J.F. / Cao, T.P. / Gully, B.S. / Le Nours, J. / Moody, D.B. / Van Rhijn, I. / Rossjohn, J.
History
DepositionAug 25, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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 receptor gamma variable 4,T cell receptor beta constant 1
D: T cell receptor delta variable 1,T cell receptor alpha chain constant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,0086
Polymers96,8054
Non-polymers2022
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)237.076, 42.461, 121.589
Angle α, β, γ (deg.)90.000, 116.132, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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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: 32593.562 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: 12602.105 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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T cell receptor ... , 2 types, 2 molecules CD

#3: Protein T cell receptor gamma variable 4,T cell receptor beta constant 1


Mass: 27987.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRGV4, TCRGV4, TRBC1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0C4DH28, UniProt: P01850
#4: Protein T cell receptor delta variable 1,T cell receptor alpha chain constant


Mass: 23622.590 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRDV1, TRAC, TCRA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1B0GX56, UniProt: P01848

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Non-polymers , 2 types, 2 molecules

#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4

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Details

Has ligand of interestN

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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: 2.84 Å3/Da / Density % sol: 56.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350, 0.2M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 3.2→41.64 Å / Num. obs: 18526 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 81.03 Å2 / CC1/2: 0.972 / Net I/σ(I): 8.8
Reflection shellResolution: 3.2→3.42 Å / Num. unique obs: 3277 / CC1/2: 0.909

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7RYL and 7KP1

7ryl

7kp1


Resolution: 3.2→41.64 Å / SU ML: 0.455 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.8987
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2858 1027 5.56 %
Rwork0.2473 17456 -
obs0.2493 18483 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 128.17 Å2
Refinement stepCycle: LAST / Resolution: 3.2→41.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5530 0 12 0 5542
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00235692
X-RAY DIFFRACTIONf_angle_d0.60077776
X-RAY DIFFRACTIONf_chiral_restr0.0424860
X-RAY DIFFRACTIONf_plane_restr0.0058988
X-RAY DIFFRACTIONf_dihedral_angle_d4.9266778
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.370.39211560.37532443X-RAY DIFFRACTION99.62
3.37-3.580.35351520.30152448X-RAY DIFFRACTION99.62
3.58-3.860.33271450.2672485X-RAY DIFFRACTION99.66
3.86-4.240.25261580.22462455X-RAY DIFFRACTION99.81
4.24-4.860.23961240.19432491X-RAY DIFFRACTION99.54
4.86-6.120.281550.23212530X-RAY DIFFRACTION99.93
6.12-41.640.26111370.24752604X-RAY DIFFRACTION99.42
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)
11.093012192080.1547767392680.1549494078040.936832747984-0.04515990987770.4526639707870.02580566314340.112169177797-0.224777304466-0.07952070428620.0845291254505-0.105748174879-0.072086786013-0.03218427099051.710742550280.5455636854820.03249767962650.03783566780210.394359348983-0.001765255437410.7624151811430.75216.908-3
20.592444466452-0.4608511561720.5691539464170.417240403219-0.2475306122251.04358586080.178816167117-0.07104184891440.445743755173-0.01090112377810.146139663097-0.0529154688188-0.0365694559992-0.03231576036792.62802424969E-50.5798872406490.03926954330380.02828877581690.656239805885-0.003905707701420.79824100806535.45324.81812.175
30.642310170866-0.2313331521720.4058948461390.5110206187990.04083866477050.63096001064-0.134388912182-0.24523103758-0.352282457473-0.0177952731031-0.09638728950530.4340371941910.451080217221-0.1157313181770.0001386944297971.00667117146-0.01436110308820.2487733499721.215215077140.1566907376020.966190141716-8.3162.61740.07
40.0583447786292-0.245617822290.09682131830421.0252595829-0.5669168930110.4470247480030.192789978351-0.2515024518310.637194632333-0.394097832986-0.358952788847-0.6574942194330.3678032675391.06671278248-0.05536737941710.724028715525-0.156668092109-0.01571293263071.69846633375-0.006401574359541.1483500753113.59211.18841.781
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 8:280 )A8 - 280
2X-RAY DIFFRACTION2( CHAIN B AND RESID 1:99 ) OR ( CHAIN A AND RESID 301:301 )B1 - 99
3X-RAY DIFFRACTION2( CHAIN B AND RESID 1:99 ) OR ( CHAIN A AND RESID 301:301 )A301
4X-RAY DIFFRACTION3( CHAIN C AND RESID 11:248 )C11 - 248
5X-RAY DIFFRACTION4( CHAIN D AND RESID 2:178 )D2 - 178

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