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- PDB-6tro: Crystal structure of the T-cell receptor GVY01 bound to HLA A2*01... -

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Basic information

Entry
Database: PDB / ID: 6tro
TitleCrystal structure of the T-cell receptor GVY01 bound to HLA A2*01-GVYDGREHTV
Components
  • (T-cell receptor ...) x 2
  • Beta-2-microglobulin
  • MAGE-A4 peptide (amino acids 230-239)
  • MHC class I antigen
KeywordsIMMUNE SYSTEM / human leukocyte antigen / MAGE-A4 / T-cell receptor
Function / homology
Function and homology information


antigen processing and presentation of peptide antigen via MHC class I / positive regulation of cell cycle / 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 / lumenal side of endoplasmic reticulum membrane ...antigen processing and presentation of peptide antigen via MHC class I / positive regulation of cell cycle / 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 / lumenal side of endoplasmic reticulum membrane / 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 / histone deacetylase binding / 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 / intracellular iron ion homeostasis / learning or memory / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / lysosomal membrane / external side of plasma membrane / focal adhesion / Neutrophil degranulation / negative regulation of apoptotic process / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / endoplasmic reticulum / negative regulation of transcription by RNA polymerase II / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / metal ion binding / identical protein binding / nucleus / membrane / plasma membrane / cytosol
Similarity search - Function
Melanoma associated antigen, N-terminal / Melanoma associated antigen family N terminal / Melanoma associated antigen family N terminal / MAGE conserved domain profile. / MAGE homology domain / Melanoma-associated antigen / MAGE homology domain, winged helix WH1 motif / MAGE homology domain, winged helix WH2 motif / MAGE homology domain / Melanoma-associated antigen ...Melanoma associated antigen, N-terminal / Melanoma associated antigen family N terminal / Melanoma associated antigen family N terminal / MAGE conserved domain profile. / MAGE homology domain / Melanoma-associated antigen / MAGE homology domain, winged helix WH1 motif / MAGE homology domain, winged helix WH2 motif / MAGE homology domain / Melanoma-associated antigen / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
MHC class I antigen / Melanoma-associated antigen 4 / Beta-2-microglobulin / HLA class I antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsColes, C.H. / McMurran, C. / Lloyd, A. / Hibbert, L. / Lupardus, P.J. / Cole, D.K. / Harper, S.
CitationJournal: J.Biol.Chem. / Year: 2020
Title: T cell receptor interactions with human leukocyte antigen govern indirect peptide selectivity for the cancer testis antigen MAGE-A4.
Authors: Coles, C.H. / McMurran, C. / Lloyd, A. / Hock, M. / Hibbert, L. / Raman, M.C.C. / Hayes, C. / Lupardus, P. / Cole, D.K. / Harper, S.
History
DepositionDec 19, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 6, 2021Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / database_2 / diffrn_source / pdbx_contact_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MHC class I antigen
B: Beta-2-microglobulin
C: MAGE-A4 peptide (amino acids 230-239)
D: T-cell receptor alpha chain
E: T-cell receptor beta chain


Theoretical massNumber of molelcules
Total (without water)96,3835
Polymers96,3835
Non-polymers00
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10590 Å2
ΔGint-50 kcal/mol
Surface area38470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)220.040, 220.040, 96.830
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein MHC class I antigen


Mass: 31951.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5B8RNS7, UniProt: Q53Z42*PLUS
#2: Protein Beta-2-microglobulin


Mass: 11879.356 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: Escherichia coli (E. coli) / References: UniProt: P61769

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T-cell receptor ... , 2 types, 2 molecules DE

#4: Protein T-cell receptor alpha chain


Mass: 23016.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#5: Protein T-cell receptor beta chain


Mass: 28401.824 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Protein/peptide / Non-polymers , 2 types, 24 molecules C

#3: Protein/peptide MAGE-A4 peptide (amino acids 230-239)


Mass: 1134.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P43358*PLUS
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.51 Å3/Da / Density % sol: 64.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1 M succinic acid, 0.1 M HEPES pH 7.0, 1 % w/v PEG MME 2k

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3→67.91 Å / Num. obs: 27736 / % possible obs: 98.6 % / Redundancy: 6.6 % / Biso Wilson estimate: 85.884 Å2 / Rpim(I) all: 0.037 / Rrim(I) all: 0.102 / Net I/σ(I): 13.5 / Num. measured all: 183925
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all% possible all
3-3.056.81.2940213820.6871.93999.6
8.14-67.93638.9872214550.0130.03492.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
xia20.5.744data scaling
PDB_EXTRACT3.25data extraction
xia20.5.744data reduction
PHASER2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HUJ, 6AVF, 5e00

3huj

6avf

5e00


Resolution: 3→67.91 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.9 / SU B: 45.777 / SU ML: 0.364 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.414 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2702 1355 4.9 %RANDOM
Rwork0.2133 ---
obs0.2162 26360 98.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 210.85 Å2 / Biso mean: 102.286 Å2 / Biso min: 60.12 Å2
Baniso -1Baniso -2Baniso -3
1--1.63 Å2-0.82 Å2-0 Å2
2---1.63 Å20 Å2
3---5.29 Å2
Refinement stepCycle: final / Resolution: 3→67.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6572 0 0 23 6595
Biso mean---73.82 -
Num. residues----814
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0136750
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175902
X-RAY DIFFRACTIONr_angle_refined_deg1.2031.6519165
X-RAY DIFFRACTIONr_angle_other_deg1.051.57713718
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7995806
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.22921.98394
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.01151099
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7391549
X-RAY DIFFRACTIONr_chiral_restr0.0370.2854
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027608
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021515
LS refinement shellResolution: 3→3.078 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 101 -
Rwork0.341 1922 -
all-2023 -
obs--99.51 %
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)
13.4651-0.5527-1.14551.44550.18912.47350.2391-0.23860.33860.22750.110.489-0.4457-0.0759-0.3490.5638-0.06010.18180.11620.11620.423675.0792-21.99473.4098
27.1023-0.92020.22184.91420.23642.50250.20060.45820.1998-0.4616-0.0030.5824-0.2333-0.5671-0.19760.4257-0.00040.12360.22040.16170.458258.8203-31.98012.497
310.5982-1.0237-0.7930.15130.49254.94041.14350.6614-1.5636-0.03220.0580.11290.41191.4444-1.20150.56430.118-0.13970.5652-0.48150.95393.6258-29.9696-2.444
46.8940.6544-2.62352.2410.22672.3311-0.08960.31480.197-0.18620.121-0.5876-0.20160.0127-0.03140.52440.06570.08110.04750.01230.2075120.9007-9.0489-22.2368
54.57350.3644-1.45122.07820.17420.72530.26190.2769-0.177-0.1668-0.1936-0.557-0.0065-0.0462-0.06830.4510.10780.00050.16840.00790.166122.0498-27.6034-31.008
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 274
2X-RAY DIFFRACTION2B0 - 99
3X-RAY DIFFRACTION3C1 - 10
4X-RAY DIFFRACTION4D2 - 217
5X-RAY DIFFRACTION5E4 - 256

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