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- PDB-6d7g: Structure of 5F3 TCR in complex with HLA-A2/MART-1 -

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Basic information

Entry
Database: PDB / ID: 6d7g
TitleStructure of 5F3 TCR in complex with HLA-A2/MART-1
Components
  • MART1 PEPTIDE-BETA-2-MICROGLOBULIN-HLA-A*02 CHIMERA
  • T-CELL RECEPTOR GAMMA VARIABLE 8,T-CELL RECEPTOR GAMMA-2 CHAIN C REGION
  • TRA@ proteinTRA (gene)
KeywordsIMMUNE SYSTEM / TCR / MHC / peptide recognition / complex
Function / homology
Function and homology information


T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding ...T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / endoplasmic reticulum exit site / beta-2-microglobulin binding / TAP binding / protection from natural killer cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / detection of bacterium / T cell 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 / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / 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 / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / negative regulation of epithelial cell proliferation / Interferon gamma signaling / positive regulation of T cell activation / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / positive regulation of type II interferon production / sensory perception of smell / E3 ubiquitin ligases ubiquitinate target proteins / negative regulation of neuron projection development / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / T cell differentiation in thymus / late endosome membrane / positive regulation of protein binding / ER-Phagosome pathway / antibacterial humoral response / iron ion transport / T cell receptor signaling pathway / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane / endoplasmic reticulum lumen / Golgi membrane / signaling receptor binding / focal adhesion / innate immune response / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum
Similarity search - Function
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 / Immunoglobulin V-Type / Beta-2-Microglobulin / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily ...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 / 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 / Immunoglobulin subtype / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin / 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
HLA class I histocompatibility antigen, A alpha chain / Beta-2-microglobulin / TRA@ protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsRoy, S. / Adams, E.J.
CitationJournal: Sci Immunol / Year: 2018
Title: Generation and molecular recognition of melanoma-associated antigen-specific human gamma delta T cells.
Authors: Benveniste, P.M. / Roy, S. / Nakatsugawa, M. / Chen, E.L.Y. / Nguyen, L. / Millar, D.G. / Ohashi, P.S. / Hirano, N. / Adams, E.J. / Zuniga-Pflucker, J.C.
History
DepositionApr 24, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Derived calculations
Category: chem_comp / pdbx_struct_assembly ...chem_comp / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _chem_comp.type / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MART1 PEPTIDE-BETA-2-MICROGLOBULIN-HLA-A*02 CHIMERA
D: TRA@ protein
E: T-CELL RECEPTOR GAMMA VARIABLE 8,T-CELL RECEPTOR GAMMA-2 CHAIN C REGION
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,2294
Polymers103,0083
Non-polymers2211
Water543
1
D: TRA@ protein
E: T-CELL RECEPTOR GAMMA VARIABLE 8,T-CELL RECEPTOR GAMMA-2 CHAIN C REGION
hetero molecules

A: MART1 PEPTIDE-BETA-2-MICROGLOBULIN-HLA-A*02 CHIMERA


Theoretical massNumber of molelcules
Total (without water)103,2294
Polymers103,0083
Non-polymers2211
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_564-y,x-y+1,z-1/31
Unit cell
Length a, b, c (Å)123.953, 123.953, 154.156
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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Components

#1: Protein MART1 PEPTIDE-BETA-2-MICROGLOBULIN-HLA-A*02 CHIMERA / MHC CLASS I ANTIGEN A*2


Mass: 47863.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P, HLA-A, HLAA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P61769, UniProt: P01892
#2: Antibody TRA@ protein / TRA (gene)


Mass: 25730.254 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRA@ / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q6PJ56
#3: Protein T-CELL RECEPTOR GAMMA VARIABLE 8,T-CELL RECEPTOR GAMMA-2 CHAIN C REGION


Mass: 29414.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRGV8, TRGC2 / Production host: Spodoptera frugiperda (fall armyworm)
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

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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: 3.32 Å3/Da / Density % sol: 62.94 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop
Details: PEG 550 MME, TRIS, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9194 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9194 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 34834 / % possible obs: 99.9 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.032 / Rrim(I) all: 0.102 / Net I/σ(I): 11.66
Reflection shellResolution: 2.75→2.849 Å / Rmerge(I) obs: 0.975 / Rpim(I) all: 0.315 / Rrim(I) all: 1.025

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASERphasing
PHENIX1.10.1_2155refinement
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→48.3 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.49
RfactorNum. reflection% reflection
Rfree0.237 1806 5.18 %
Rwork0.211 --
obs0.212 34834 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 66.48 Å2
Refinement stepCycle: LAST / Resolution: 2.75→48.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6005 0 14 3 6022
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0136180
X-RAY DIFFRACTIONf_angle_d1.3138442
X-RAY DIFFRACTIONf_dihedral_angle_d16.1173601
X-RAY DIFFRACTIONf_chiral_restr0.077941
X-RAY DIFFRACTIONf_plane_restr0.0091080
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7503-2.82470.33681470.27142495X-RAY DIFFRACTION100
2.8247-2.90780.30251480.25552527X-RAY DIFFRACTION100
2.9078-3.00160.30181590.25352510X-RAY DIFFRACTION100
3.0016-3.10890.28471230.25842552X-RAY DIFFRACTION100
3.1089-3.23340.29441270.23772538X-RAY DIFFRACTION100
3.2334-3.38050.25711530.22592517X-RAY DIFFRACTION100
3.3805-3.55860.25051370.22912541X-RAY DIFFRACTION100
3.5586-3.78150.27081240.21742563X-RAY DIFFRACTION100
3.7815-4.07340.20191120.19372566X-RAY DIFFRACTION100
4.0734-4.4830.21641310.17262553X-RAY DIFFRACTION100
4.483-5.13110.17961580.16782526X-RAY DIFFRACTION100
5.1311-6.46220.22151450.21462556X-RAY DIFFRACTION100
6.4622-48.30680.24631420.22342584X-RAY DIFFRACTION100
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)
10.1740.05910.65390.00020.63413.00970.17550.3619-0.0798-0.1069-0.12650.21370.1499-0.4493-0.00260.4915-0.0405-0.04420.6759-0.03210.5405-48.837836.2657-18.9598
21.2018-0.1290.11081.84770.5942.51290.20860.3971-0.4072-0.116-0.08640.1090.7758-0.061-0.09180.6496-0.0331-0.12190.6536-0.13710.5966-48.842624.8256-32.1633
32.8286-0.58030.15671.42540.16972.77790.18860.13950.11550.0858-0.04110.0730.0659-0.0315-0.11250.386-0.06540.0230.37310.00330.4231-42.704636.5131-9.838
41.18750.4188-0.17712.1891-0.47552.233-0.00340.6214-0.0039-0.14670.09920.11990.01120.4079-0.11520.46640.0931-0.03181.0039-0.03210.534-36.006940.9511-43.2964
51.59540.2151-0.14980.54370.58781.81330.0471-0.3968-0.18350.0615-0.0436-0.0427-0.06170.36440.0390.3137-0.0148-0.04020.84250.10060.5208-58.877356.9497-33.3118
62.39590.91270.67131.27180.69551.4320.4604-0.83690.22580.2408-0.4604-0.09780.1474-0.6936-0.04880.4976-0.1935-0.03641.2844-0.09770.5317-55.292466.43331.6614
71.92970.531-1.20710.48460.44323.03430.1551-0.43260.09420.0496-0.2740.0717-0.0625-0.20620.08530.32830.0007-0.01280.77030.07370.481-81.316154.733-28.636
81.42430.22860.16340.68990.81470.79760.0109-2.01061.2218-1.43910.19290.1370.4329-2.1822-0.03780.32580.2775-0.01092.1502-0.75941.2392-72.077671.1872-1.1458
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 1 THROUGH 111 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 112 THROUGH 1001 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 1002 THROUGH 1185 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 1186 THROUGH 1276 )
5X-RAY DIFFRACTION5CHAIN 'D' AND (RESID 1 THROUGH 108 )
6X-RAY DIFFRACTION6CHAIN 'D' AND (RESID 109 THROUGH 201 )
7X-RAY DIFFRACTION7CHAIN 'E' AND (RESID 6 THROUGH 128 )
8X-RAY DIFFRACTION8CHAIN 'E' AND (RESID 129 THROUGH 226 )

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