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- PDB-9gv6: Structure of TCR in complex with peptide-HLA -

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Basic information

Entry
Database: PDB / ID: 9gv6
TitleStructure of TCR in complex with peptide-HLA
Components
  • Beta-2-microglobulin
  • MHC class I antigen
  • Peptide
  • TCR Beta
  • TCR alpha
KeywordsIMMUNE SYSTEM / TCR / HLA / MHC
Function / homology
Function and homology information


antigen processing and presentation of peptide antigen via MHC class I / 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 ...antigen processing and presentation of peptide antigen via MHC class I / 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 / 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 / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / lysosomal membrane / external side of plasma membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
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. ...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
Similarity search - Domain/homology
MHC class I antigen / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.77 Å
AuthorsKaruppiah, V.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Other private United Kingdom
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Determining T-cell receptor binding orientation and Peptide-HLA interactions using cross-linking mass spectrometry.
Authors: Powell, T. / Karuppiah, V. / Shaikh, S.A. / Pengelly, R. / Mai, N. / Barnbrook, K. / Sharma, A. / Harper, S. / Ebner, M. / Creese, A.J.
History
DepositionSep 23, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2025Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

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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: Peptide
D: TCR alpha
E: TCR Beta
G: MHC class I antigen
H: Beta-2-microglobulin
I: Peptide
J: TCR alpha
K: TCR Beta


Theoretical massNumber of molelcules
Total (without water)189,52510
Polymers189,52510
Non-polymers00
Water19811
1
A: MHC class I antigen
B: Beta-2-microglobulin
C: Peptide
D: TCR alpha
E: TCR Beta


Theoretical massNumber of molelcules
Total (without water)94,7635
Polymers94,7635
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: MHC class I antigen
H: Beta-2-microglobulin
I: Peptide
J: TCR alpha
K: TCR Beta


Theoretical massNumber of molelcules
Total (without water)94,7635
Polymers94,7635
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.120, 93.530, 388.950
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 AGBHDJEK

#1: Protein MHC class I antigen


Mass: 31951.316 Da / Num. of mol.: 2
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
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 2 / Fragment: UNP residues 21-119
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
#4: Protein TCR alpha


Mass: 21873.287 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)
#5: Protein TCR Beta


Mass: 27929.297 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)

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Protein/peptide / Non-polymers , 2 types, 13 molecules CI

#3: Protein/peptide Peptide


Mass: 1129.288 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 3.56 Å3/Da / Density % sol: 65.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium citrate tribasic dihydrate, 0.1 M Bis-Tris propane pH 7.5, and 20 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.77→90.94 Å / Num. obs: 69770 / % possible obs: 99.62 % / Redundancy: 14.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.212 / Rpim(I) all: 0.057 / Rrim(I) all: 0.22 / Net I/σ(I): 8.1
Reflection shellResolution: 2.77→2.82 Å / Redundancy: 9.2 % / Rmerge(I) obs: 3.438 / Mean I/σ(I) obs: 0.3 / Num. unique obs: 3197 / CC1/2: 0.366 / Rpim(I) all: 1.158 / Rrim(I) all: 3.642 / % possible all: 94.03

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.77→90.94 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.925 / SU B: 50.565 / SU ML: 0.382 / Cross valid method: THROUGHOUT / ESU R: 0.608 / ESU R Free: 0.345 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27357 3484 5 %RANDOM
Rwork0.21709 ---
obs0.21976 66086 99.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 108.509 Å2
Baniso -1Baniso -2Baniso -3
1-5.4 Å20 Å2-0 Å2
2---0.02 Å20 Å2
3----5.38 Å2
Refinement stepCycle: 1 / Resolution: 2.77→90.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13154 0 0 11 13165
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01213520
X-RAY DIFFRACTIONr_bond_other_d0.0010.01612140
X-RAY DIFFRACTIONr_angle_refined_deg1.7671.8218368
X-RAY DIFFRACTIONr_angle_other_deg0.6071.77427964
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3751622
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.41596
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.404102178
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0810.21922
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216376
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023348
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.9915.2116518
X-RAY DIFFRACTIONr_mcbond_other4.995.2116518
X-RAY DIFFRACTIONr_mcangle_it7.8039.3578130
X-RAY DIFFRACTIONr_mcangle_other7.8029.3588131
X-RAY DIFFRACTIONr_scbond_it5.1865.5827002
X-RAY DIFFRACTIONr_scbond_other5.1865.5817001
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.24310.06210239
X-RAY DIFFRACTIONr_long_range_B_refined11.06548.5914224
X-RAY DIFFRACTIONr_long_range_B_other11.06548.614225
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.77→2.842 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.629 224 -
Rwork0.62 4498 -
obs--92.19 %
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)
10.6770.19980.51442.13841.30492.7858-0.04680.00630.04170.69640.1221-0.175-0.03490.188-0.07530.4882-0.0341-0.05510.6952-0.03530.1218-18.4442.703755.6502
23.30811.41780.3556.84951.42131.0175-0.00880.12530.33960.55730.07430.5383-0.3266-0.2376-0.06550.66340.02120.04480.6754-0.04930.2001-29.961717.289160.7193
30.03290.27320.46472.51784.27747.27330.050.0518-0.01670.27180.127-0.08730.42830.2282-0.1770.3815-0.0722-0.01060.68260.00250.4839-24.0806-10.669341.3196
40.8067-0.26830.39831.32292.0296.8169-0.00990.2675-0.0328-0.2991-0.037-0.2534-0.18020.23470.04690.1342-0.04520.06830.6948-0.02070.4333-14.3875-23.98426.3563
50.8812-0.383-0.25661.84921.60674.17930.010.22520.0586-0.3279-0.14820.0705-0.3992-0.09190.13830.0752-0.0504-0.03850.735-0.0690.2455-31.1988-14.73222.3595
61.4337-0.4461.24660.1547-0.48612.20720.12980.0413-0.2215-0.1406-0.01130.05660.20020.1591-0.11851.46650.0217-0.13880.7772-0.0050.205112.8005-48.270596.8366
75.1692-2.51840.61394.1632-0.96510.5405-0.08570.2054-0.0435-0.29570.0243-0.41820.14350.5360.06131.24530.0426-0.04781.02920.01370.257132.1145-47.729896.2523
87.4215-3.41810.34161.5809-0.06924.16540.0964-0.3584-0.1639-0.00460.22920.06610.07840.2548-0.32560.90020.0598-0.06230.56450.05830.52971.4078-37.770683.3839
92.4960.46592.58211.4194-0.02675.43420.0223-0.0131-0.33150.25360.09690.37020.4995-0.4268-0.11920.9088-0.00250.08270.60410.03460.5493-23.4907-46.509455.1912
101.7583-0.35431.58851.6036-0.16393.43620.05290.3305-0.23620.2808-0.008-0.03070.34180.4397-0.04490.669-0.02340.0220.6628-0.00240.1798-9.7027-38.448744.7695
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 276
2X-RAY DIFFRACTION2B0 - 99
3X-RAY DIFFRACTION3C1 - 9
4X-RAY DIFFRACTION4D3 - 188
5X-RAY DIFFRACTION5E3 - 247
6X-RAY DIFFRACTION6G1 - 276
7X-RAY DIFFRACTION7H0 - 99
8X-RAY DIFFRACTION8I1 - 9
9X-RAY DIFFRACTION9J3 - 188
10X-RAY DIFFRACTION10K3 - 247

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