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- PDB-9gv7: Structure of reverse docking TCR in complex with peptide-HLA -

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Basic information

Entry
Database: PDB / ID: 9gv7
TitleStructure of reverse docking TCR in complex with peptide-HLA
Components
  • Beta-2-microglobulin
  • MHC class I antigen
  • Peptide
  • TCR Alpha
  • TCR Beta
KeywordsIMMUNE SYSTEM / TCR / HLA / reverse docking / MHC
Function / homology
Function and homology information


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 / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent ...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 / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / 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 / 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 / positive regulation of T cell mediated cytotoxicity / cellular response to nicotine / multicellular organismal-level iron ion homeostasis / Modulation by Mtb of host immune system / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / ER-Phagosome pathway / negative regulation of neuron projection development / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / Amyloid fiber formation / endoplasmic reticulum lumen / 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: 1.86 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,7157
Polymers94,5915
Non-polymers1242
Water8,539474
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10920 Å2
ΔGint-40 kcal/mol
Surface area36830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.130, 144.130, 106.790
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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Protein , 4 types, 4 molecules ABDE

#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
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 1 / 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: 22114.492 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 TCR Beta


Mass: 27567.783 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 , 1 types, 1 molecules C

#3: Protein/peptide Peptide


Mass: 1078.219 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 2 types, 476 molecules

#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 474 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 3.39 Å3/Da / Density % sol: 63.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MMT pH 9, 25% PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.86→124.82 Å / Num. obs: 105638 / % possible obs: 100 % / Redundancy: 31.52 % / CC1/2: 0.9997 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.016 / Rrim(I) all: 0.095 / Net I/σ(I): 24.2
Reflection shellResolution: 1.86→1.89 Å / Redundancy: 19.03 % / Rmerge(I) obs: 2.135 / Mean I/σ(I) obs: 1.12 / Num. unique obs: 5255 / CC1/2: 0.5557 / Rpim(I) all: 0.502 / Rrim(I) all: 2.194 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
xia2.multiplexdata reduction
xia2.multiplexdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.86→124.82 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.947 / SU B: 5.078 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21202 5187 4.9 %RANDOM
Rwork0.18031 ---
obs0.18184 100403 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.091 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20.16 Å20 Å2
2--0.32 Å20 Å2
3----1.02 Å2
Refinement stepCycle: 1 / Resolution: 1.86→124.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6530 0 8 474 7012
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0126717
X-RAY DIFFRACTIONr_bond_other_d0.0020.0166025
X-RAY DIFFRACTIONr_angle_refined_deg1.8091.8259111
X-RAY DIFFRACTIONr_angle_other_deg0.6521.77513885
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1755812
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.063549
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.593101091
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0920.2948
X-RAY DIFFRACTIONr_gen_planes_refined0.010.028148
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021660
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_it3.0462.8623257
X-RAY DIFFRACTIONr_mcbond_other3.0452.8623257
X-RAY DIFFRACTIONr_mcangle_it4.1085.134063
X-RAY DIFFRACTIONr_mcangle_other4.1095.1324064
X-RAY DIFFRACTIONr_scbond_it3.9823.2173460
X-RAY DIFFRACTIONr_scbond_other3.9823.2173461
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7445.7265048
X-RAY DIFFRACTIONr_long_range_B_refined8.21129.967231
X-RAY DIFFRACTIONr_long_range_B_other8.20728.247130
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.86→1.908 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 405 -
Rwork0.304 7439 -
obs--100 %
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)
11.2938-0.22980.00680.6622-0.33370.71120.07190.05580.21620.0785-0.07060.1127-0.2374-0.1319-0.00140.090.0350.0060.1135-0.02540.1039-89.750451.916124.7888
21.4086-0.03870.3283.3254-0.75992.17940.01960.3280.1002-0.25530.08680.1965-0.1719-0.176-0.10640.10030.09940.00460.23250.00070.1482-103.907354.863211.9971
32.59253.762-2.91096.7433-5.13883.920.17590.328-0.07920.152-0.03890.2064-0.12390.0005-0.1370.02060.0584-0.03590.2604-0.12330.1076-79.524634.037623.9753
42.9783-0.938-1.99250.89050.51681.488-0.1686-0.1825-0.4034-0.0241-0.0562-0.17250.20640.25410.22480.1030.0511-0.01580.19930.04320.3072-46.604422.080614.6313
51.5962-0.0936-0.87540.26210.0531.05780.0117-0.2781-0.04220.0135-0.0082-0.1497-0.00180.2778-0.00350.0406-0.0402-0.00950.17620.04940.1647-37.765339.366212.7047
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 301
2X-RAY DIFFRACTION2B0 - 99
3X-RAY DIFFRACTION3C1 - 11
4X-RAY DIFFRACTION4D1 - 191
5X-RAY DIFFRACTION5E3 - 301

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