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- PDB-9wft: Crystal structure of A0PKV-1 TCR in complex with HLA-A*11:01 boun... -

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Basic information

Entry
Database: PDB / ID: 9wft
TitleCrystal structure of A0PKV-1 TCR in complex with HLA-A*11:01 bound to G12V-9 peptide(VVGAVGVGK)
Components
  • A0PKV-1 TCR alpha chain
  • A0PKV-1 TCR beta chain
  • Beta-2-microglobulin
  • G12V9
  • HLA class I histocompatibility antigen, A alpha chain
KeywordsIMMUNE SYSTEM / pMHC / TCR / Complex
Function / homology
Function and homology information


positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / 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 / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna ...positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / 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 / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / CD8 receptor binding / protection from natural killer cell mediated cytotoxicity / TAP binding / endoplasmic reticulum exit site / detection of bacterium / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / beta-2-microglobulin binding / T cell receptor binding / regulation of natural killer cell mediated immunity / early endosome lumen / positive regulation of T cell mediated cytotoxicity / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / regulation of iron ion transport / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / HFE-transferrin receptor complex / positive regulation of type II interferon production / MHC class I peptide loading complex / transferrin transport / negative regulation of receptor-mediated endocytosis / cellular response to iron ion / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / peptide antigen assembly with MHC class II protein complex / MHC class I protein complex / negative regulation of epithelial cell proliferation / cellular response to nicotine / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / specific granule lumen / positive regulation of immune response / antigen processing and presentation of exogenous peptide antigen via MHC class II / peptide antigen binding / T cell receptor signaling pathway / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of T cell activation / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / sensory perception of smell / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / tertiary granule lumen / positive regulation of cellular senescence / MHC class II protein complex binding / DAP12 signaling / late endosome membrane / E3 ubiquitin ligases ubiquitinate target proteins / ER-Phagosome pathway / early endosome membrane / antibacterial humoral response / amyloid fibril formation / protein homotetramerization / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / external side of plasma membrane / signaling receptor binding / Golgi membrane / innate immune response / focal adhesion / lysosomal membrane / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / : / RNA binding / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane
Similarity search - Function
MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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 / : ...MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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
HLA class I histocompatibility antigen, A alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Kirsten murine sarcoma virus
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.09 Å
AuthorsJin, X.Y. / Zhang, Z.Y. / Xi, Y.H. / Gu, Y.H. / Qi, J.X. / Chai, Y. / Tan, S.G. / Gao, G.F.
Funding support China, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022YFC2302900 China
Chinese Academy of SciencesYSBR-083 China
National Natural Science Foundation of China (NSFC)32222031 China
CitationJournal: To Be Published
Title: Commensal Clostridium spp. harbor mimetic CTL-epitopes eliciting T cells cross-recognizing KRAS-G12V tumor neoantigen
Authors: Jin, X.Y. / Wang, W.L. / Zhang, Z.Y. / Gu, Y.H. / Xi, Y.H. / Jiang, M. / Peng, Y.Q. / Yao, P.J. / Tang, L.F. / Ma, K.K. / Wang, J. / Li, F.Y. / Li, X.W. / Jin, W.J. / Chen, Y. / Chai, Y. / ...Authors: Jin, X.Y. / Wang, W.L. / Zhang, Z.Y. / Gu, Y.H. / Xi, Y.H. / Jiang, M. / Peng, Y.Q. / Yao, P.J. / Tang, L.F. / Ma, K.K. / Wang, J. / Li, F.Y. / Li, X.W. / Jin, W.J. / Chen, Y. / Chai, Y. / Qi, J.X. / Zhang, C.W.H. / Liu, K.F. / Wang, J. / Gao, G.F. / Tan, S.G.
History
DepositionAug 22, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: HLA class I histocompatibility antigen, A alpha chain
L: Beta-2-microglobulin
P: G12V9
A: A0PKV-1 TCR beta chain
B: A0PKV-1 TCR alpha chain


Theoretical massNumber of molelcules
Total (without water)97,1775
Polymers97,1775
Non-polymers00
Water97354
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.241, 54.569, 98.893
Angle α, β, γ (deg.)96.234, 94.056, 112.504
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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Protein , 4 types, 4 molecules HLAB

#1: Protein HLA class I histocompatibility antigen, A alpha chain / MHC class I antigen / Human leukocyte antigen A / HLA-A


Mass: 31986.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Production host: Escherichia coli (E. coli) / References: UniProt: P04439
#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
#4: Protein A0PKV-1 TCR beta chain


Mass: 28594.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#5: Protein A0PKV-1 TCR alpha chain


Mass: 23931.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)

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Protein/peptide / Non-polymers , 2 types, 55 molecules P

#3: Protein/peptide G12V9


Mass: 785.951 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kirsten murine sarcoma virus / Production host: Escherichia coli (E. coli)
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.19 Å3/Da / Density % sol: 43.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: 0.1 M Tris pH 8.2, 22% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97861 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 1, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97861 Å / Relative weight: 1
ReflectionResolution: 3.09→48.79 Å / Num. obs: 27466 / % possible obs: 91.1 % / Redundancy: 1.7 % / Biso Wilson estimate: 39.21 Å2 / CC1/2: 0.953 / Rmerge(I) obs: 0.162 / Rrim(I) all: 0.229 / Net I/σ(I): 4.96
Reflection shellResolution: 3.09→3.28 Å / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 1.91 / Num. unique obs: 4474 / CC1/2: 0.687 / Rrim(I) all: 0.608 / % possible all: 92.9

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
PHENIXv1.21-5207refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.09→48.79 Å / SU ML: 0.4642 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 27.5842
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2732 726 5 %
Rwork0.1844 13785 -
obs0.189 14511 96.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.37 Å2
Refinement stepCycle: LAST / Resolution: 3.09→48.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6645 0 0 54 6699
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00886821
X-RAY DIFFRACTIONf_angle_d1.03029264
X-RAY DIFFRACTIONf_chiral_restr0.0529958
X-RAY DIFFRACTIONf_plane_restr0.00841230
X-RAY DIFFRACTIONf_dihedral_angle_d17.08042486
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.09-3.330.31411450.21312765X-RAY DIFFRACTION97.13
3.33-3.660.30961440.20262732X-RAY DIFFRACTION95.14
3.66-4.190.26571480.1832802X-RAY DIFFRACTION97.84
4.19-5.280.24391450.16142760X-RAY DIFFRACTION96.16
5.28-48.790.26141440.18092726X-RAY DIFFRACTION95.03

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