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- PDB-9wfs: Crystal structure of 3-2E TCR in complex with HLA-A*11:01 bound t... -

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Basic information

Entry
Database: PDB / ID: 9wfs
TitleCrystal structure of 3-2E TCR in complex with HLA-A*11:01 bound to A0PXA8 peptide(ITGAVGIAK)
Components
  • 3-2E TCR alpha chain
  • 3-2E TCR beta chain
  • Adenylosuccinate synthetase
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A alpha chain
KeywordsIMMUNE SYSTEM / pMHC / TCR / Complex
Function / homology
Function and homology information


adenylosuccinate synthase / adenylosuccinate synthase activity / IMP metabolic process / 'de novo' AMP biosynthetic process / 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 ...adenylosuccinate synthase / adenylosuccinate synthase activity / IMP metabolic process / 'de novo' AMP biosynthetic process / 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 / GTP binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / magnesium ion binding / cell surface / endoplasmic reticulum / protein homodimerization activity / : / RNA binding
Similarity search - Function
Adenylosuccinate synthase, active site / Adenylosuccinate synthetase active site. / Adenylosuccinate synthase, GTP-binding site / Adenylosuccinate synthetase, domain 2 / Adenylosuccinate synthetase, domain 3 / Adenylosuccinate synthetase GTP-binding site. / Adenylosuccinate synthetase / Adenylosuccinate synthetase, domain 1 / Adenylosuccinate synthetase / Adenylosuccinate synthetase ...Adenylosuccinate synthase, active site / Adenylosuccinate synthetase active site. / Adenylosuccinate synthase, GTP-binding site / Adenylosuccinate synthetase, domain 2 / Adenylosuccinate synthetase, domain 3 / Adenylosuccinate synthetase GTP-binding site. / Adenylosuccinate synthetase / Adenylosuccinate synthetase, domain 1 / Adenylosuccinate synthetase / Adenylosuccinate synthetase / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Adenylosuccinate synthetase / HLA class I histocompatibility antigen, A alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
Clostridium novyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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

Downloads & links

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Assembly

Deposited unit
A: 3-2E TCR alpha chain
B: 3-2E TCR beta chain
H: HLA class I histocompatibility antigen, A alpha chain
L: Beta-2-microglobulin
P: Adenylosuccinate synthetase


Theoretical massNumber of molelcules
Total (without water)97,5225
Polymers97,5225
Non-polymers00
Water86548
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)119.095, 119.095, 313.054
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Space group name HallP622(x,y,z+1/3)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/3
#3: y,-x+y,z+2/3
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z
#9: y,x,-z+2/3
#10: -y,-x,-z+2/3
#11: -x+y,y,-z
#12: x,x-y,-z+1/3

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Components

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Protein , 4 types, 4 molecules ABHL

#1: Protein 3-2E TCR alpha chain


Mass: 23873.344 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)
#2: Protein 3-2E TCR beta chain


Mass: 28953.244 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)
#3: 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
#4: 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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Protein/peptide / Non-polymers , 2 types, 49 molecules P

#5: Protein/peptide Adenylosuccinate synthetase / AMPSase / AdSS / IMP--aspartate ligase


Mass: 830.004 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium novyi (strain NT) (bacteria)
Gene: purA, NT01CX_0905 / Production host: Escherichia coli (E. coli) / References: UniProt: A0PXA8, adenylosuccinate synthase
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 3.29 Å3/Da / Density % sol: 62.57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 0.1M Sodium Cacodylate pH 7.2, 8% w/v gamma-PGA, 14% Polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Sep 15, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 2.997→104.351 Å / Num. obs: 49672 / % possible obs: 99.4 % / Redundancy: 17.7 % / Biso Wilson estimate: 66.31 Å2 / CC1/2: 0.995 / Net I/σ(I): 10.66
Reflection shellResolution: 3→3.18 Å / Mean I/σ(I) obs: 1.64 / Num. unique obs: 8074 / CC1/2: 0.665 / % possible all: 99.7

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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→86.12 Å / SU ML: 0.5125 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.9956
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2974 1353 4.98 %
Rwork0.2396 25791 -
obs0.2425 27144 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 72.38 Å2
Refinement stepCycle: LAST / Resolution: 3→86.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6573 0 0 48 6621
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00866738
X-RAY DIFFRACTIONf_angle_d1.04259151
X-RAY DIFFRACTIONf_chiral_restr0.0555969
X-RAY DIFFRACTIONf_plane_restr0.00821203
X-RAY DIFFRACTIONf_dihedral_angle_d18.35072464
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.10.42521330.39252517X-RAY DIFFRACTION99.59
3.1-3.230.40771320.33672534X-RAY DIFFRACTION99.29
3.23-3.370.37941310.30142495X-RAY DIFFRACTION99.17
3.37-3.550.29481320.28262533X-RAY DIFFRACTION99.37
3.55-3.780.34221320.27412533X-RAY DIFFRACTION99.4
3.78-4.070.32561340.23472550X-RAY DIFFRACTION98.89
4.07-4.480.30381340.22442558X-RAY DIFFRACTION98.97
4.48-5.120.26781370.21132591X-RAY DIFFRACTION99.31
5.13-6.450.3341400.21712649X-RAY DIFFRACTION99.43
6.46-86.120.20271480.18592831X-RAY DIFFRACTION99.23

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