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- PDB-9we1: Crystal structure of HLA-A*11:01 bound to G12V-9-T2 peptide(VTGAVGVGK) -

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Basic information

Entry
Database: PDB / ID: 9we1
TitleCrystal structure of HLA-A*11:01 bound to G12V-9-T2 peptide(VTGAVGVGK)
Components
  • Beta-2-microglobulin
  • G12V9-T2
  • HLA class I histocompatibility antigen, A alpha chain
KeywordsIMMUNE SYSTEM / pMHC
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
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 19, 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: HLA class I histocompatibility antigen, A alpha chain
B: Beta-2-microglobulin
C: G12V9-T2


Theoretical massNumber of molelcules
Total (without water)44,6543
Polymers44,6543
Non-polymers00
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-13 kcal/mol
Surface area18740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.381, 67.187, 76.446
Angle α, β, γ (deg.)90.000, 98.914, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#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
#3: Protein/peptide G12V9-T2


Mass: 787.924 Da / Num. of mol.: 1 / Mutation: V2T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kirsten murine sarcoma virus / Production host: Escherichia coli (E. coli)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O
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: 2.81 Å3/Da / Density % sol: 56.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M Imidazole pH 7.0, 20% w/v PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 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: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.7→50.2 Å / Num. obs: 54877 / % possible obs: 100 % / Redundancy: 4.9 % / Biso Wilson estimate: 22.11 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.039 / Χ2: 0.88 / Net I/σ(I): 11.3
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.919 / Mean I/σ(I) obs: 2 / Num. unique obs: 7964 / CC1/2: 0.429 / Rpim(I) all: 0.468 / Χ2: 0.55 / % possible all: 100

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Processing

Software
NameVersionClassification
autoPROCdata processing
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
PHENIXv1.21-5207refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→27.67 Å / SU ML: 0.2722 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.3181
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2864 2728 4.99 %
Rwork0.2533 51986 -
obs0.255 54714 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.88 Å2
Refinement stepCycle: LAST / Resolution: 1.7→27.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3120 0 0 203 3323
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00653203
X-RAY DIFFRACTIONf_angle_d0.84854345
X-RAY DIFFRACTIONf_chiral_restr0.0528441
X-RAY DIFFRACTIONf_plane_restr0.0081576
X-RAY DIFFRACTIONf_dihedral_angle_d15.40551186
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.730.37951410.35212684X-RAY DIFFRACTION99.02
1.73-1.760.34561450.34282728X-RAY DIFFRACTION99.24
1.76-1.80.37851530.32632675X-RAY DIFFRACTION99.79
1.8-1.830.33031490.31292745X-RAY DIFFRACTION99.66
1.83-1.880.32791250.30772721X-RAY DIFFRACTION100
1.88-1.920.39531430.32452767X-RAY DIFFRACTION99.93
1.92-1.980.33841330.30482736X-RAY DIFFRACTION99.9
1.98-2.030.29591520.29122740X-RAY DIFFRACTION99.93
2.03-2.10.32041470.2792693X-RAY DIFFRACTION100
2.1-2.170.3151500.28522733X-RAY DIFFRACTION100
2.17-2.260.3291550.28292740X-RAY DIFFRACTION99.79
2.26-2.360.31231270.2772735X-RAY DIFFRACTION99.93
2.36-2.490.32571460.27952738X-RAY DIFFRACTION100
2.49-2.640.37391350.29122739X-RAY DIFFRACTION99.97
2.65-2.850.31651490.2862739X-RAY DIFFRACTION99.79
2.85-3.140.29461340.26562756X-RAY DIFFRACTION99.9
3.14-3.590.32071330.24542773X-RAY DIFFRACTION99.86
3.59-4.520.23951540.20192764X-RAY DIFFRACTION99.69
4.52-27.670.18511570.18132780X-RAY DIFFRACTION98.89

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