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- PDB-9wve: Crystal structure of HLA-A*11:01 in complex with KRAS G12A 10-mer... -

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Basic information

Entry
Database: PDB / ID: 9wve
TitleCrystal structure of HLA-A*11:01 in complex with KRAS G12A 10-mer peptide (VVVGAAGVGK)
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A alpha chain
  • VAL-VAL-VAL-GLY-ALA-ALA-GLY-VAL-GLY-LYS
KeywordsIMMUNE SYSTEM / Complex
Function / homology
Function and homology information


positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding ...positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding / endoplasmic reticulum exit site / TAP binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / protection from natural killer cell mediated cytotoxicity / 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 / detection of bacterium / T cell receptor binding / negative regulation of iron ion transport / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / negative regulation of receptor-mediated endocytosis / 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 / lumenal side of endoplasmic reticulum membrane / 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 erythrocyte differentiation / regulation of iron ion transport / 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 / peptide antigen binding / positive regulation of T cell activation / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / positive regulation of type II interferon production / 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 / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / antibacterial humoral response / DAP12 signaling / T cell differentiation in thymus / T cell receptor signaling pathway / negative regulation of neuron projection development / E3 ubiquitin ligases ubiquitinate target proteins / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / signaling receptor binding / innate immune response / external side of plasma membrane / lysosomal membrane / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / RNA binding
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsJiali, Z. / Linlin, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Commun Biol / Year: 2025
Title: Structure guided analysis of KRAS G12 mutants in HLA-A*11:01 reveals a length encoded immunogenic advantage in G12D.
Authors: Zhu, J. / Chen, Z. / Xu, X. / Wang, Y. / Liu, P. / Wen, M. / Wang, Q. / He, Y. / Jin, H. / Xue, H. / Wang, S. / Xu, K. / Zhao, L.
History
DepositionSep 19, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 24, 2025Provider: repository / Type: Initial release
Revision 1.1Jan 21, 2026Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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: VAL-VAL-VAL-GLY-ALA-ALA-GLY-VAL-GLY-LYS
D: HLA class I histocompatibility antigen, A alpha chain
E: Beta-2-microglobulin
F: VAL-VAL-VAL-GLY-ALA-ALA-GLY-VAL-GLY-LYS
G: HLA class I histocompatibility antigen, A alpha chain
H: Beta-2-microglobulin
I: VAL-VAL-VAL-GLY-ALA-ALA-GLY-VAL-GLY-LYS
J: HLA class I histocompatibility antigen, A alpha chain
K: Beta-2-microglobulin
L: VAL-VAL-VAL-GLY-ALA-ALA-GLY-VAL-GLY-LYS


Theoretical massNumber of molelcules
Total (without water)188,03612
Polymers188,03612
Non-polymers00
Water1,29772
1
A: HLA class I histocompatibility antigen, A alpha chain
B: Beta-2-microglobulin
C: VAL-VAL-VAL-GLY-ALA-ALA-GLY-VAL-GLY-LYS


Theoretical massNumber of molelcules
Total (without water)47,0093
Polymers47,0093
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-18 kcal/mol
Surface area18910 Å2
MethodPISA
2
D: HLA class I histocompatibility antigen, A alpha chain
E: Beta-2-microglobulin
F: VAL-VAL-VAL-GLY-ALA-ALA-GLY-VAL-GLY-LYS


Theoretical massNumber of molelcules
Total (without water)47,0093
Polymers47,0093
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-18 kcal/mol
Surface area19010 Å2
MethodPISA
3
G: HLA class I histocompatibility antigen, A alpha chain
H: Beta-2-microglobulin
I: VAL-VAL-VAL-GLY-ALA-ALA-GLY-VAL-GLY-LYS


Theoretical massNumber of molelcules
Total (without water)47,0093
Polymers47,0093
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-20 kcal/mol
Surface area18980 Å2
MethodPISA
4
J: HLA class I histocompatibility antigen, A alpha chain
K: Beta-2-microglobulin
L: VAL-VAL-VAL-GLY-ALA-ALA-GLY-VAL-GLY-LYS


Theoretical massNumber of molelcules
Total (without water)47,0093
Polymers47,0093
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-19 kcal/mol
Surface area18980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.875, 121.573, 132.587
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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.: 4
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: 14165.771 Da / Num. of mol.: 4
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
VAL-VAL-VAL-GLY-ALA-ALA-GLY-VAL-GLY-LYS


Mass: 857.029 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.55 Å3/Da / Density % sol: 51.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 23% PEG3350, 0.1M Bis-Tris, PH5.8, 0.2M Lithium sulfate

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Data collection

DiffractionMean temperature: 80 K / Ambient temp details: liquid nitrogen / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97861 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 15, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97861 Å / Relative weight: 1
ReflectionResolution: 2.8→44.8 Å / Num. obs: 47986 / % possible obs: 99.9 % / Redundancy: 5.3 % / CC1/2: 0.993 / Rmerge(I) obs: 0.218 / Rpim(I) all: 0.103 / Rrim(I) all: 0.242 / Χ2: 1.01 / Net I/σ(I): 6.9 / Num. measured all: 256236
Reflection shellResolution: 2.8→2.89 Å / % possible obs: 100 % / Redundancy: 5.2 % / Rmerge(I) obs: 2.145 / Num. measured all: 22597 / Num. unique obs: 4385 / CC1/2: 0.385 / Rpim(I) all: 1.046 / Rrim(I) all: 2.393 / Χ2: 0.96 / Net I/σ(I) obs: 0.7

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→44.8 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2671 2001 4.18 %
Rwork0.2468 --
obs0.2476 47828 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→44.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12384 0 0 72 12456
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112711
X-RAY DIFFRACTIONf_angle_d1.21717252
X-RAY DIFFRACTIONf_dihedral_angle_d6.2431714
X-RAY DIFFRACTIONf_chiral_restr0.0661766
X-RAY DIFFRACTIONf_plane_restr0.0142285
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.870.42261420.41223229X-RAY DIFFRACTION99
2.87-2.950.42531310.3843245X-RAY DIFFRACTION100
2.95-3.030.35751480.35753232X-RAY DIFFRACTION100
3.03-3.130.39951410.34433234X-RAY DIFFRACTION100
3.13-3.240.33611350.32033234X-RAY DIFFRACTION100
3.24-3.370.32581470.30193243X-RAY DIFFRACTION100
3.37-3.530.30521380.27533246X-RAY DIFFRACTION100
3.53-3.710.31171480.2633261X-RAY DIFFRACTION100
3.71-3.950.26781420.24553244X-RAY DIFFRACTION100
3.95-4.250.23151420.22163296X-RAY DIFFRACTION100
4.25-4.680.21521490.19573249X-RAY DIFFRACTION99
4.68-5.350.2021400.18983300X-RAY DIFFRACTION100
5.35-6.740.24571480.2313342X-RAY DIFFRACTION100
6.74-44.80.20561500.19683472X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 29.8341 Å / Origin y: 11.5917 Å / Origin z: -30.4172 Å
111213212223313233
T0.5448 Å2-0.0133 Å20.1784 Å2-0.6491 Å2-0.1396 Å2--0.6225 Å2
L0.5524 °20.17 °20.0015 °2-1.29 °2-0.3657 °2--0.211 °2
S0.3294 Å °0.0239 Å °0.1696 Å °0.1644 Å °-0.2581 Å °0.5394 Å °-0.0682 Å °0.0157 Å °-0.0692 Å °
Refinement TLS groupSelection details: all

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