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- PDB-9uv8: Crystal structure of HLA-A*11:01 in complex with KRAS G12D 9-mer ... -

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Basic information

Entry
Database: PDB / ID: 9uv8
TitleCrystal structure of HLA-A*11:01 in complex with KRAS G12D 9-mer peptide (VVGADGVGK)
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A alpha chain
  • KRAS G12D-9mer (VVGADGVGK)
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: 1.79 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
DepositionMay 9, 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: KRAS G12D-9mer (VVGADGVGK)


Theoretical massNumber of molelcules
Total (without water)46,9543
Polymers46,9543
Non-polymers00
Water5,873326
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-15 kcal/mol
Surface area18910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.249, 80.002, 57.692
Angle α, β, γ (deg.)90.00, 116.40, 90.00
Int Tables number4
Space group name H-MP1211

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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: 14165.771 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 KRAS G12D-9mer (VVGADGVGK)


Mass: 801.908 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)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / 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: 2.6 Å3/Da / Density % sol: 52.75 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 27% PEG3350,0.1M Bis-Tris,0.2M Lithium sulfate,additve 0.1M Spermidine

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Data collection

DiffractionMean temperature: 80 K / Ambient temp details: liquid N2 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97861 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 22, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97861 Å / Relative weight: 1
ReflectionResolution: 1.79→51.67 Å / Num. obs: 42599 / % possible obs: 98.3 % / Redundancy: 4.7 % / Biso Wilson estimate: 15.31 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.046 / Rrim(I) all: 0.1 / Χ2: 1.02 / Net I/σ(I): 13.9
Reflection shellResolution: 1.79→1.88 Å / Rmerge(I) obs: 0.556 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 5880 / CC1/2: 0.693 / Rpim(I) all: 0.327 / Rrim(I) all: 0.649 / Χ2: 0.95

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→51.67 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2309 1963 4.63 %
Rwork0.1917 --
obs0.1935 42435 97.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.79→51.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3128 0 0 326 3454
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083211
X-RAY DIFFRACTIONf_angle_d1.094354
X-RAY DIFFRACTIONf_dihedral_angle_d16.3111189
X-RAY DIFFRACTIONf_chiral_restr0.063441
X-RAY DIFFRACTIONf_plane_restr0.02577
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.830.32211150.26452573X-RAY DIFFRACTION88
1.83-1.880.3031370.25462903X-RAY DIFFRACTION98
1.88-1.940.26431440.24132929X-RAY DIFFRACTION99
1.94-20.27921550.2262928X-RAY DIFFRACTION99
2-2.070.23641300.21872922X-RAY DIFFRACTION99
2.07-2.150.27281450.21292913X-RAY DIFFRACTION99
2.15-2.250.24581380.2022909X-RAY DIFFRACTION99
2.25-2.370.23741300.2012922X-RAY DIFFRACTION99
2.37-2.520.24331450.19182960X-RAY DIFFRACTION100
2.52-2.710.21971490.18532910X-RAY DIFFRACTION99
2.71-2.990.19191450.17372947X-RAY DIFFRACTION99
2.99-3.420.22131400.16752910X-RAY DIFFRACTION99
3.42-4.30.20511450.16232910X-RAY DIFFRACTION97
4.31-51.670.21431450.18642836X-RAY DIFFRACTION94
Refinement TLS params.Method: refined / Origin x: -6.93 Å / Origin y: -1.045 Å / Origin z: -7.5825 Å
111213212223313233
T0.1051 Å20.0064 Å2-0.0115 Å2-0.1109 Å2-0.0057 Å2--0.1001 Å2
L0.2937 °20.1742 °2-0.1003 °2-0.3773 °20.057 °2--0.0798 °2
S0.006 Å °0.0183 Å °-0.0414 Å °0.0208 Å °0.0126 Å °-0.0179 Å °0.0017 Å °-0.0128 Å °0.0011 Å °
Refinement TLS groupSelection details: all

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