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- PDB-8k4t: Crystal structure of HLA-A*11:01 in complex with KRAS G12C peptid... -

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Basic information

Entry
Database: PDB / ID: 8k4t
TitleCrystal structure of HLA-A*11:01 in complex with KRAS G12C peptide (VVVGACGVGK)
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A alpha chain
  • KRAS G12C peptide (VVVGACGVGK)
KeywordsIMMUNE SYSTEM / cancer immunotherapy
Function / homology
Function and homology information


forebrain astrocyte development / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / 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 / negative regulation of epithelial cell differentiation / CD8 receptor binding ...forebrain astrocyte development / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / 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 / negative regulation of epithelial cell differentiation / CD8 receptor binding / type I pneumocyte differentiation / regulation of synaptic transmission, GABAergic / epithelial tube branching involved in lung morphogenesis / Rac protein signal transduction / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding / positive regulation of Rac protein signal transduction / skeletal muscle cell differentiation / endoplasmic reticulum exit site / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP binding / RAS signaling downstream of NF1 loss-of-function variants / protection from natural killer cell mediated cytotoxicity / RUNX3 regulates p14-ARF / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / Signalling to RAS / Activated NTRK2 signals through FRS2 and FRS3 / SHC-related events triggered by IGF1R / glial cell proliferation / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / detection of bacterium / MET activates RAS signaling / T cell receptor binding / SHC-mediated cascade:FGFR2 / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / SHC-mediated cascade:FGFR4 / Signaling by CSF3 (G-CSF) / Signaling by FGFR4 in disease / Erythropoietin activates RAS / SHC-mediated cascade:FGFR1 / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / protein-membrane adaptor activity / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / p38MAPK events / Tie2 Signaling / positive regulation of glial cell proliferation / FRS-mediated FGFR1 signaling / homeostasis of number of cells within a tissue / Signaling by FGFR2 in disease / striated muscle cell differentiation / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / Signaling by FLT3 fusion proteins / FLT3 Signaling / Signaling by FGFR1 in disease / EGFR Transactivation by Gastrin / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / GRB2 events in ERBB2 signaling / Downstream signal transduction / Ras activation upon Ca2+ influx through NMDA receptor / SHC1 events in ERBB2 signaling / Insulin receptor signalling cascade / Constitutive Signaling by Overexpressed ERBB2 / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / : / : / positive regulation of receptor binding / early endosome lumen / VEGFR2 mediated cell proliferation / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / small monomeric GTPase / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / FCERI mediated MAPK activation / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / RAF activation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / MHC class II protein complex / negative regulation of forebrain neuron differentiation / regulation of long-term neuronal synaptic plasticity
Similarity search - Function
Small GTPase, Ras-type / small GTPase Ras family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I alpha chain, alpha1 alpha2 domains / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Class I Histocompatibility antigen, domains alpha 1 and 2 / Small GTPase ...Small GTPase, Ras-type / small GTPase Ras family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I alpha chain, alpha1 alpha2 domains / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Class I Histocompatibility antigen, domains alpha 1 and 2 / Small GTPase / Ras family / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Rab subfamily of small GTPases / MHC classes I/II-like antigen recognition protein / : / Small GTP-binding protein domain / 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
GTPase KRas / 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: 2.3 Å
AuthorsXu, Y.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2021YFA1302200 China
CitationJournal: To Be Published
Title: Crystal structure of HLA-A*11:01 in complex with KRAS G12C peptide (VVVGACGVGK)
Authors: Xu, Y.
History
DepositionJul 20, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 29, 2025Provider: 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: KRAS G12C peptide (VVVGACGVGK)
D: HLA class I histocompatibility antigen, A alpha chain
E: Beta-2-microglobulin
F: KRAS G12C peptide (VVVGACGVGK)


Theoretical massNumber of molelcules
Total (without water)94,0826
Polymers94,0826
Non-polymers00
Water00
1
A: HLA class I histocompatibility antigen, A alpha chain
B: Beta-2-microglobulin
C: KRAS G12C peptide (VVVGACGVGK)


Theoretical massNumber of molelcules
Total (without water)47,0413
Polymers47,0413
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3840 Å2
ΔGint-18 kcal/mol
Surface area18790 Å2
MethodPISA
2
D: HLA class I histocompatibility antigen, A alpha chain
E: Beta-2-microglobulin
F: KRAS G12C peptide (VVVGACGVGK)


Theoretical massNumber of molelcules
Total (without water)47,0413
Polymers47,0413
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3880 Å2
ΔGint-16 kcal/mol
Surface area18770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.708, 63.579, 75.507
Angle α, β, γ (deg.)105.864, 92.656, 97.701
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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


Mass: 31986.250 Da / Num. of mol.: 2
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.: 2
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 G12C peptide (VVVGACGVGK)


Mass: 889.094 Da / Num. of mol.: 2 / Mutation: G12C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KRAS, KRAS2, RASK2 / Production host: Escherichia coli (E. coli) / References: UniProt: P01116
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: 2.51 Å3/Da / Density % sol: 51.07 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion
Details: Ammonium sulfate,Sodium cacodylate pH 6.0, PEG 4000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 37232 / % possible obs: 97.32 % / Redundancy: 3.5 % / Biso Wilson estimate: 49.69 Å2 / CC1/2: 0.999 / Net I/σ(I): 21.53
Reflection shellResolution: 2.3→2.382 Å / Num. unique obs: 3676 / CC1/2: 0.883

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata scaling
Cootmodel building
PHENIX1.17.1_3660phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→28.78 Å / SU ML: 0.4036 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 38.4226
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.316 3904 5.38 %
Rwork0.2576 68712 -
obs0.2607 37232 94.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.7 Å2
Refinement stepCycle: LAST / Resolution: 2.3→28.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6213 0 0 0 6213
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00216379
X-RAY DIFFRACTIONf_angle_d0.50938655
X-RAY DIFFRACTIONf_chiral_restr0.0397881
X-RAY DIFFRACTIONf_plane_restr0.00331145
X-RAY DIFFRACTIONf_dihedral_angle_d23.4818857
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.320.57191290.45112274X-RAY DIFFRACTION87.83
2.32-2.350.44981420.41862468X-RAY DIFFRACTION95.81
2.35-2.380.45671380.40922432X-RAY DIFFRACTION95.97
2.38-2.420.45891410.39242548X-RAY DIFFRACTION95.15
2.42-2.450.42351440.39142462X-RAY DIFFRACTION95.81
2.45-2.490.39021390.38432437X-RAY DIFFRACTION95.69
2.49-2.530.45251410.37012520X-RAY DIFFRACTION95.86
2.53-2.570.44031410.37212487X-RAY DIFFRACTION94.81
2.57-2.610.3781330.3462403X-RAY DIFFRACTION94.77
2.61-2.660.41431440.35042524X-RAY DIFFRACTION95.56
2.66-2.710.32031420.3462501X-RAY DIFFRACTION95.69
2.71-2.770.34711350.33272433X-RAY DIFFRACTION93.93
2.77-2.830.34221390.32732457X-RAY DIFFRACTION95.79
2.83-2.890.34211420.33462540X-RAY DIFFRACTION95.85
2.89-2.960.38321390.31282427X-RAY DIFFRACTION96.18
2.96-3.040.34861440.3262569X-RAY DIFFRACTION96.34
3.04-3.130.39951400.32332491X-RAY DIFFRACTION96.23
3.13-3.240.33651440.29642492X-RAY DIFFRACTION96.27
3.24-3.350.38861410.282457X-RAY DIFFRACTION95.94
3.35-3.480.37711390.2712477X-RAY DIFFRACTION94.78
3.48-3.640.39671360.26412463X-RAY DIFFRACTION94.85
3.64-3.830.31291410.24032420X-RAY DIFFRACTION92.92
3.83-4.070.29381430.22752393X-RAY DIFFRACTION93.17
4.08-4.390.24821370.20422447X-RAY DIFFRACTION93.69
4.39-4.830.25341380.18712430X-RAY DIFFRACTION93.18
4.83-5.520.25621380.19922384X-RAY DIFFRACTION93.34
5.52-6.940.30461400.21622428X-RAY DIFFRACTION92.11
6.94-28.780.1681340.15382348X-RAY DIFFRACTION91.05

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