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- PDB-8k50: Crystal structure of HLA-A*11:01 in complex with KRAS G12V peptid... -

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Basic information

Entry
Database: PDB / ID: 8k50
TitleCrystal structure of HLA-A*11:01 in complex with KRAS G12V peptide (VVVGARGVGK)
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A alpha chain
  • KRAS G12V peptide (VVVGAVGVGK)
KeywordsIMMUNE SYSTEM / cancer immunotherapy
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 / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / response to mineralocorticoid / GMP binding / positive regulation of CD8-positive, alpha-beta T cell proliferation / 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 / response to mineralocorticoid / GMP binding / positive regulation of CD8-positive, alpha-beta T cell proliferation / forebrain astrocyte development / LRR domain binding / regulation of synaptic transmission, GABAergic / negative regulation of epithelial cell differentiation / CD8 receptor binding / response to isolation stress / antigen processing and presentation of exogenous peptide antigen via MHC class I / response to gravity / epithelial tube branching involved in lung morphogenesis / beta-2-microglobulin binding / type I pneumocyte differentiation / Rac protein signal transduction / endoplasmic reticulum exit site / TAP binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of Rac protein signal transduction / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / protection from natural killer cell mediated cytotoxicity / myoblast proliferation / RAS signaling downstream of NF1 loss-of-function variants / skeletal muscle cell differentiation / RUNX3 regulates p14-ARF / positive regulation of glial cell proliferation / 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 / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / cardiac muscle cell proliferation / Signalling to RAS / detection of bacterium / Activated NTRK2 signals through FRS2 and FRS3 / SHC-related events triggered by IGF1R / Estrogen-stimulated signaling through PRKCZ / glial cell proliferation / SHC-mediated cascade:FGFR3 / 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 / SHC-mediated cascade:FGFR4 / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Erythropoietin activates RAS / SHC-mediated cascade:FGFR1 / Signaling by FGFR4 in disease / FRS-mediated FGFR3 signaling / Signaling by CSF3 (G-CSF) / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / FRS-mediated FGFR1 signaling / p38MAPK events / Signaling by FGFR3 in disease / protein-membrane adaptor activity / Tie2 Signaling / striated muscle cell differentiation / Signaling by FGFR2 in disease / 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 / Downstream signal transduction / GRB2 events in ERBB2 signaling / homeostasis of number of cells within a tissue / Insulin receptor signalling cascade / Ras activation upon Ca2+ influx through NMDA receptor / SHC1 events in ERBB2 signaling / response to glucocorticoid / Constitutive Signaling by Overexpressed ERBB2 / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / VEGFR2 mediated cell proliferation / transferrin transport / small monomeric GTPase / cellular response to iron ion / Endosomal/Vacuolar pathway / FCERI mediated MAPK activation / 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
Similarity search - Function
Small GTPase, Ras-type / Small GTPase Ras domain 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 / Class I Histocompatibility antigen, domains alpha 1 and 2 / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase ...Small GTPase, Ras-type / Small GTPase Ras domain 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 / Class I Histocompatibility antigen, domains alpha 1 and 2 / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / 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: 2.8 Å
AuthorsXu, K.
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 G12R peptide (VVVGARGVGK)
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

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, A alpha chain
B: Beta-2-microglobulin
C: KRAS G12V peptide (VVVGAVGVGK)
D: HLA class I histocompatibility antigen, A alpha chain
E: Beta-2-microglobulin
F: KRAS G12V peptide (VVVGAVGVGK)
G: HLA class I histocompatibility antigen, A alpha chain
H: Beta-2-microglobulin
I: KRAS G12V peptide (VVVGAVGVGK)
J: HLA class I histocompatibility antigen, A alpha chain
K: Beta-2-microglobulin
L: KRAS G12V peptide (VVVGAVGVGK)


Theoretical massNumber of molelcules
Total (without water)188,14812
Polymers188,14812
Non-polymers00
Water00
1
A: HLA class I histocompatibility antigen, A alpha chain
B: Beta-2-microglobulin
C: KRAS G12V peptide (VVVGAVGVGK)


Theoretical massNumber of molelcules
Total (without water)47,0373
Polymers47,0373
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-18 kcal/mol
Surface area18860 Å2
MethodPISA
2
D: HLA class I histocompatibility antigen, A alpha chain
E: Beta-2-microglobulin
F: KRAS G12V peptide (VVVGAVGVGK)


Theoretical massNumber of molelcules
Total (without water)47,0373
Polymers47,0373
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-19 kcal/mol
Surface area19010 Å2
MethodPISA
3
G: HLA class I histocompatibility antigen, A alpha chain
H: Beta-2-microglobulin
I: KRAS G12V peptide (VVVGAVGVGK)


Theoretical massNumber of molelcules
Total (without water)47,0373
Polymers47,0373
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-20 kcal/mol
Surface area18670 Å2
MethodPISA
4
J: HLA class I histocompatibility antigen, A alpha chain
K: Beta-2-microglobulin
L: KRAS G12V peptide (VVVGAVGVGK)


Theoretical massNumber of molelcules
Total (without water)47,0373
Polymers47,0373
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-17 kcal/mol
Surface area18820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.289, 121.845, 133.376
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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.: 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
KRAS G12V peptide (VVVGAVGVGK)


Mass: 885.082 Da / Num. of mol.: 4 / Mutation: G12V
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: 51.02 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / Details: Ammonium sulfate, Sodium cacodylate, PEG 4000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 47325 / % possible obs: 99.79 % / Redundancy: 13.2 % / Biso Wilson estimate: 48.85 Å2 / CC1/2: 0.998 / Net I/σ(I): 16.98
Reflection shellResolution: 2.8→2.9 Å / Num. unique obs: 4698 / CC1/2: 0.917

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660phasing
PHENIX1.17.1_3660refinement
Cootmodel building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→44.98 Å / SU ML: 0.3659 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.4461
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2809 3777 4.18 %
Rwork0.2226 86581 -
obs0.225 47325 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.99 Å2
Refinement stepCycle: LAST / Resolution: 2.8→44.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12534 0 0 0 12534
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002612864
X-RAY DIFFRACTIONf_angle_d0.511217443
X-RAY DIFFRACTIONf_chiral_restr0.04081774
X-RAY DIFFRACTIONf_plane_restr0.00322307
X-RAY DIFFRACTIONf_dihedral_angle_d23.42171730
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.830.39491340.32873201X-RAY DIFFRACTION98.73
2.83-2.870.26771290.29053217X-RAY DIFFRACTION99.79
2.87-2.910.36481380.29013218X-RAY DIFFRACTION99.88
2.91-2.950.35611580.29373202X-RAY DIFFRACTION99.91
2.95-2.990.32561320.27653179X-RAY DIFFRACTION99.85
2.99-3.040.35881410.27423219X-RAY DIFFRACTION99.91
3.04-3.090.33261490.27173163X-RAY DIFFRACTION99.61
3.09-3.140.39441260.27243232X-RAY DIFFRACTION99.76
3.14-3.20.30541580.25943199X-RAY DIFFRACTION99.79
3.2-3.260.33591380.24543201X-RAY DIFFRACTION99.73
3.26-3.330.33461230.25133243X-RAY DIFFRACTION99.94
3.33-3.40.29571510.23863188X-RAY DIFFRACTION99.91
3.4-3.480.35171480.23683220X-RAY DIFFRACTION99.94
3.48-3.570.23871270.22723197X-RAY DIFFRACTION99.88
3.57-3.660.25391520.23013217X-RAY DIFFRACTION99.94
3.66-3.770.26911470.23123229X-RAY DIFFRACTION99.91
3.77-3.890.25751490.22893187X-RAY DIFFRACTION99.94
3.89-4.030.35141270.21013221X-RAY DIFFRACTION99.88
4.03-4.190.311430.21333196X-RAY DIFFRACTION99.97
4.19-4.380.25571400.20113191X-RAY DIFFRACTION99.94
4.38-4.610.21461360.18673243X-RAY DIFFRACTION99.91
4.61-4.90.23851450.17753213X-RAY DIFFRACTION100
4.9-5.280.29771340.19013214X-RAY DIFFRACTION99.88
5.28-5.810.23311370.19913226X-RAY DIFFRACTION99.88
5.81-6.650.28531410.22043189X-RAY DIFFRACTION99.94
6.65-8.370.22741390.19543213X-RAY DIFFRACTION99.88
8.37-44.980.19431350.18643163X-RAY DIFFRACTION98.3

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