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- PDB-8vjz: HLA-A*03:01 with WT KRAS-10mer -

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Basic information

Entry
Database: PDB / ID: 8vjz
TitleHLA-A*03:01 with WT KRAS-10mer
Components
  • Beta-2-microglobulin
  • GTPase KRas, N-terminally processed
  • HLA class I histocompatibility antigen, A alpha chain
KeywordsIMMUNE SYSTEM / HLA-A*03:01 presenting peptide from KRAS (VVVGAGGVGK)
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 / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / SHC1 events in ERBB4 signaling / 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) / Erythropoietin activates RAS / Signaling by FGFR4 in disease / 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 / positive regulation of glial cell proliferation / Tie2 Signaling / 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 / EGFR Transactivation by Gastrin / Signaling by FGFR1 in disease / 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 / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / RAF activation / 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 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 / 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 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 / 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: 1.9 Å
AuthorsSim, M.J.W. / Sun, P.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
Citation
Journal: Eur.J.Immunol. / Year: 2024
Title: Identification and structural characterization of a mutant KRAS-G12V specific TCR restricted by HLA-A3.
Authors: Sim, M.J.W. / Hanada, K.I. / Stotz, Z. / Yu, Z. / Lu, J. / Brennan, P. / Quastel, M. / Gillespie, G.M. / Long, E.O. / Yang, J.C. / Sun, P.D.
#1: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
History
DepositionJan 8, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2024Provider: 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: GTPase KRas, N-terminally processed
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6414
Polymers44,5493
Non-polymers921
Water7,674426
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4790 Å2
ΔGint-20 kcal/mol
Surface area18980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.637, 154.637, 85.365
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number177
Space group name H-MP622
Symmetry operation#1: x,y,z
#2: x-y,x,z
#3: y,-x+y,z
#4: -y,x-y,z
#5: -x+y,-x,z
#6: x-y,-y,-z
#7: -x,-x+y,-z
#8: -x,-y,z
#9: y,x,-z
#10: -y,-x,-z
#11: -x+y,y,-z
#12: x,x-y,-z
Components on special symmetry positions
IDModelComponents
11A-597-

HOH

21A-798-

HOH

31A-815-

HOH

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Components

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


Mass: 31958.188 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: 11748.160 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 GTPase KRas, N-terminally processed


Mass: 843.003 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KRAS, KRAS2, RASK2 / Production host: synthetic construct (others) / References: UniProt: P01116
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 426 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.31 Å3/Da / Density % sol: 62.8 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.1M ammonium citrate tribasic pH7, 12% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 2.1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.1 Å / Relative weight: 1
ReflectionResolution: 1.9→37.14 Å / Num. obs: 47684 / % possible obs: 99.49 % / Redundancy: 1.11 % / Biso Wilson estimate: 22.64 Å2 / CC1/2: 1 / CC star: 1 / Net I/σ(I): 32.18
Reflection shellResolution: 1.9→1.968 Å / Mean I/σ(I) obs: 7.71 / Num. unique obs: 4611 / CC1/2: 1

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→37.14 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 20.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2141 2434 5.11 %
Rwork0.1834 --
obs0.185 47639 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→37.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3140 0 6 426 3572
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083254
X-RAY DIFFRACTIONf_angle_d0.9234417
X-RAY DIFFRACTIONf_dihedral_angle_d6.541442
X-RAY DIFFRACTIONf_chiral_restr0.059451
X-RAY DIFFRACTIONf_plane_restr0.017585
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.940.28511280.24622610X-RAY DIFFRACTION99
1.94-1.980.26351290.21782590X-RAY DIFFRACTION99
1.98-2.020.27051350.20642609X-RAY DIFFRACTION99
2.02-2.080.23341270.19822636X-RAY DIFFRACTION99
2.08-2.130.21681450.19242607X-RAY DIFFRACTION99
2.13-2.190.23181370.19142628X-RAY DIFFRACTION100
2.19-2.270.22991500.18962620X-RAY DIFFRACTION100
2.27-2.350.22431480.20142629X-RAY DIFFRACTION100
2.35-2.440.23371310.19942649X-RAY DIFFRACTION100
2.44-2.550.24791550.1972623X-RAY DIFFRACTION100
2.55-2.690.23071440.192662X-RAY DIFFRACTION100
2.69-2.850.21361480.19552658X-RAY DIFFRACTION100
2.85-3.070.23251560.18752654X-RAY DIFFRACTION100
3.07-3.380.2251360.18062697X-RAY DIFFRACTION100
3.38-3.870.18851490.17012712X-RAY DIFFRACTION100
3.87-4.880.19241690.14572719X-RAY DIFFRACTION100
4.88-37.140.17191470.18282902X-RAY DIFFRACTION99

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