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- PDB-8rro: G12V-TCR complex with HLA-A3 -

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Basic information

Entry
Database: PDB / ID: 8rro
TitleG12V-TCR complex with HLA-A3
Components
  • Beta-2-microglobulin
  • G12V-TCR alpha chain
  • G12V-TCR beta chain
  • GTPase KRas, N-terminally processed
  • HLA class I histocompatibility antigen, A alpha chain
KeywordsIMMUNE SYSTEM / HLA-A*03:01 with KRAS-G12V-10mer
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: 3.5 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 23, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: G12V-TCR alpha chain
B: G12V-TCR beta chain
C: HLA class I histocompatibility antigen, A alpha chain
D: Beta-2-microglobulin
E: GTPase KRas, N-terminally processed
F: G12V-TCR alpha chain
G: G12V-TCR beta chain
H: HLA class I histocompatibility antigen, A alpha chain
I: Beta-2-microglobulin
J: GTPase KRas, N-terminally processed
K: G12V-TCR alpha chain
L: G12V-TCR beta chain
M: HLA class I histocompatibility antigen, A alpha chain
N: Beta-2-microglobulin
O: GTPase KRas, N-terminally processed
P: G12V-TCR alpha chain
Q: G12V-TCR beta chain
R: HLA class I histocompatibility antigen, A alpha chain
S: Beta-2-microglobulin
T: GTPase KRas, N-terminally processed
U: G12V-TCR alpha chain
V: G12V-TCR beta chain
W: HLA class I histocompatibility antigen, A alpha chain
X: Beta-2-microglobulin
Y: GTPase KRas, N-terminally processed
Z: G12V-TCR alpha chain
a: G12V-TCR beta chain
b: HLA class I histocompatibility antigen, A alpha chain
c: Beta-2-microglobulin
d: GTPase KRas, N-terminally processed
e: G12V-TCR alpha chain
f: G12V-TCR beta chain
g: HLA class I histocompatibility antigen, A alpha chain
h: Beta-2-microglobulin
i: GTPase KRas, N-terminally processed
j: G12V-TCR alpha chain
k: G12V-TCR beta chain
l: HLA class I histocompatibility antigen, A alpha chain
m: Beta-2-microglobulin
n: GTPase KRas, N-terminally processed


Theoretical massNumber of molelcules
Total (without water)768,82640
Polymers768,82640
Non-polymers00
Water181
1
A: G12V-TCR alpha chain
B: G12V-TCR beta chain
C: HLA class I histocompatibility antigen, A alpha chain
D: Beta-2-microglobulin
E: GTPase KRas, N-terminally processed


Theoretical massNumber of molelcules
Total (without water)96,1035
Polymers96,1035
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: G12V-TCR alpha chain
G: G12V-TCR beta chain
H: HLA class I histocompatibility antigen, A alpha chain
I: Beta-2-microglobulin
J: GTPase KRas, N-terminally processed


Theoretical massNumber of molelcules
Total (without water)96,1035
Polymers96,1035
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
K: G12V-TCR alpha chain
L: G12V-TCR beta chain
M: HLA class I histocompatibility antigen, A alpha chain
N: Beta-2-microglobulin
O: GTPase KRas, N-terminally processed


Theoretical massNumber of molelcules
Total (without water)96,1035
Polymers96,1035
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
P: G12V-TCR alpha chain
Q: G12V-TCR beta chain
R: HLA class I histocompatibility antigen, A alpha chain
S: Beta-2-microglobulin
T: GTPase KRas, N-terminally processed


Theoretical massNumber of molelcules
Total (without water)96,1035
Polymers96,1035
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
U: G12V-TCR alpha chain
V: G12V-TCR beta chain
W: HLA class I histocompatibility antigen, A alpha chain
X: Beta-2-microglobulin
Y: GTPase KRas, N-terminally processed


Theoretical massNumber of molelcules
Total (without water)96,1035
Polymers96,1035
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
Z: G12V-TCR alpha chain
a: G12V-TCR beta chain
b: HLA class I histocompatibility antigen, A alpha chain
c: Beta-2-microglobulin
d: GTPase KRas, N-terminally processed


Theoretical massNumber of molelcules
Total (without water)96,1035
Polymers96,1035
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
e: G12V-TCR alpha chain
f: G12V-TCR beta chain
g: HLA class I histocompatibility antigen, A alpha chain
h: Beta-2-microglobulin
i: GTPase KRas, N-terminally processed


Theoretical massNumber of molelcules
Total (without water)96,1035
Polymers96,1035
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
j: G12V-TCR alpha chain
k: G12V-TCR beta chain
l: HLA class I histocompatibility antigen, A alpha chain
m: Beta-2-microglobulin
n: GTPase KRas, N-terminally processed


Theoretical massNumber of molelcules
Total (without water)96,1035
Polymers96,1035
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)131.477, 195.787, 442.856
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 4 types, 32 molecules AFKPUZejBGLQVafkCHMRWbglDINSXchm

#1: Protein
G12V-TCR alpha chain


Mass: 23022.637 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Protein
G12V-TCR beta chain


Mass: 28139.695 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Protein
HLA class I histocompatibility antigen, A alpha chain / Human leukocyte antigen A / HLA-A


Mass: 32176.463 Da / Num. of mol.: 8
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
#4: Protein
Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 8 / Fragment: UNP residues 21-119
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

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Protein/peptide / Non-polymers , 2 types, 9 molecules EJOTYdin

#5: Protein/peptide
GTPase KRas, N-terminally processed


Mass: 885.082 Da / Num. of mol.: 8 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01116
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.77 Å3/Da / Density % sol: 67.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: 0.1M Bis-Tris Propane (pH 6.5), 0.2M Na2SO4, 14-20% 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: Dec 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.1 Å / Relative weight: 1
ReflectionResolution: 3.5→46.46 Å / Num. obs: 137380 / % possible obs: 84.39 % / Redundancy: 1.1 % / CC1/2: 1 / CC star: 1 / Net I/σ(I): 3.46
Reflection shellResolution: 3.5→3.626 Å / Mean I/σ(I) obs: 0.25 / Num. unique obs: 11066 / CC1/2: 1

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→46.46 Å / SU ML: 0.56 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2859 6098 5 %
Rwork0.2378 --
obs0.2402 122022 84.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.5→46.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms53223 0 0 1 53224
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_dihedral_angle_d6.7077307
X-RAY DIFFRACTIONf_chiral_restr0.0747855
X-RAY DIFFRACTIONf_plane_restr0.0129699
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.540.3672720.38431350X-RAY DIFFRACTION30
3.54-3.580.405870.37381603X-RAY DIFFRACTION35
3.58-3.620.37441040.37762300X-RAY DIFFRACTION50
3.63-3.670.38041480.37882762X-RAY DIFFRACTION61
3.67-3.720.42271420.34852800X-RAY DIFFRACTION62
3.72-3.770.39321470.3532880X-RAY DIFFRACTION64
3.77-3.820.39621590.34493147X-RAY DIFFRACTION69
3.82-3.880.37371660.35133051X-RAY DIFFRACTION67
3.88-3.940.35871650.3413124X-RAY DIFFRACTION69
3.94-4.010.36391790.33263747X-RAY DIFFRACTION82
4.01-4.080.34531960.33083871X-RAY DIFFRACTION85
4.08-4.150.3562010.3284024X-RAY DIFFRACTION88
4.15-4.230.35712410.30494166X-RAY DIFFRACTION93
4.23-4.320.30752440.29394272X-RAY DIFFRACTION95
4.32-4.410.3382240.27494483X-RAY DIFFRACTION98
4.41-4.510.30652610.26424415X-RAY DIFFRACTION98
4.51-4.620.29952450.25744512X-RAY DIFFRACTION99
4.62-4.750.28052420.24684527X-RAY DIFFRACTION99
4.75-4.890.27972570.23014533X-RAY DIFFRACTION99
4.89-5.050.29162520.22184545X-RAY DIFFRACTION100
5.05-5.230.28432310.22644545X-RAY DIFFRACTION99
5.23-5.440.26642470.22134485X-RAY DIFFRACTION98
5.44-5.680.26992140.22134420X-RAY DIFFRACTION96
5.68-5.980.27372510.21224586X-RAY DIFFRACTION99
5.98-6.360.2832190.21594578X-RAY DIFFRACTION99
6.36-6.840.27922050.21154623X-RAY DIFFRACTION99
6.84-7.530.27912530.19784611X-RAY DIFFRACTION100
7.53-8.610.22982320.16534666X-RAY DIFFRACTION100
8.61-10.830.20032620.1414583X-RAY DIFFRACTION97
10.83-46.460.23952520.20754715X-RAY DIFFRACTION96

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