[English] 日本語
Yorodumi
- PDB-8k4v: Crystal structure of HLA-A*11:01 in complex with KRAS G12R peptid... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8k4v
TitleCrystal structure of HLA-A*11:01 in complex with KRAS G12R peptide (VVVGARGVGK)
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A alpha chain
  • KRAS G12R peptide (VVVGARGVGK)
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: 3.095 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 G12R peptide (VVVGARGVGK)
Authors: Xu, Y.
History
DepositionJul 20, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 29, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HLA class I histocompatibility antigen, A alpha chain
B: Beta-2-microglobulin
C: KRAS G12R peptide (VVVGARGVGK)
D: HLA class I histocompatibility antigen, A alpha chain
E: Beta-2-microglobulin
F: KRAS G12R peptide (VVVGARGVGK)
G: HLA class I histocompatibility antigen, A alpha chain
H: Beta-2-microglobulin
I: KRAS G12R peptide (VVVGARGVGK)
J: HLA class I histocompatibility antigen, A alpha chain
K: Beta-2-microglobulin
L: KRAS G12R peptide (VVVGARGVGK)


Theoretical massNumber of molelcules
Total (without water)188,38112
Polymers188,38112
Non-polymers00
Water00
1
A: HLA class I histocompatibility antigen, A alpha chain
B: Beta-2-microglobulin
C: KRAS G12R peptide (VVVGARGVGK)


Theoretical massNumber of molelcules
Total (without water)47,0953
Polymers47,0953
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-21 kcal/mol
Surface area19050 Å2
MethodPISA
2
D: HLA class I histocompatibility antigen, A alpha chain
E: Beta-2-microglobulin
F: KRAS G12R peptide (VVVGARGVGK)


Theoretical massNumber of molelcules
Total (without water)47,0953
Polymers47,0953
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-18 kcal/mol
Surface area18970 Å2
MethodPISA
3
G: HLA class I histocompatibility antigen, A alpha chain
H: Beta-2-microglobulin
I: KRAS G12R peptide (VVVGARGVGK)


Theoretical massNumber of molelcules
Total (without water)47,0953
Polymers47,0953
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-21 kcal/mol
Surface area19070 Å2
MethodPISA
4
J: HLA class I histocompatibility antigen, A alpha chain
K: Beta-2-microglobulin
L: KRAS G12R peptide (VVVGARGVGK)


Theoretical massNumber of molelcules
Total (without water)47,0953
Polymers47,0953
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-20 kcal/mol
Surface area19080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.648, 121.602, 155.814
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
12
22
32
42
13
23
33

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
101GLYGLYLYSLYS(chain 'A' and (resid 25 through 93 or resid 95 through 299))AA25 - 922 - 69
111SERSERTRPTRP(chain 'A' and (resid 25 through 93 or resid 95 through 299))AA95 - 29872 - 275
201GLYGLYLYSLYS(chain 'D' and (resid 25 through 93 or resid 95 through 299))DD25 - 922 - 69
211SERSERTRPTRP(chain 'D' and (resid 25 through 93 or resid 95 through 299))DD95 - 29872 - 275
301GLYGLYLYSLYS(chain 'G' and (resid 25 through 93 or resid 95 through 299))GG25 - 922 - 69
311SERSERTRPTRP(chain 'G' and (resid 25 through 93 or resid 95 through 299))GG95 - 29872 - 275
401GLYGLYLYSLYS(chain 'J' and (resid 25 through 93 or resid 95 through 299))JJ25 - 922 - 69
411SERSERTRPTRP(chain 'J' and (resid 25 through 93 or resid 95 through 299))JJ95 - 29872 - 275
102METMETMETMETchain 'B'BB0 - 991 - 100
212METMETMETMETchain 'E'EE0 - 991 - 100
322METMETMETMETchain 'H'HH0 - 991 - 100
432METMETMETMETchain 'K'KK0 - 991 - 100
103VALVALVALVALchain 'F'FF1 - 31 - 3
113GLYGLYLYSLYSchain 'F'FF7 - 107 - 10
203VALVALVALVALchain 'I'II1 - 31 - 3
213GLYGLYLYSLYSchain 'I'II7 - 107 - 10
303VALVALVALVALchain 'L'LL1 - 31 - 3
313GLYGLYLYSLYSchain 'L'LL7 - 107 - 10

NCS ensembles :
ID
1
2
3

-
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 G12R peptide (VVVGARGVGK)


Mass: 943.145 Da / Num. of mol.: 4 / Mutation: G12R
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.98 Å3/Da / Density % sol: 58.77 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / Details: Ammonium sulfate, Sodium cacodylate, PEG 4000

-
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: 3.095→50 Å / Num. obs: 41628 / % possible obs: 99.1 % / Redundancy: 13 % / Biso Wilson estimate: 52.9 Å2 / CC1/2: 0.981 / Net I/σ(I): 5.51
Reflection shellResolution: 3.095→3.205 Å / Num. unique obs: 52883 / CC1/2: 0.716

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660phasing
Cootmodel building
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.095→25.39 Å / SU ML: 0.5311 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 40.1212
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3474 3762 4.78 %
Rwork0.2957 74937 -
obs0.2981 41628 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.74 Å2
Refinement stepCycle: LAST / Resolution: 3.095→25.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12540 0 0 0 12540
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002412897
X-RAY DIFFRACTIONf_angle_d0.570717488
X-RAY DIFFRACTIONf_chiral_restr0.04151774
X-RAY DIFFRACTIONf_plane_restr0.00392316
X-RAY DIFFRACTIONf_dihedral_angle_d23.69481736
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.095-3.130.44421230.41162540X-RAY DIFFRACTION90.61
3.13-3.170.37651530.38672779X-RAY DIFFRACTION99.52
3.17-3.220.42361250.37342786X-RAY DIFFRACTION99.22
3.22-3.260.41511390.37172797X-RAY DIFFRACTION99.76
3.26-3.310.441300.37252810X-RAY DIFFRACTION99.73
3.31-3.360.41271460.37092775X-RAY DIFFRACTION99.83
3.36-3.420.43621370.35582801X-RAY DIFFRACTION99.8
3.42-3.480.3691310.33572828X-RAY DIFFRACTION99.76
3.48-3.540.36421560.31372737X-RAY DIFFRACTION99.59
3.54-3.610.33081520.33422790X-RAY DIFFRACTION99.49
3.61-3.680.38451240.32162787X-RAY DIFFRACTION99.62
3.68-3.760.42081380.30182785X-RAY DIFFRACTION99.73
3.76-3.850.41511320.29472818X-RAY DIFFRACTION99.53
3.85-3.950.38351500.29572762X-RAY DIFFRACTION99.39
3.95-4.050.30771390.29222777X-RAY DIFFRACTION99.56
4.05-4.170.35071480.28462761X-RAY DIFFRACTION99.45
4.17-4.30.31021480.26272750X-RAY DIFFRACTION99.35
4.3-4.460.30231220.25272835X-RAY DIFFRACTION99.7
4.46-4.640.25961450.25042767X-RAY DIFFRACTION99.73
4.64-4.840.27431400.24652783X-RAY DIFFRACTION99.39
4.84-5.10.3061500.26792772X-RAY DIFFRACTION99.66
5.1-5.410.29881400.26192784X-RAY DIFFRACTION99.63
5.42-5.830.3421420.28652791X-RAY DIFFRACTION99.52
5.83-6.410.36551490.29792782X-RAY DIFFRACTION99.63
6.41-7.310.39171360.28632780X-RAY DIFFRACTION99.62
7.31-9.140.3241380.24752788X-RAY DIFFRACTION99.39
9.14-25.390.3021290.26012772X-RAY DIFFRACTION98.71

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more