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- PDB-6jtp: Crystal structure of HLA-C08 in complex with a tumor mut9m peptide -

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Basic information

Entry
Database: PDB / ID: 6jtp
TitleCrystal structure of HLA-C08 in complex with a tumor mut9m peptide
Components
  • 9-mer peptide
  • Beta-2-microglobulin
  • HLA class I antigen, Cw8.2 alpha chain
KeywordsIMMUNE SYSTEM / major histocompatibility complex / antigen / HLA
Function / homology
Function and homology information


forebrain astrocyte development / negative regulation of epithelial cell differentiation / type I pneumocyte differentiation / regulation of synaptic transmission, GABAergic / epithelial tube branching involved in lung morphogenesis / antigen processing and presentation of peptide antigen via MHC class I / Rac protein signal transduction / positive regulation of Rac protein signal transduction / skeletal muscle cell differentiation / Signaling by RAS GAP mutants ...forebrain astrocyte development / negative regulation of epithelial cell differentiation / type I pneumocyte differentiation / regulation of synaptic transmission, GABAergic / epithelial tube branching involved in lung morphogenesis / antigen processing and presentation of peptide antigen via MHC class I / Rac protein signal transduction / positive regulation of Rac protein signal transduction / skeletal muscle cell differentiation / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / RAS signaling downstream of NF1 loss-of-function variants / RUNX3 regulates p14-ARF / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / 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 / MET activates RAS signaling / 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 / Signaling by ERBB2 TMD/JMD mutants / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / Signaling by high-kinase activity BRAF mutants / MHC class I peptide loading complex / response to molecule of bacterial origin / Signaling by SCF-KIT / HFE-transferrin receptor complex / Constitutive Signaling by EGFRvIII / MAP2K and MAPK activation / T cell mediated cytotoxicity / Signaling by ERBB2 ECD mutants / visual learning / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production
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-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases ...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-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HLA class I antigen / GTPase KRas / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBai, P. / Zhou, Q. / Wei, P. / Lei, Y.
CitationJournal: Oncoimmunology / Year: 2021
Title: Immune-based mutation classification enables neoantigen prioritization and immune feature discovery in cancer immunotherapy.
Authors: Bai, P. / Li, Y. / Zhou, Q. / Xia, J. / Wei, P.C. / Deng, H. / Wu, M. / Chan, S.K. / Kappler, J.W. / Zhou, Y. / Tran, E. / Marrack, P. / Yin, L.
History
DepositionApr 11, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Feb 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HLA class I antigen, Cw8.2 alpha chain
B: Beta-2-microglobulin
C: 9-mer peptide


Theoretical massNumber of molelcules
Total (without water)44,1133
Polymers44,1133
Non-polymers00
Water9,350519
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-13 kcal/mol
Surface area19270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.280, 75.920, 78.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HLA class I antigen, Cw8.2 alpha chain / MHC class I antigen / MHC class I histocompatibility antigen


Mass: 31733.967 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-Cw, HLA-C / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: C1K0Y1
#2: Protein Beta-2-microglobulin


Mass: 11616.964 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 K-12 (bacteria) / References: UniProt: P61769
#3: Protein/peptide 9-mer peptide


Mass: 761.802 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01116*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 519 / Source method: isolated from a natural source / Formula: H2O
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: 2.28 Å3/Da / Density % sol: 46.02 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M ammonium acetate, 0.1M HEPES (pH 7.5), 25% w/v polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.9→42.55 Å / Num. obs: 32450 / % possible obs: 96 % / Redundancy: 2 % / CC1/2: 0.995 / Rmerge(I) obs: 0.04092 / Net I/σ(I): 7.15
Reflection shellResolution: 1.9→1.968 Å / Redundancy: 2 % / Rmerge(I) obs: 0.1168 / Mean I/σ(I) obs: 4.02 / Num. unique obs: 3174 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→42.55 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.63
RfactorNum. reflection% reflection
Rfree0.2828 1936 6.18 %
Rwork0.2396 --
obs0.2424 31350 96.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→42.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3115 0 0 519 3634
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083207
X-RAY DIFFRACTIONf_angle_d0.9094355
X-RAY DIFFRACTIONf_dihedral_angle_d19.8151907
X-RAY DIFFRACTIONf_chiral_restr0.053438
X-RAY DIFFRACTIONf_plane_restr0.005579
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.94760.55831100.57481687X-RAY DIFFRACTION78
1.9476-2.00020.44631290.41262072X-RAY DIFFRACTION96
2.0002-2.05910.30521420.26062109X-RAY DIFFRACTION99
2.0591-2.12550.30291350.2392129X-RAY DIFFRACTION99
2.1255-2.20150.32121490.22812148X-RAY DIFFRACTION100
2.2015-2.28960.52371090.42971632X-RAY DIFFRACTION76
2.2896-2.39380.29391360.22422166X-RAY DIFFRACTION100
2.3938-2.520.27381510.23332193X-RAY DIFFRACTION100
2.52-2.67790.2541390.22442159X-RAY DIFFRACTION100
2.6779-2.88460.32241450.21322174X-RAY DIFFRACTION100
2.8846-3.17480.22071410.20192199X-RAY DIFFRACTION100
3.1748-3.6340.20371500.18262209X-RAY DIFFRACTION100
3.634-4.57760.1991460.15962203X-RAY DIFFRACTION99
4.5776-42.56460.22191540.18492334X-RAY DIFFRACTION100

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