+Open data
-Basic information
Entry | Database: PDB / ID: 6mpp | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | HLA-A*01:01 complex with NRAS Q61K peptide by NMR | ||||||||||||
Components |
| ||||||||||||
Keywords | IMMUNE SYSTEM | ||||||||||||
Function / homology | Function and homology information myoblast differentiation / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I ...myoblast differentiation / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / endoplasmic reticulum exit site / tertiary granule membrane / RAS signaling downstream of NF1 loss-of-function variants / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP binding / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / protection from natural killer cell mediated cytotoxicity / SHC1 events in ERBB4 signaling / Signalling to RAS / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / beta-2-microglobulin binding / SHC-mediated cascade:FGFR2 / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / T cell receptor binding / SHC-mediated cascade:FGFR4 / Signaling by FGFR4 in disease / detection of bacterium / Erythropoietin activates RAS / SHC-mediated cascade:FGFR1 / FRS-mediated FGFR2 signaling / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / Signaling by FGFR2 in disease / FRS-mediated FGFR4 signaling / p38MAPK events / Signaling by FGFR3 in disease / Tie2 Signaling / FRS-mediated FGFR1 signaling / positive regulation of endothelial cell proliferation / GRB2 events in EGFR signaling / FLT3 Signaling / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / Signaling by FGFR1 in disease / Ras activation upon Ca2+ influx through NMDA receptor / GRB2 events in ERBB2 signaling / CD209 (DC-SIGN) signaling / NCAM signaling for neurite out-growth / SHC1 events in ERBB2 signaling / Downstream signal transduction / Constitutive Signaling by Overexpressed ERBB2 / Insulin receptor signalling cascade / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / small monomeric GTPase / VEGFR2 mediated cell proliferation / negative regulation of receptor binding / G protein activity / DAP12 interactions / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / 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 / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / FCERI mediated MAPK activation / Signaling by ERBB2 TMD/JMD mutants / RAF activation / Signaling by high-kinase activity BRAF mutants / cellular response to iron(III) ion / Constitutive Signaling by EGFRvIII / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / MAP2K and MAPK activation / Signaling by ERBB2 ECD mutants / Signaling by SCF-KIT / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / regulation of iron ion transport / Signaling by ERBB2 KD Mutants / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | SOLUTION NMR / distance geometry | ||||||||||||
Authors | Flores-Solis, D. / McShan, A.C. / Sgourakis, N.G. | ||||||||||||
Funding support | United States, 3items
| ||||||||||||
Citation | Journal: To Be Published Title: MHC-I complex determined by NMR Authors: Flores-Solis, D. / McShan, A.C. / Sgourakis, N.G. | ||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6mpp.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6mpp.ent.gz | 1 MB | Display | PDB format |
PDBx/mmJSON format | 6mpp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6mpp_validation.pdf.gz | 403 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6mpp_full_validation.pdf.gz | 505 KB | Display | |
Data in XML | 6mpp_validation.xml.gz | 70.2 KB | Display | |
Data in CIF | 6mpp_validation.cif.gz | 90 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mp/6mpp ftp://data.pdbj.org/pub/pdb/validation_reports/mp/6mpp | HTTPS FTP |
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: Protein | Mass: 32181.514 Da / Num. of mol.: 1 / Fragment: residues 25-303 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: P30443, UniProt: P04439*PLUS |
---|---|
#2: Protein/peptide | Mass: 1139.233 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P01111*PLUS |
#3: Protein | Mass: 11879.356 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 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
|
-Sample preparation
Details |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Sample |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||
Sample conditions | Details: 50 mM NaCl 20 mM NaPO4 / Ionic strength: 20 mM / Label: NMR_Buffer / pH: 7.2 / PH err: 0.05 / Pressure: 1 atm / Temperature: 298 K / Temperature err: 0.1 |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE III HD / Manufacturer: Bruker / Model: AVANCE III HD / Field strength: 800 MHz |
---|
-Processing
NMR software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: distance geometry / Software ordinal: 2 / Details: Structure is calculated based on NMR constraints | ||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 50000 / Conformers submitted total number: 10 |