- PDB-6mpp: HLA-A*01:01 complex with NRAS Q61K peptide by NMR -
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Basic information
Entry
Database: PDB / ID: 6mpp
Title
HLA-A*01:01 complex with NRAS Q61K peptide by NMR
Components
Beta-2-microglobulin
HLA class I histocompatibility antigen, A-1 alpha chain
NRAS Q61K peptide
Keywords
IMMUNE SYSTEM
Function / homology
Function and homology information
myoblast differentiation / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / 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 / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / 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 / 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 / SHC-mediated cascade:FGFR2 / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / T cell receptor binding / SHC-mediated cascade:FGFR4 / Signaling by FGFR4 in disease / SHC-mediated cascade:FGFR1 / Erythropoietin activates RAS / detection of bacterium / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR4 signaling / p38MAPK events / Tie2 Signaling / FRS-mediated FGFR1 signaling / Signaling by FGFR2 in disease / positive regulation of endothelial cell proliferation / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / FLT3 Signaling / Ras activation upon Ca2+ influx through NMDA receptor / Signaling by FGFR1 in disease / 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 / small monomeric GTPase / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / G protein activity / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / VEGFR2 mediated cell proliferation / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / 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 / 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 / Signaling by ERBB2 TMD/JMD mutants / RAF activation / cellular response to iron(III) ion / Signaling by high-kinase activity BRAF mutants / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / Constitutive Signaling by EGFRvIII / negative regulation of forebrain neuron differentiation / MAP2K and MAPK activation / Signaling by ERBB2 ECD mutants / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / regulation of iron ion transport / response to molecule of bacterial origin / Signaling by ERBB2 KD Mutants / MHC class I peptide loading complex / Signaling by SCF-KIT / HFE-transferrin receptor complex Similarity search - Function
Small GTPase, Ras-type / small GTPase Ras family profile. / : / 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 / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / MHC class I alpha chain, alpha1 alpha2 domains ...Small GTPase, Ras-type / small GTPase Ras family profile. / : / 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 / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / MHC class I alpha chain, alpha1 alpha2 domains / Small GTPase / Ras family / Class I Histocompatibility antigen, domains alpha 1 and 2 / Rab subfamily of small GTPases / Beta-2-Microglobulin / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Mainly Beta / Alpha Beta Similarity search - Domain/homology
GTPase NRas / HLA class I histocompatibility antigen, A alpha chain / HLA class I histocompatibility antigen, A alpha chain / Beta-2-microglobulin Similarity search - Component
HLAclassIhistocompatibilityantigen, A-1alphachain / MHC class I antigen A*1
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
NRASQ61Kpeptide
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
Beta-2-microglobulin
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
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Experimental details
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Experiment
Experiment
Method: SOLUTION NMR
NMR experiment
Conditions-ID
Experiment-ID
Solution-ID
Sample state
Spectrometer-ID
Type
1
5
1
isotropic
1
2D 1H-15N HSQC
1
6
2
isotropic
1
2D 1H-15N HSQC
1
17
3
isotropic
1
2D 1H-15N HSQC
1
7
2
isotropic
1
2D 1H-13C HSQC aliphatic
1
22
4
isotropic
1
2D 1H-1H filtered-TOCSY
1
8
3
isotropic
1
2D 1H-13C HSQC
1
1
1
isotropic
1
3D HNCO
1
2
1
isotropic
1
3D HNCA
1
3
1
isotropic
1
3D HN(CA)CB
1
4
1
isotropic
1
3DHN(COCA)CB
1
16
2
isotropic
1
3D Cmethyl-CmethylHmethyl
1
14
2
isotropic
1
3D N-CmethylHmethyl
1
13
2
isotropic
1
3D N-NHamide
1
12
2
isotropic
1
3D Hmethyl-CmethylHmethyl
1
21
4
isotropic
1
3D 1H-13C filtered-NOESY
1
15
3
isotropic
1
3D Caromatic-CmethylHmethyl
1
10
3
isotropic
1
3D Hmethyl-CaroHaro
1
18
3
isotropic
1
3D Cmethyl-CmethylHmethyl
1
19
3
isotropic
1
3D N-CmethylHmethyl
1
20
3
isotropic
1
3D Hmethyl-CmethylHmethyl
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Sample preparation
Details
Type
Solution-ID
Contents
Details
Label
Solvent system
solution
1
300 uM [U-99% 13C; U-99% 15N] MHC-I HLA-A01:01, 300 uM NRAS Q16K, 300 uM Hb2M, 90% H2O/10% D2O
ProtonatedSampleforbackboneexperiments
Protonated_A01
90% H2O/10% D2O
solution
2
180 uM [U-15N; U-2H]; [U-15N; U-2H; Methyl-1H; Methyl-13C]-Ala, Ile, Leu & Val MHC-I HLA-A01:01, 180 uM NRAS Q16K, 180 uM Hb2M, 90% H2O/10% D2O
AILV_A01
90% H2O/10% D2O
solution
4
170 uM [U-15N; U-2H]; [U-15N; U-2H; Methyl-1H; Methyl-13C]-Ala, Ile, Leu & Val MHC-I HLA-A01:01, 170 uM NRAS Q16K, 170 uM Hb2M, 100% D2O
AILV_A01_D2O
100% D2O
solution
3
210 uM [U-15N; U-2H]; [U-15N; U-2H; Methyl-1H; Methyl-13C]-Ala, Ile, Leu & Val; [U-13C; U-15N]-Phe & Tyr MHC-I HLA-A01:01, 210 uM [U-15N] NRAS Q16K, 210 uM [U-2H] Hb2M, 90% H2O/10% D2O
FYAILV_A01_15N_NRAS
90% H2O/10% D2O
Sample
Conc. (mg/ml)
Component
Isotopic labeling
Solution-ID
300uM
MHC-I HLA-A01:01
[U-99% 13C; U-99% 15N]
1
300uM
NRASQ16K
naturalabundance
1
300uM
Hb2M
naturalabundance
1
180uM
MHC-I HLA-A01:01
[U-15N; U-2H]; [U-15N; U-2H; Methyl-1H; Methyl-13C]-Ala, Ile, Leu & Val
2
180uM
NRASQ16K
naturalabundance
2
180uM
Hb2M
naturalabundance
2
170uM
MHC-I HLA-A01:01
[U-15N; U-2H]; [U-15N; U-2H; Methyl-1H; Methyl-13C]-Ala, Ile, Leu & Val
4
170uM
NRASQ16K
naturalabundance
4
170uM
Hb2M
naturalabundance
4
210uM
MHC-I HLA-A01:01
[U-15N; U-2H]; [U-15N; U-2H; Methyl-1H; Methyl-13C]-Ala, Ile, Leu & Val; [U-13C; U-15N]-Phe & Tyr
3
210uM
NRASQ16K
[U-15N]
3
210uM
Hb2M
[U-2H]
3
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
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NMR measurement
NMR spectrometer
Type: Bruker AVANCE III HD / Manufacturer: Bruker / Model: AVANCE III HD / Field strength: 800 MHz
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Processing
NMR software
Name
Version
Developer
Classification
CS-ROSETTA
Shen, Vernon, BakerandBax
refinement
Sparky
NMRFAM
Goddard
chemicalshiftassignment
Sparky
NMRFAM
Goddard
peakpicking
CS-ROSETTA
Shen, Vernon, BakerandBax
structurecalculation
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
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