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- PDB-6mpp: HLA-A*01:01 complex with NRAS Q61K peptide by NMR -

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Basic information

Entry
Database: PDB / ID: 6mpp
TitleHLA-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
KeywordsIMMUNE SYSTEM
Function / homology
Function and homology information


positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / 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 / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / CD8 receptor binding ...positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / 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 / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / CD8 receptor binding / protection from natural killer cell mediated cytotoxicity / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / beta-2-microglobulin binding / tertiary granule membrane / endoplasmic reticulum exit site / RAS signaling downstream of NF1 loss-of-function variants / TAP binding / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / Signalling to RAS / detection of bacterium / 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 / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / 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 FLT3 ITD and TKD mutants / T cell receptor binding / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / p38MAPK events / Signaling by FGFR3 in disease / FRS-mediated FGFR1 signaling / Tie2 Signaling / Signaling by FGFR2 in disease / positive regulation of endothelial cell proliferation / GRB2 events in EGFR signaling / Signaling by FLT3 fusion proteins / SHC1 events in EGFR signaling / 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 / Insulin receptor signalling cascade / SHC1 events in ERBB2 signaling / Ras activation upon Ca2+ influx through NMDA receptor / Constitutive Signaling by Overexpressed ERBB2 / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / VEGFR2 mediated cell proliferation / small monomeric GTPase / Endosomal/Vacuolar pathway / T cell mediated cytotoxicity / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / FCERI mediated MAPK activation / lumenal side of endoplasmic reticulum membrane / regulation of iron ion transport / cellular response to iron(III) ion / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / Signaling by ERBB2 TMD/JMD mutants / response to molecule of bacterial origin / HFE-transferrin receptor complex / transferrin transport / MHC class I peptide loading complex / RAF activation / cellular response to iron ion / Signaling by SCF-KIT / negative regulation of receptor-mediated endocytosis / Constitutive Signaling by EGFRvIII / Signaling by high-kinase activity BRAF mutants / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / Signaling by ERBB2 ECD mutants / MAP2K and MAPK activation / MHC class I protein complex
Similarity search - Function
Small GTPase, Ras-type / Small GTPase Ras domain 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 / 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-type / Small GTPase Ras domain 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 / 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 / Immunoglobulins / 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
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry
AuthorsFlores-Solis, D. / McShan, A.C. / Sgourakis, N.G.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/Office of the DirectorHIE-S10OD018455 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI2573-01 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R35GM125034-01 United States
CitationJournal: To Be Published
Title: MHC-I complex determined by NMR
Authors: Flores-Solis, D. / McShan, A.C. / Sgourakis, N.G.
History
DepositionOct 8, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 16, 2022Group: Database references / Structure summary / Category: database_2 / entity / struct
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _struct.title
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, A-1 alpha chain
B: NRAS Q61K peptide
C: Beta-2-microglobulin


Theoretical massNumber of molelcules
Total (without water)45,2003
Polymers45,2003
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area4470 Å2
ΔGint-21 kcal/mol
Surface area19930 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 50000structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein HLA class I histocompatibility antigen, A-1 alpha chain / 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 NRAS Q61K 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 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
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
151isotropic12D 1H-15N HSQC
162isotropic12D 1H-15N HSQC
1173isotropic12D 1H-15N HSQC
172isotropic12D 1H-13C HSQC aliphatic
1224isotropic12D 1H-1H filtered-TOCSY
183isotropic12D 1H-13C HSQC
111isotropic13D HNCO
121isotropic13D HNCA
131isotropic13D HN(CA)CB
141isotropic13D HN(COCA)CB
1162isotropic13D Cmethyl-CmethylHmethyl
1142isotropic13D N-CmethylHmethyl
1132isotropic13D N-NHamide
1122isotropic13D Hmethyl-CmethylHmethyl
1214isotropic13D 1H-13C filtered-NOESY
1153isotropic13D Caromatic-CmethylHmethyl
1103isotropic13D Hmethyl-CaroHaro
1183isotropic13D Cmethyl-CmethylHmethyl
1193isotropic13D N-CmethylHmethyl
1203isotropic13D Hmethyl-CmethylHmethyl

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution1300 uM [U-99% 13C; U-99% 15N] MHC-I HLA-A01:01, 300 uM NRAS Q16K, 300 uM Hb2M, 90% H2O/10% D2OProtonated Sample for backbone experimentsProtonated_A0190% H2O/10% D2O
solution2180 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% D2OAILV_A0190% H2O/10% D2O
solution4170 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% D2OAILV_A01_D2O100% D2O
solution3210 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% D2OFYAILV_A01_15N_NRAS90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
300 uMMHC-I HLA-A01:01[U-99% 13C; U-99% 15N]1
300 uMNRAS Q16Knatural abundance1
300 uMHb2Mnatural abundance1
180 uMMHC-I HLA-A01:01[U-15N; U-2H]; [U-15N; U-2H; Methyl-1H; Methyl-13C]-Ala, Ile, Leu & Val2
180 uMNRAS Q16Knatural abundance2
180 uMHb2Mnatural abundance2
170 uMMHC-I HLA-A01:01[U-15N; U-2H]; [U-15N; U-2H; Methyl-1H; Methyl-13C]-Ala, Ile, Leu & Val4
170 uMNRAS Q16Knatural abundance4
170 uMHb2Mnatural abundance4
210 uMMHC-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 & Tyr3
210 uMNRAS Q16K[U-15N]3
210 uMHb2M[U-2H]3
Sample conditionsDetails: 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 spectrometerType: Bruker AVANCE III HD / Manufacturer: Bruker / Model: AVANCE III HD / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CS-ROSETTAShen, Vernon, Baker and Baxrefinement
SparkyNMRFAMGoddardchemical shift assignment
SparkyNMRFAMGoddardpeak picking
CS-ROSETTAShen, Vernon, Baker and Baxstructure calculation
RefinementMethod: distance geometry / Software ordinal: 2 / Details: Structure is calculated based on NMR constraints
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50000 / Conformers submitted total number: 10

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