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- PDB-6w4f: NMR-driven structure of KRAS4B-GDP homodimer on a lipid bilayer n... -

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Basic information

Entry
Database: PDB / ID: 6w4f
TitleNMR-driven structure of KRAS4B-GDP homodimer on a lipid bilayer nanodisc
Components
  • Apolipoprotein A-I
  • GTPase KRas
KeywordsONCOPROTEIN / GTPase / nanodisc
Function / homology
Function and homology information


Defective ABCA1 causes TGD / high-density lipoprotein particle receptor binding / HDL clearance / spherical high-density lipoprotein particle / Scavenging by Class B Receptors / positive regulation of hydrolase activity / negative regulation of response to cytokine stimulus / protein oxidation / regulation of intestinal cholesterol absorption / vitamin transport ...Defective ABCA1 causes TGD / high-density lipoprotein particle receptor binding / HDL clearance / spherical high-density lipoprotein particle / Scavenging by Class B Receptors / positive regulation of hydrolase activity / negative regulation of response to cytokine stimulus / protein oxidation / regulation of intestinal cholesterol absorption / vitamin transport / cholesterol import / blood vessel endothelial cell migration / high-density lipoprotein particle binding / negative regulation of heterotypic cell-cell adhesion / ABC transporters in lipid homeostasis / apolipoprotein A-I receptor binding / apolipoprotein receptor binding / negative regulation of cytokine production involved in immune response / negative regulation of cell adhesion molecule production / HDL assembly / negative regulation of very-low-density lipoprotein particle remodeling / peptidyl-methionine modification / phosphatidylcholine biosynthetic process / glucocorticoid metabolic process / acylglycerol homeostasis / phosphatidylcholine-sterol O-acyltransferase activator activity / positive regulation of phospholipid efflux / Chylomicron remodeling / positive regulation of cholesterol metabolic process / cellular response to lipoprotein particle stimulus / Chylomicron assembly / : / high-density lipoprotein particle clearance / chylomicron / phospholipid efflux / high-density lipoprotein particle remodeling / phospholipid homeostasis / reverse cholesterol transport / chemorepellent activity / high-density lipoprotein particle assembly / lipid storage / low-density lipoprotein particle / lipoprotein biosynthetic process / cholesterol transfer activity / cholesterol transport / high-density lipoprotein particle / very-low-density lipoprotein particle / regulation of Cdc42 protein signal transduction / triglyceride homeostasis / endothelial cell proliferation / HDL remodeling / cholesterol efflux / forebrain astrocyte development / Scavenging by Class A Receptors / negative regulation of interleukin-1 beta production / adrenal gland development / negative chemotaxis / cholesterol binding / negative regulation of epithelial cell differentiation / type I pneumocyte differentiation / regulation of synaptic transmission, GABAergic / epithelial tube branching involved in lung morphogenesis / cholesterol biosynthetic process / positive regulation of Rho protein signal transduction / Rac protein signal transduction / positive regulation of Rac protein signal transduction / skeletal muscle cell differentiation / amyloid-beta formation / 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 / endocytic vesicle / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / positive regulation of cholesterol efflux / SHC1 events in ERBB4 signaling / negative regulation of tumor necrosis factor-mediated signaling pathway / 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 / Scavenging of heme from plasma / 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 / Retinoid metabolism and transport / SHC-mediated cascade:FGFR1 / positive regulation of phagocytosis / FRS-mediated FGFR3 signaling
Similarity search - Function
Apolipoprotein A/E / : / Apolipoprotein A1/A4/E domain / Small GTPase, Ras-type / small GTPase Ras family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family ...Apolipoprotein A/E / : / Apolipoprotein A1/A4/E domain / Small GTPase, Ras-type / small GTPase Ras family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-17F / GUANOSINE-5'-DIPHOSPHATE / 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / GTPase KRas / Apolipoprotein A-I
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsLee, K. / Fang, Z. / Enomoto, M. / Gasmi-Seabrook, G.M. / Zheng, L. / Marshall, C.B. / Ikura, M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2020
Title: Two Distinct Structures of Membrane-Associated Homodimers of GTP- and GDP-Bound KRAS4B Revealed by Paramagnetic Relaxation Enhancement.
Authors: Lee, K.Y. / Fang, Z. / Enomoto, M. / Gasmi-Seabrook, G. / Zheng, L. / Koide, S. / Ikura, M. / Marshall, C.B.
History
DepositionMar 10, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Apolipoprotein A-I
D: Apolipoprotein A-I
B: GTPase KRas
C: GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,47488
Polymers88,5554
Non-polymers63,91984
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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Protein , 2 types, 4 molecules ADBC

#1: Protein Apolipoprotein A-I / ApoA-I / Apolipoprotein A1


Mass: 23234.295 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APOA1 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: P02647
#2: Protein GTPase KRas / K-Ras 2 / Ki-Ras / c-K-ras / c-Ki-ras


Mass: 21042.959 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KRAS, KRAS2, RASK2 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: P01116

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Non-polymers , 4 types, 84 molecules

#3: Chemical...
ChemComp-PCW / 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / (Z,Z)-4-HYDROXY-N,N,N-TRIMETHYL-10-OXO-7-[(1-OXO-9-OCTADECENYL)OXY]-3,5,9-TRIOXA-4-PHOSPHAHEPTACOS-18-EN-1-AMINIUM-4-OXIDE


Mass: 787.121 Da / Num. of mol.: 64 / Source method: obtained synthetically / Formula: C44H85NO8P / Comment: DOPC, phospholipid*YM
#4: Chemical
ChemComp-17F / O-[(S)-({(2R)-2,3-bis[(9Z)-octadec-9-enoyloxy]propyl}oxy)(hydroxy)phosphoryl]-L-serine / 1,2-Dioleoyl-sn-glycero-3-phospho-L-serine


Mass: 788.043 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C42H78NO10P / Comment: phospholipid*YM
#5: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-13C TROSY
121isotropic12D 1H-15N HSQC

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Sample preparation

DetailsType: solution
Contents: 80 uM ILV 13C-methyl; Lys 15N-amide KRAS4B, 90% H2O/10% D2O
Label: 15N_13C_sample / Solvent system: 90% H2O/10% D2O
SampleConc.: 80 uM / Component: KRAS4B / Isotopic labeling: ILV 13C-methyl; Lys 15N-amide
Sample conditionsIonic strength: 100 mM / Label: conditions_1 / pH: 7.4 / Pressure: 1 atm / Temperature: 288 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificdata analysis
HADDOCKBonvinrefinement
HADDOCKBonvinstructure calculation
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxpeak picking
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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