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- PDB-6w4e: NMR-driven structure of KRAS4B-GTP homodimer on a lipid bilayer n... -

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Basic information

Entry
Database: PDB / ID: 6w4e
TitleNMR-driven structure of KRAS4B-GTP 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 / peptidyl-methionine modification / HDL clearance / spherical high-density lipoprotein particle / negative regulation of response to cytokine stimulus / protein oxidation / vitamin transport / cholesterol import / negative regulation of heterotypic cell-cell adhesion ...Defective ABCA1 causes TGD / high-density lipoprotein particle receptor binding / peptidyl-methionine modification / HDL clearance / spherical high-density lipoprotein particle / negative regulation of response to cytokine stimulus / protein oxidation / vitamin transport / cholesterol import / negative regulation of heterotypic cell-cell adhesion / Scavenging by Class B Receptors / apolipoprotein A-I receptor binding / negative regulation of cell adhesion molecule production / apolipoprotein receptor binding / ABC transporters in lipid homeostasis / negative regulation of cytokine production involved in immune response / HDL assembly / high-density lipoprotein particle binding / phosphatidylcholine biosynthetic process / negative regulation of very-low-density lipoprotein particle remodeling / acylglycerol homeostasis / phosphatidylcholine-sterol O-acyltransferase activator activity / cholesterol transport / positive regulation of phospholipid efflux / Chylomicron remodeling / lipoprotein metabolic process / cellular response to lipoprotein particle stimulus / Chylomicron assembly / phospholipid homeostasis / high-density lipoprotein particle clearance / phospholipid efflux / chylomicron / high-density lipoprotein particle remodeling / reverse cholesterol transport / positive regulation of cholesterol metabolic process / high-density lipoprotein particle assembly / chemorepellent activity / cholesterol transfer activity / low-density lipoprotein particle / high-density lipoprotein particle / very-low-density lipoprotein particle / cholesterol efflux / regulation of Cdc42 protein signal transduction / HDL remodeling / triglyceride homeostasis / negative chemotaxis / Scavenging by Class A Receptors / negative regulation of interleukin-1 beta production / response to mineralocorticoid / GMP binding / cholesterol binding / amyloid-beta formation / LRR domain binding / response to isolation stress / positive regulation of Rho protein signal transduction / response to gravity / myoblast proliferation / cardiac muscle cell proliferation / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / positive regulation of cholesterol efflux / RAS signaling downstream of NF1 loss-of-function variants / RUNX3 regulates p14-ARF / positive regulation of substrate adhesion-dependent cell spreading / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / endocytic vesicle / positive regulation of stress fiber assembly / cholesterol metabolic process / SHC1 events in ERBB4 signaling / negative regulation of tumor necrosis factor-mediated signaling pathway / Scavenging of heme from plasma / Signalling to RAS / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / Retinoid metabolism and transport / Dengue virus activates/modulates innate and adaptive immune responses / MET activates RAS signaling / positive regulation of Ras protein signal transduction / 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 / Signaling by CSF3 (G-CSF) / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / p38MAPK events / heat shock protein binding / cholesterol homeostasis / endocytic vesicle lumen
Similarity search - Function
Apolipoprotein A/E / : / Apolipoprotein A1/A4/E domain / Small GTPase, Ras-type / Small GTPase Ras domain 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 domain 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 / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / 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 15, 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 1.2May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)152,84088
Polymers88,7294
Non-polymers64,11284
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 3000structures 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: 21130.037 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-GSP / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE


Mass: 539.246 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3S
#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
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 3000 / Conformers submitted total number: 20

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