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- PDB-2msd: NMR data-driven model of GTPase KRas-GNP tethered to a lipid-bila... -

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Basic information

Entry
Database: PDB / ID: 2msd
TitleNMR data-driven model of GTPase KRas-GNP tethered to a lipid-bilayer nanodisc
Components
  • Apolipoprotein A-I
  • GTPase KRas
KeywordsLIPID BINDING PROTEIN / K-Ras / Nanodisc / PRE / Docking
Function / homology
Function and homology information


endocrine signaling / Defective ABCA1 causes TGD / high-density lipoprotein particle receptor binding / peptidyl-methionine modification / HDL clearance / spherical high-density lipoprotein particle / Scavenging by Class B Receptors / negative regulation of response to cytokine stimulus / protein oxidation / regulation of intestinal cholesterol absorption ...endocrine signaling / Defective ABCA1 causes TGD / high-density lipoprotein particle receptor binding / peptidyl-methionine modification / HDL clearance / spherical high-density lipoprotein particle / Scavenging by Class B Receptors / negative regulation of response to cytokine stimulus / protein oxidation / regulation of intestinal cholesterol absorption / vitamin transport / blood vessel endothelial cell migration / cholesterol import / negative regulation of heterotypic cell-cell adhesion / ABC transporters in lipid homeostasis / apolipoprotein A-I receptor binding / apolipoprotein receptor binding / high-density lipoprotein particle binding / negative regulation of cell adhesion molecule production / negative regulation of cytokine production involved in immune response / HDL assembly / negative regulation of very-low-density lipoprotein particle remodeling / phosphatidylcholine biosynthetic process / glucocorticoid metabolic process / acylglycerol homeostasis / phosphatidylcholine-sterol O-acyltransferase activator activity / positive regulation of phospholipid efflux / Chylomicron remodeling / cellular response to lipoprotein particle stimulus / Chylomicron assembly / high-density lipoprotein particle clearance / phospholipid efflux / chylomicron / high-density lipoprotein particle remodeling / positive regulation of cholesterol metabolic process / reverse cholesterol transport / lipid storage / phospholipid homeostasis / high-density lipoprotein particle assembly / chemorepellent activity / 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 / endothelial cell proliferation / HDL remodeling / cholesterol efflux / Scavenging by Class A Receptors / triglyceride homeostasis / adrenal gland development / response to mineralocorticoid / GMP binding / negative regulation of interleukin-1 beta production / negative chemotaxis / forebrain astrocyte development / cholesterol binding / LRR domain binding / regulation of synaptic transmission, GABAergic / negative regulation of epithelial cell differentiation / cholesterol biosynthetic process / response to isolation stress / amyloid-beta formation / positive regulation of Rho protein signal transduction / response to gravity / epithelial tube branching involved in lung morphogenesis / type I pneumocyte differentiation / Rac protein signal transduction / positive regulation of Rac protein signal transduction / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / myoblast proliferation / skeletal muscle cell differentiation / RAS signaling downstream of NF1 loss-of-function variants / RUNX3 regulates p14-ARF / positive regulation of glial cell proliferation / endocytic vesicle / SOS-mediated signalling / 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 / cardiac muscle cell proliferation / Signalling to RAS / Activated NTRK2 signals through FRS2 and FRS3 / SHC-related events triggered by IGF1R / Scavenging of heme from plasma / Estrogen-stimulated signaling through PRKCZ / glial cell proliferation / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / SHC-mediated cascade:FGFR2 / cholesterol metabolic process / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants
Similarity search - Function
Apolipoprotein A/E / : / Apolipoprotein A1/A4/E domain / Small GTPase Rab domain profile. / Small GTPase Rho domain profile. / 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 ...Apolipoprotein A/E / : / Apolipoprotein A1/A4/E domain / Small GTPase Rab domain profile. / Small GTPase Rho domain profile. / 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 / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / V-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog, isoform CRA_b / GTPase KRas / Apolipoprotein A-I
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsMazhab-Jafari, M. / Stathopoulos, P. / Marshall, C. / Ikura, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Oncogenic and RASopathy-associated K-RAS mutations relieve membrane-dependent occlusion of the effector-binding site.
Authors: Mazhab-Jafari, M.T. / Marshall, C.B. / Smith, M.J. / Gasmi-Seabrook, G.M. / Stathopulos, P.B. / Inagaki, F. / Kay, L.E. / Neel, B.G. / Ikura, M.
History
DepositionJul 29, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2015Group: Database references
Revision 1.2Dec 11, 2019Group: Data collection / Database references ...Data collection / Database references / Experimental preparation / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_name_com.name ..._entity.pdbx_description / _entity_name_com.name / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_seq_type / _pdbx_nmr_sample_details.contents / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_db_isoform / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.details / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.3May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)131,26085
Polymers67,7293
Non-polymers63,53182
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 3000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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Protein , 2 types, 3 molecules ACB

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


Mass: 23234.295 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 68-265
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APOA1 / Plasmid: pGBHPS MSP / Production host: Escherichia coli (E. coli) / References: UniProt: P02647
#2: Protein GTPase KRas / K-Ras 2 / Ki-Ras / c-K-ras / c-Ki-ras


Mass: 21260.250 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-185
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KRAS, KRAS2, RASK2 / Plasmid: pET-28 / Production host: Escherichia coli (E. coli) / References: UniProt: P01116, UniProt: A0A024RAV5*PLUS

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Non-polymers , 4 types, 82 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-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: This is a hybrid model generated by Haddock docking simulation that is based on i) NMR data that includes PRE-measurements between lipids (i.e. nanodisc) and the protien (i.e. K-RasGNP) ii) ...Details: This is a hybrid model generated by Haddock docking simulation that is based on i) NMR data that includes PRE-measurements between lipids (i.e. nanodisc) and the protien (i.e. K-RasGNP) ii) crystolagraphic information (K-RasGNP) and iii) theoretical computation (i.e. nanodisc).
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-13C HMQC
1222D 1H-13C HMQC
NMR detailsText: All PRE measurements were carrried out on the C-delta of Ile residues.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.6 mM U-15N, Ile C-delta-13C K-Ras-1, 0.6 mM membrane scaffold protein-2, 20 mM TRIS-3, 100 mM sodium chloride-4, 2 mM TCEP-5, 0.6 mM PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER-6, 5 mM Magnesium-7, 18.75 mM 1,2-dioleoyl-sn-glycero-3-phosphocholine-8, 5 mM 1,2-dioleoyl-sn-glycero-3-phospho-L-serine-9, 1.25 mM 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine-N-[4-(p-maleimidomethyl)cyclohexane-carboxamide]-10, 90% H2O/10% D2O90% H2O/10% D2O
20.6 mM U-15N, Ile C-delta-13C K-Ras-11, 0.6 mM membrane scaffold protein-12, 20 mM TRIS-13, 100 mM sodium chloride-14, 5 mM Magnesium-15, 0.6 mM PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER-16, 2 mM TCEP-17, 18.75 mM 1,2-dioleoyl-sn-glycero-3-phosphocholine-18, 5 mM 1,2-dioleoyl-sn-glycero-3-phospho-L-serine-19, 1.25 mM 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine-N-[4-(p-maleimidomethyl)cyclohexane-carboxamide]-20, 0.65 mM 1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-diethylenetriaminepentaacetic acid (gadolinium salt)-21, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMK-Ras-1U-15N, Ile C-delta-13C1
0.6 mMmembrane scaffold protein-21
20 mMTRIS-31
100 mMsodium chloride-41
2 mMTCEP-51
0.6 mMPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER-61
5 mMMagnesium-71
18.75 mM1,2-dioleoyl-sn-glycero-3-phosphocholine-81
5 mM1,2-dioleoyl-sn-glycero-3-phospho-L-serine-91
1.25 mM1,2-dioleoyl-sn-glycero-3-phosphoethanolamine-N-[4-(p-maleimidomethyl)cyclohexane-carboxamide]-101
0.6 mMK-Ras-11U-15N, Ile C-delta-13C2
0.6 mMmembrane scaffold protein-122
20 mMTRIS-132
100 mMsodium chloride-142
5 mMMagnesium-152
0.6 mMPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER-162
2 mMTCEP-172
18.75 mM1,2-dioleoyl-sn-glycero-3-phosphocholine-182
5 mM1,2-dioleoyl-sn-glycero-3-phospho-L-serine-192
1.25 mM1,2-dioleoyl-sn-glycero-3-phosphoethanolamine-N-[4-(p-maleimidomethyl)cyclohexane-carboxamide]-202
0.65 mM1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-diethylenetriaminepentaacetic acid (gadolinium salt)-212
Sample conditionsIonic strength: 0.105 / pH: 7.4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
HADDOCKAlexandre Bonvinstructure solution
TopSpinBruker Biospincollection
CHARMM-GUICHARMM-GUI (S. Jo, T. Kim, V.G. Iyer, and W. Im)structure solution
SparkyGoddarddata analysis
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 3000 / Conformers submitted total number: 10

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