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- PDB-5wpl: KRas G12V, bound to GppNHp and miniprotein 225-11 -

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Basic information

Entry
Database: PDB / ID: 5wpl
TitleKRas G12V, bound to GppNHp and miniprotein 225-11
Components
  • GTPase HRasHRAS
  • Ras-binding peptide
KeywordsSIGNALING PROTEIN / Inhibitor / Complex
Function / homology
Function and homology information


GTPase complex / oncogene-induced cell senescence / positive regulation of ruffle assembly / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / negative regulation of GTPase activity / positive regulation of miRNA metabolic process / T-helper 1 type immune response / positive regulation of wound healing / defense response to protozoan / Signaling by RAS GAP mutants ...GTPase complex / oncogene-induced cell senescence / positive regulation of ruffle assembly / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / negative regulation of GTPase activity / positive regulation of miRNA metabolic process / T-helper 1 type immune response / positive regulation of wound healing / defense response to protozoan / 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 / positive regulation of protein targeting to membrane / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / Signalling to RAS / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / adipose tissue development / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / positive regulation of phospholipase C activity / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Schwann cell development / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / protein-membrane adaptor activity / Signaling by FGFR4 in disease / SHC-mediated cascade:FGFR1 / Erythropoietin activates RAS / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / p38MAPK events / FRS-mediated FGFR1 signaling / Tie2 Signaling / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / EPHB-mediated forward signaling / SHC1 events in EGFR signaling / myelination / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / Ras activation upon Ca2+ influx through NMDA receptor / FLT3 Signaling / Signaling by FGFR1 in disease / GRB2 events in ERBB2 signaling / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / SHC1 events in ERBB2 signaling / Downstream signal transduction / Insulin receptor signalling cascade / Constitutive Signaling by Overexpressed ERBB2 / intrinsic apoptotic signaling pathway / small monomeric GTPase / G protein activity / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / VEGFR2 mediated cell proliferation / positive regulation of epithelial cell proliferation / regulation of actin cytoskeleton organization / FCERI mediated MAPK activation / regulation of long-term neuronal synaptic plasticity / animal organ morphogenesis / positive regulation of JNK cascade / Signaling by ERBB2 TMD/JMD mutants / RAF activation / Signaling by high-kinase activity BRAF mutants / cellular response to gamma radiation / Constitutive Signaling by EGFRvIII / positive regulation of MAP kinase activity / MAP2K and MAPK activation / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / Signaling by SCF-KIT / positive regulation of GTPase activity / endocytosis / Regulation of RAS by GAPs / Negative regulation of MAPK pathway / RAS processing / GDP binding / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / chemotaxis / positive regulation of fibroblast proliferation / MAPK cascade / cellular senescence / Signaling by BRAF and RAF1 fusions / positive regulation of type II interferon production / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / DAP12 signaling
Similarity search - Function
Small GTPase, Ras-type / small GTPase Ras family profile. / 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 / P-loop containing nucleoside triphosphate hydrolase ...Small GTPase, Ras-type / small GTPase Ras family profile. / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GTPase HRas
Similarity search - Component
Biological speciesHomo sapiens (human)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 Å
AuthorsLee, S.-J. / Shim, S.Y. / McGee, J.H. / Verdine, G.L.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Exceptionally high-affinity Ras binders that remodel its effector domain.
Authors: McGee, J.H. / Shim, S.Y. / Lee, S.J. / Swanson, P.K. / Jiang, S.Y. / Durney, M.A. / Verdine, G.L.
History
DepositionAug 5, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 3, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Mar 14, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GTPase HRas
B: Ras-binding peptide
C: Ras-binding peptide
D: GTPase HRas
E: Ras-binding peptide
F: Ras-binding peptide
G: GTPase HRas
H: Ras-binding peptide
I: Ras-binding peptide
J: GTPase HRas
K: Ras-binding peptide
L: Ras-binding peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,74229
Polymers106,21112
Non-polymers2,53117
Water4,107228
1
A: GTPase HRas
B: Ras-binding peptide
C: Ras-binding peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2208
Polymers26,5533
Non-polymers6675
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-51 kcal/mol
Surface area11360 Å2
MethodPISA
2
D: GTPase HRas
E: Ras-binding peptide
F: Ras-binding peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1396
Polymers26,5533
Non-polymers5873
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-48 kcal/mol
Surface area10930 Å2
MethodPISA
3
G: GTPase HRas
H: Ras-binding peptide
I: Ras-binding peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1647
Polymers26,5533
Non-polymers6114
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-48 kcal/mol
Surface area10890 Å2
MethodPISA
4
J: GTPase HRas
K: Ras-binding peptide
L: Ras-binding peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2208
Polymers26,5533
Non-polymers6675
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-51 kcal/mol
Surface area11010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.861, 234.507, 48.143
Angle α, β, γ (deg.)90.000, 90.130, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Protein/peptide , 2 types, 12 molecules ADGJBCEFHIKL

#1: Protein
GTPase HRas / HRAS / H-Ras-1 / Ha-Ras / Transforming protein p21 / c-H-ras / p21ras


Mass: 18960.357 Da / Num. of mol.: 4 / Fragment: residues 1-166
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HRAS, HRAS1 / Production host: Escherichia coli (E. coli) / References: UniProt: P01112
#2: Protein/peptide
Ras-binding peptide


Mass: 3796.214 Da / Num. of mol.: 8 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)

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Non-polymers , 4 types, 245 molecules

#3: Chemical
ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 228 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M ammonium sulfate and 20-25% PEG3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 47914 / % possible obs: 98.1 % / Redundancy: 3.6 % / Net I/σ(I): 12.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
REFMAC5.8.0151refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→48.14 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.895 / SU B: 7.406 / SU ML: 0.185 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.31 / ESU R Free: 0.23
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2583 2364 4.9 %RANDOM
Rwork0.2048 ---
obs0.2075 45476 97.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 89.75 Å2 / Biso mean: 26.683 Å2 / Biso min: 5.34 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.15→48.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7071 0 141 228 7440
Biso mean--19.36 23.2 -
Num. residues----871
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0197355
X-RAY DIFFRACTIONr_bond_other_d0.0020.026771
X-RAY DIFFRACTIONr_angle_refined_deg1.6731.9729992
X-RAY DIFFRACTIONr_angle_other_deg1.014315518
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6275856
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.85523.351382
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.704151216
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6941572
X-RAY DIFFRACTIONr_chiral_restr0.0960.21065
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028247
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021761
LS refinement shellResolution: 2.15→2.206 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 152 -
Rwork0.283 2658 -
all-2810 -
obs--78.91 %

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