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- PDB-5ufq: K-RasG12D(GNP)/R11.1.6 complex -

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Basic information

Entry
Database: PDB / ID: 5ufq
TitleK-RasG12D(GNP)/R11.1.6 complex
Components
  • GTPase KRas
  • R11.1.6
KeywordsHydrolase/DE NOVO PROTEIN / Ras / GTPase / complex / inhibitor / Hydrolase-DE NOVO PROTEIN complex
Function / homology
Function and homology information


response to mineralocorticoid / GMP binding / forebrain astrocyte development / LRR domain binding / regulation of synaptic transmission, GABAergic / negative regulation of epithelial cell differentiation / response to isolation stress / response to gravity / epithelial tube branching involved in lung morphogenesis / type I pneumocyte differentiation ...response to mineralocorticoid / GMP binding / forebrain astrocyte development / LRR domain binding / regulation of synaptic transmission, GABAergic / negative regulation of epithelial cell differentiation / response to isolation stress / 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 / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / cardiac muscle cell proliferation / Signalling to RAS / Activated NTRK2 signals through FRS2 and FRS3 / SHC-related events triggered by IGF1R / Estrogen-stimulated signaling through PRKCZ / glial cell proliferation / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / SHC-mediated cascade:FGFR2 / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR4 / Erythropoietin activates RAS / SHC-mediated cascade:FGFR1 / Signaling by FGFR4 in disease / FRS-mediated FGFR3 signaling / Signaling by CSF3 (G-CSF) / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / p38MAPK events / FRS-mediated FGFR1 signaling / Signaling by FGFR3 in disease / protein-membrane adaptor activity / Tie2 Signaling / striated muscle cell differentiation / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / Signaling by FLT3 fusion proteins / FLT3 Signaling / Signaling by FGFR1 in disease / EGFR Transactivation by Gastrin / NCAM signaling for neurite out-growth / homeostasis of number of cells within a tissue / CD209 (DC-SIGN) signaling / GRB2 events in ERBB2 signaling / Downstream signal transduction / Insulin receptor signalling cascade / SHC1 events in ERBB2 signaling / Ras activation upon Ca2+ influx through NMDA receptor / response to glucocorticoid / Constitutive Signaling by Overexpressed ERBB2 / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / VEGFR2 mediated cell proliferation / small monomeric GTPase / FCERI mediated MAPK activation / liver development / Signaling by ERBB2 TMD/JMD mutants / female pregnancy / RAF activation / Signaling by SCF-KIT / Signaling by high-kinase activity BRAF mutants / Constitutive Signaling by EGFRvIII / regulation of long-term neuronal synaptic plasticity / MAP2K and MAPK activation / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / visual learning / cytoplasmic side of plasma membrane / cytokine-mediated signaling pathway / Regulation of RAS by GAPs / Signaling by CSF1 (M-CSF) in myeloid cells / RAS processing / Negative regulation of MAPK pathway / 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 / GDP binding / Signaling by BRAF and RAF1 fusions / positive regulation of cellular senescence / DAP12 signaling / MAPK cascade / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants
Similarity search - Function
OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / 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 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) ...OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / 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 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Beta Barrel / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GTPase KRas
Similarity search - Component
Biological speciesHomo sapiens (human)
Sulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.199 Å
AuthorsParker, J.A. / Mattos, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1517295 United States
CitationJournal: Sci Rep / Year: 2017
Title: An engineered protein antagonist of K-Ras/B-Raf interaction.
Authors: Kauke, M.J. / Traxlmayr, M.W. / Parker, J.A. / Kiefer, J.D. / Knihtila, R. / McGee, J. / Verdine, G. / Mattos, C. / Wittrup, K.D.
History
DepositionJan 5, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GTPase KRas
B: GTPase KRas
C: R11.1.6
D: R11.1.6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,94116
Polymers52,4014
Non-polymers1,54012
Water2,054114
1
B: GTPase KRas
D: R11.1.6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9718
Polymers26,2012
Non-polymers7706
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: GTPase KRas
C: R11.1.6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9718
Polymers26,2012
Non-polymers7706
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-7 kcal/mol
Surface area10910 Å2
MethodPISA
3
B: GTPase KRas
hetero molecules

D: R11.1.6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9718
Polymers26,2012
Non-polymers7706
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area1530 Å2
ΔGint-9 kcal/mol
Surface area10940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.717, 42.707, 100.235
Angle α, β, γ (deg.)90.00, 113.33, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein GTPase KRas / K-Ras 2 / Ki-Ras / c-K-ras / c-Ki-ras


Mass: 18942.320 Da / Num. of mol.: 2 / Fragment: UNP residues 1-166 / Mutation: G12D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KRAS, KRAS2, RASK2 / Production host: Escherichia coli (E. coli) / References: UniProt: P01116
#2: Protein R11.1.6


Mass: 7258.335 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Production host: Escherichia coli (E. coli)

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Non-polymers , 6 types, 126 molecules

#3: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#7: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 2.25 Å3/Da / Density % sol: 45.21 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: calcium chloride, cadmium chloride, cobalt(II) chloride hexahydrate, PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.199→45.174 Å / Num. obs: 23511 / % possible obs: 97.68 % / Redundancy: 7.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.1016 / Net I/σ(I): 21.83
Reflection shellResolution: 2.199→2.278 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.3521 / Mean I/σ(I) obs: 4.5 / CC1/2: 0.972 / % possible all: 93.48

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
PHENIX1.8.4_1496phasing
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 3GFT and PDB ID 1SSO

3gft

1sso


Resolution: 2.199→45.174 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 32.44
RfactorNum. reflection% reflection
Rfree0.2634 1996 8.5 %
Rwork0.2003 --
obs0.2056 23486 97.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.199→45.174 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3504 0 74 114 3692
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093644
X-RAY DIFFRACTIONf_angle_d1.1524948
X-RAY DIFFRACTIONf_dihedral_angle_d15.1081314
X-RAY DIFFRACTIONf_chiral_restr0.044549
X-RAY DIFFRACTIONf_plane_restr0.005621
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1991-2.25410.31271320.23361448X-RAY DIFFRACTION92
2.2541-2.3150.30911380.24621470X-RAY DIFFRACTION96
2.315-2.38320.3361420.23521525X-RAY DIFFRACTION97
2.3832-2.46010.25271390.23131492X-RAY DIFFRACTION97
2.4601-2.5480.32361430.23561546X-RAY DIFFRACTION97
2.548-2.650.27681420.23691523X-RAY DIFFRACTION97
2.65-2.77060.29521400.24761511X-RAY DIFFRACTION98
2.7706-2.91660.35291450.24251546X-RAY DIFFRACTION98
2.9166-3.09930.31821410.2271525X-RAY DIFFRACTION98
3.0993-3.33860.26141460.2231563X-RAY DIFFRACTION99
3.3386-3.67440.28821440.20021555X-RAY DIFFRACTION99
3.6744-4.20580.2211470.16611576X-RAY DIFFRACTION99
4.2058-5.29750.19841460.1561571X-RAY DIFFRACTION99
5.2975-45.1740.23651510.17831639X-RAY DIFFRACTION99

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