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- PDB-5xco: Crystal structure of human K-Ras G12D Mutant in complex with GDP ... -

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Basic information

Entry
Database: PDB / ID: 5xco
TitleCrystal structure of human K-Ras G12D Mutant in complex with GDP and Cyclic Inhibitory Peptide
Components
  • ACE-ARG-ARG-ARG-ARG-CYS-PRO-LEU-TYR-ILE-SER-TYR-ASP-PRO-VAL-CYS-ARG-ARG-ARG-ARG-NH2
  • GTPase KRas
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Hydrolase / Complex / Inhibitor / Small GTPase / Oncogene / Signaling / HYDROLASE-HYDROLASE INHIBITOR 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 / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / positive regulation of Rac protein signal transduction / Activation of RAS in B cells / myoblast proliferation / RAS signaling downstream of NF1 loss-of-function variants / RUNX3 regulates p14-ARF / positive regulation of glial cell proliferation / skeletal muscle cell differentiation / 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 / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / glial cell proliferation / MET activates RAS signaling / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / 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 / FRS-mediated FGFR1 signaling / Signaling by FGFR3 in disease / protein-membrane adaptor activity / striated muscle cell differentiation / Tie2 Signaling / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / Signaling by FLT3 fusion proteins / SHC1 events in EGFR signaling / FLT3 Signaling / Signaling by FGFR1 in disease / EGFR Transactivation by Gastrin / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / GRB2 events in ERBB2 signaling / homeostasis of number of cells within a tissue / 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 / Constitutive Signaling by EGFRvIII / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / regulation of long-term neuronal synaptic plasticity / visual learning / cytoplasmic side of plasma membrane / cytokine-mediated signaling pathway / Signaling by CSF1 (M-CSF) in myeloid cells / Regulation of RAS by GAPs / Negative regulation of MAPK pathway / Signaling by RAF1 mutants / RAS processing / 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
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 ...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
GUANOSINE-5'-DIPHOSPHATE / GTPase KRas
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage T7 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsSogabe, S. / Miwa, M.
CitationJournal: ACS Med Chem Lett / Year: 2017
Title: Crystal Structure of a Human K-Ras G12D Mutant in Complex with GDP and the Cyclic Inhibitory Peptide KRpep-2d
Authors: Sogabe, S. / Kamada, Y. / Miwa, M. / Niida, A. / Sameshima, T. / Kamaura, M. / Yonemori, K. / Sasaki, S. / Sakamoto, J. / Sakamoto, K.
History
DepositionMar 23, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GTPase KRas
B: ACE-ARG-ARG-ARG-ARG-CYS-PRO-LEU-TYR-ILE-SER-TYR-ASP-PRO-VAL-CYS-ARG-ARG-ARG-ARG-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5334
Polymers22,0282
Non-polymers5052
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-14 kcal/mol
Surface area9730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.529, 51.529, 129.741
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-385-

HOH

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Components

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


Mass: 19473.926 Da / Num. of mol.: 1 / Fragment: UNP residues 1-169 / 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/peptide ACE-ARG-ARG-ARG-ARG-CYS-PRO-LEU-TYR-ILE-SER-TYR-ASP-PRO-VAL-CYS-ARG-ARG-ARG-ARG-NH2


Mass: 2554.086 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Enterobacteria phage T7 (virus)
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.26 Å3/Da / Density % sol: 45.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1M Hepes, 50% PEG 200

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.25→50 Å / Num. obs: 56366 / % possible obs: 100 % / Redundancy: 9.3 % / Rsym value: 0.041 / Net I/σ(I): 54.4
Reflection shellResolution: 1.25→1.27 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2780 / Rsym value: 0.964 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QL3

4ql3


Resolution: 1.25→44.63 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.247 / SU ML: 0.026 / Cross valid method: THROUGHOUT / ESU R: 0.042 / ESU R Free: 0.045 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19403 2766 4.9 %RANDOM
Rwork0.17077 ---
obs0.17191 53531 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.106 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.02 Å2-0 Å2
2--0.03 Å20 Å2
3----0.1 Å2
Refinement stepCycle: 1 / Resolution: 1.25→44.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1539 0 33 138 1710
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191681
X-RAY DIFFRACTIONr_bond_other_d0.0140.021561
X-RAY DIFFRACTIONr_angle_refined_deg1.5921.9872284
X-RAY DIFFRACTIONr_angle_other_deg1.10433629
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0045211
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.26723.16790
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.75815317
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7431519
X-RAY DIFFRACTIONr_chiral_restr0.0950.2247
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022639
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02356
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8921.427781
X-RAY DIFFRACTIONr_mcbond_other0.8731.428779
X-RAY DIFFRACTIONr_mcangle_it1.4592.141978
X-RAY DIFFRACTIONr_mcangle_other1.4542.141978
X-RAY DIFFRACTIONr_scbond_it1.3561.691900
X-RAY DIFFRACTIONr_scbond_other1.3581.689901
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1722.451296
X-RAY DIFFRACTIONr_long_range_B_refined3.55415.5832289
X-RAY DIFFRACTIONr_long_range_B_other3.5115.3092271
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.249→1.281 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 202 -
Rwork0.273 3866 -
obs--98.81 %
Refinement TLS params.Method: refined / Origin x: 12.5793 Å / Origin y: -10.8222 Å / Origin z: -10.4998 Å
111213212223313233
T0.061 Å2-0.0123 Å2-0.0029 Å2-0.0213 Å20.0018 Å2--0.0025 Å2
L0.1494 °20.0951 °20.0432 °2-0.2943 °2-0.1351 °2--0.1771 °2
S0.0384 Å °0.0039 Å °-0.0153 Å °0.0282 Å °-0.0224 Å °-0.0019 Å °-0.0007 Å °-0.007 Å °-0.0161 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 169
2X-RAY DIFFRACTION1A201
3X-RAY DIFFRACTION1B0 - 20

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