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- PDB-1zw6: Crystal Structure of the GTP-bound form of RasQ61G -

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Basic information

Entry
Database: PDB / ID: 1zw6
TitleCrystal Structure of the GTP-bound form of RasQ61G
ComponentsTransforming protein p21/H-Ras-1
KeywordsONCOPROTEIN / GTPase / GTP / Ras / G-protein
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 / positive regulation of JNK cascade / regulation of long-term neuronal synaptic plasticity / animal organ morphogenesis / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsFord, B. / Hornak, V. / Kleinman, H. / Nassar, N.
Citation
Journal: Structure / Year: 2006
Title: Structure of a transient intermediate for GTP hydrolysis by ras.
Authors: Ford, B. / Hornak, V. / Kleinman, H. / Nassar, N.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: The structural basis for the transition from Ras-GTP to Ras-GDP
Authors: Hall, B.E. / Bar-Sagi, D. / Nassar, N.
History
DepositionJun 3, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_symmetry / _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_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Transforming protein p21/H-Ras-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4957
Polymers18,8201
Non-polymers6756
Water3,009167
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.776, 88.776, 134.392
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-204-

MG

21A-335-

HOH

31A-341-

HOH

41A-346-

HOH

51A-358-

HOH

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Components

#1: Protein Transforming protein p21/H-Ras-1 / c-H-ras


Mass: 18820.115 Da / Num. of mol.: 1 / Mutation: Q61G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HRAS, HRAS1 / Plasmid: pProEx-HTb / Production host: Escherichia coli (E. coli) / Strain (production host): CodonPlus(DE3) / References: UniProt: P01112
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.61 Å3/Da / Density % sol: 54.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 22% PEG4000, 200mM Ca Acetate, 100 mM Tris-HCl, 10 mM MgCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 6, 2004 / Details: Monochromator
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→30.8 Å / Num. all: 30980 / Num. obs: 30980 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Biso Wilson estimate: 24 Å2 / Rsym value: 0.086 / Net I/σ(I): 24.1
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 6 % / Mean I/σ(I) obs: 3.8 / Num. unique all: 32638 / Rsym value: 0.465 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→30.79 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.834 / SU ML: 0.032 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.067 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17403 1653 5.1 %RANDOM
Rwork0.14419 ---
all0.146 30980 --
obs0.146 30980 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.236 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å2-0.03 Å20 Å2
2---0.07 Å20 Å2
3---0.1 Å2
Refine analyzeLuzzati coordinate error obs: 0.159 Å
Refinement stepCycle: LAST / Resolution: 1.5→30.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1355 0 37 167 1559
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221408
X-RAY DIFFRACTIONr_bond_other_d0.0020.021248
X-RAY DIFFRACTIONr_angle_refined_deg1.4891.9871903
X-RAY DIFFRACTIONr_angle_other_deg2.34832909
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.7125.12167
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.01724.15677
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.7515256
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5371514
X-RAY DIFFRACTIONr_chiral_restr0.0830.2206
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021549
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02285
X-RAY DIFFRACTIONr_nbd_refined0.2080.2279
X-RAY DIFFRACTIONr_nbd_other0.1970.21300
X-RAY DIFFRACTIONr_nbtor_refined0.180.2687
X-RAY DIFFRACTIONr_nbtor_other0.0910.2818
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.2121
X-RAY DIFFRACTIONr_metal_ion_refined0.1280.28
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3970.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2660.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2610.226
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.3340.23
X-RAY DIFFRACTIONr_mcbond_it1.5731.5855
X-RAY DIFFRACTIONr_mcbond_other0.4951.5343
X-RAY DIFFRACTIONr_mcangle_it2.11921331
X-RAY DIFFRACTIONr_scbond_it2.9133639
X-RAY DIFFRACTIONr_scangle_it4.0644.5572
X-RAY DIFFRACTIONr_rigid_bond_restr1.52932892
X-RAY DIFFRACTIONr_sphericity_free6.5033172
X-RAY DIFFRACTIONr_sphericity_bonded2.48732635
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.197 127 -
Rwork0.152 2250 -
obs--98.96 %

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