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- PDB-1iaq: C-H-RAS P21 PROTEIN MUTANT WITH THR 35 REPLACED BY SER (T35S) COM... -

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Basic information

Entry
Database: PDB / ID: 1iaq
TitleC-H-RAS P21 PROTEIN MUTANT WITH THR 35 REPLACED BY SER (T35S) COMPLEXED WITH GUANOSINE-5'-[B,G-IMIDO] TRIPHOSPHATE
ComponentsTRANSFORMING PROTEIN P21/H-RAS-1
KeywordsSIGNALING PROTEIN / GTP-binding / Proto-oncogene
Function / homology
Function and homology information


phospholipase C activator activity / GTPase complex / oncogene-induced cell senescence / positive regulation of miRNA metabolic process / positive regulation of ruffle assembly / T-helper 1 type immune response / positive regulation of wound healing / defense response to protozoan / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / Signaling by RAS GAP mutants ...phospholipase C activator activity / GTPase complex / oncogene-induced cell senescence / positive regulation of miRNA metabolic process / positive regulation of ruffle assembly / T-helper 1 type immune response / positive regulation of wound healing / defense response to protozoan / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / 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 / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / positive regulation of protein targeting to membrane / SHC1 events in ERBB4 signaling / adipose tissue development / Signalling to RAS / Activated NTRK2 signals through FRS2 and FRS3 / SHC-related events triggered by IGF1R / Schwann cell development / Estrogen-stimulated signaling through PRKCZ / 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 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 / Signaling by FGFR2 in disease / myelination / EPHB-mediated forward signaling / 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 / CD209 (DC-SIGN) signaling / GRB2 events in ERBB2 signaling / intrinsic apoptotic signaling pathway / Downstream signal transduction / Insulin receptor signalling cascade / SHC1 events in ERBB2 signaling / Ras activation upon Ca2+ influx through NMDA receptor / Constitutive Signaling by Overexpressed ERBB2 / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / animal organ morphogenesis / VEGFR2 mediated cell proliferation / positive regulation of epithelial cell proliferation / small monomeric GTPase / regulation of actin cytoskeleton organization / positive regulation of JNK cascade / FCERI mediated MAPK activation / Signaling by ERBB2 TMD/JMD mutants / RAF activation / cellular response to gamma radiation / 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 / positive regulation of type II interferon production / endocytosis / positive regulation of fibroblast proliferation / chemotaxis / Regulation of RAS by GAPs / 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 / cellular senescence / Signaling by BRAF and RAF1 fusions / insulin receptor signaling pathway / DAP12 signaling / T cell receptor signaling pathway / MAPK cascade / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / regulation of cell population proliferation / G protein activity
Similarity search - Function
Small GTPase, Ras-type / Small GTPase Ras domain 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 / Rossmann fold ...Small GTPase, Ras-type / Small GTPase Ras domain 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 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 / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsSpoerner, M. / Herrmann, C. / Vetter, I.R. / Kalbitzer, H.R. / Wittinghofer, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Dynamic properties of the Ras switch I region and its importance for binding to effectors.
Authors: Spoerner, M. / Herrmann, C. / Vetter, I.R. / Kalbitzer, H.R. / Wittinghofer, A.
History
DepositionMar 23, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 6, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Nov 10, 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.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.value / _struct_conn.pdbx_dist_value / _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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRANSFORMING PROTEIN P21/H-RAS-1
B: TRANSFORMING PROTEIN P21/H-RAS-1
C: TRANSFORMING PROTEIN P21/H-RAS-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2239
Polymers56,5833
Non-polymers1,6406
Water00
1
A: TRANSFORMING PROTEIN P21/H-RAS-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4083
Polymers18,8611
Non-polymers5472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TRANSFORMING PROTEIN P21/H-RAS-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4083
Polymers18,8611
Non-polymers5472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: TRANSFORMING PROTEIN P21/H-RAS-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4083
Polymers18,8611
Non-polymers5472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.890, 79.060, 94.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TRANSFORMING PROTEIN P21/H-RAS-1 / C-H-RAS


Mass: 18861.166 Da / Num. of mol.: 3 / Fragment: CATALYTIC DOMAIN (RESIDUES 1-166) / Mutation: T35S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HRAS OR HRAS1 / Plasmid: PTAC / Production host: Escherichia coli (E. coli) / Strain (production host): CK600K / 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-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG1500, calcium chloride, Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
124 %PEG15001reservoir
250 mM1reservoirCaCl2
3100 mMTris1reservoir
420 mg/mlprotein1drop

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12981
22981
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5481 Å
Detector
TypeIDDetectorDateDetails
MARRESEARCH1IMAGE PLATEFeb 3, 2000monochromator
SIEMENS HI-STAR2AREA DETECTORJul 23, 1999monochromator
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1GRAPHITESINGLE WAVELENGTHMx-ray1
2GRAPHITESINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1.5481 Å / Relative weight: 1
ReflectionResolution: 2.9→34.1 Å / Num. all: 10369 / Num. obs: 60892 / % possible obs: 95.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.2 % / Biso Wilson estimate: 52.5 Å2 / Rmerge(I) obs: 0.204 / Net I/σ(I): 7.13
Reflection shellResolution: 2.9→3 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.387 / Mean I/σ(I) obs: 1.8 / Num. unique all: 1051 / % possible all: 91.6
Reflection
*PLUS
Lowest resolution: 50 Å / Num. obs: 10369 / Num. measured all: 60892
Reflection shell
*PLUS
% possible obs: 91.6 %

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
MAR345data collection
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5p21

5p21


Resolution: 2.9→25 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.282 1072 RANDOM
Rwork0.242 --
all-9016 -
obs-9016 -
Displacement parametersBiso mean: 58 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.57 Å0.79 Å
Refinement stepCycle: LAST / Resolution: 2.9→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3589 0 99 0 3688
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_improper_angle_d0.62
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.035
RfactorNum. reflection
Rfree0.37 112
Rwork0.361 -
obs-1083
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 25 Å / σ(F): 2 / Rfactor obs: 0.242
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 58 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.62
LS refinement shell
*PLUS
Highest resolution: 2.9 Å / Rfactor Rfree: 0.37 / Rfactor Rwork: 0.361

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