[English] 日本語
Yorodumi
- PDB-3lo5: Crystal Structure of the dominant negative S17N mutant of Ras -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3lo5
TitleCrystal Structure of the dominant negative S17N mutant of Ras
ComponentsGTPase HRasHRAS
KeywordsONCOPROTEIN / Ras / nucleotide exchange / dominant negative / Mg2+ / Acetylation / Cell membrane / Disease mutation / Golgi apparatus / GTP-binding / Lipoprotein / Membrane / Methylation / Nucleotide-binding / Palmitate / Prenylation / Proto-oncogene / S-nitrosylation
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
GUANOSINE-5'-DIPHOSPHATE / GTPase HRas
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.568 Å
AuthorsNassar, N. / Singh, K. / Garcia-Diaz, M.
CitationJournal: Biochemistry / Year: 2010
Title: Structure of the Dominant Negative S17N Mutant of Ras
Authors: Nassar, N. / Singh, K. / Garcia-Diaz, M.
History
DepositionFeb 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GTPase HRas
C: GTPase HRas
E: GTPase HRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,29311
Polymers56,7073
Non-polymers1,5868
Water1,18966
1
A: GTPase HRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3853
Polymers18,9021
Non-polymers4832
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: GTPase HRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4824
Polymers18,9021
Non-polymers5793
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: GTPase HRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4264
Polymers18,9021
Non-polymers5233
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.475, 102.184, 117.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11E-168-

CA

21C-181-

HOH

31E-179-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
12
22
32
13
23
33

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 1:25 )
211chain C and (resseq 1:25 )
311chain E and (resseq 1:25 )
112chain A and (resseq 40:57 )
212chain C and (resseq 40:56 )
312chain E and (resseq 41:56 )
113chain A and (resseq 75:163 )
213chain C and (resseq 75:163 )
313chain E and (resseq 115:163 )

NCS ensembles :
ID
1
2
3

-
Components

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


Mass: 18902.217 Da / Num. of mol.: 3 / Fragment: H-Ras (UNP residues 1-166) / Mutation: S17N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H-Ras, HRAS, HRAS1 / Plasmid: pProEx-HTb2 / Production host: Escherichia coli (E. coli) / Strain (production host): CodonPlus / References: UniProt: P01112
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 15% (v/v) PEG400, 13% (w/v) PEG8000, 0.2 M calcium acetate, and 0.1 M Tris-HCl pH = 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: 2007 / Details: Si-monochromator
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→44.7 Å / Num. all: 17942 / Num. obs: 17942 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Biso Wilson estimate: 56.6 Å2 / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 17.5
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 3.2 / Rsym value: 0.579 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Q21

4q21


Resolution: 2.568→41.81 Å / SU ML: 1.25 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2964 914 5.1 %Random
Rwork0.2377 ---
obs0.2406 17939 98.56 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.296 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 37.3 Å2
Refine analyzeLuzzati coordinate error free: 0.37 Å
Refinement stepCycle: LAST / Resolution: 2.568→41.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3499 0 93 66 3658
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033635
X-RAY DIFFRACTIONf_angle_d0.7344921
X-RAY DIFFRACTIONf_dihedral_angle_d16.1511327
X-RAY DIFFRACTIONf_chiral_restr0.045565
X-RAY DIFFRACTIONf_plane_restr0.002624
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A181X-RAY DIFFRACTIONPOSITIONAL
12C181X-RAY DIFFRACTIONPOSITIONAL0.012
13E181X-RAY DIFFRACTIONPOSITIONAL0.011
21A134X-RAY DIFFRACTIONPOSITIONAL
22C134X-RAY DIFFRACTIONPOSITIONAL0.051
23E122X-RAY DIFFRACTIONPOSITIONAL0.033
31A703X-RAY DIFFRACTIONPOSITIONAL
32C703X-RAY DIFFRACTIONPOSITIONAL0.019
33E381X-RAY DIFFRACTIONPOSITIONAL0.013
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5676-2.70290.35381230.29032204X-RAY DIFFRACTION91
2.7029-2.87230.32961230.28582426X-RAY DIFFRACTION100
2.8723-3.0940.31221410.26912427X-RAY DIFFRACTION100
3.094-3.40520.28741260.22712460X-RAY DIFFRACTION100
3.4052-3.89760.27711250.22032466X-RAY DIFFRACTION100
3.8976-4.90940.27851350.20022474X-RAY DIFFRACTION100
4.9094-41.81550.27841410.23152568X-RAY DIFFRACTION99
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
1refined2.8431-0.13560.44951.7262-0.93731.8191-0.11020.11040.3408-0.0298-0.04240.075-0.1448-0.0120.05250.0472-0.01990.02460.1448-0.08870.0497-11.8215-30.2536-59.8049
23.82711.447-0.4884-0.12750.21221.1192-0.0616-0.3331.0917-0.20080.18080.7003-0.13310.5972-0.28380.14310.163-0.0980.3562-0.25910.5361
32.7608-0.0970.65331.9721-0.17322.26660.0836-0.2804-0.34460.14450.12660.08340.2834-0.0291-0.16490.1403-0.05150.01980.205-0.05350.1351
42.18061.27475.09320.8825-0.19013.36970.77740.88640.44610.05360.16720.0924-0.2608-1.62890.10370.2857-0.03790.28070.81690.06380.2246
52.3036-1.0239-0.33784.75740.67381.79410.30870.3741-0.2218-0.6906-0.68610.4047-0.2985-0.30970.29990.16550.1343-0.08510.3804-0.1534-0.0064
68.43726.3901-6.11719.99195.19672.7935-0.72391.4758-0.5827-1.07020.2049-1.0282-0.2959-1.61810.23780.2430.09740.05350.5146-0.01860.1773
Refinement TLS groupSelection details: chain F

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more