[English] 日本語
Yorodumi
- PDB-3tvd: Crystal Structure of Mouse RhoA-GTP complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3tvd
TitleCrystal Structure of Mouse RhoA-GTP complex
ComponentsTransforming protein RhoA
KeywordsSIGNALING PROTEIN / Alpha helical / Protein_GTP complex / Helical protein / GTP binding protein / Regulates signal transduction pathway / GTP / Nil / Membrane
Function / homology
Function and homology information


EPHA-mediated growth cone collapse / PCP/CE pathway / RHO GTPases activate PKNs / SLIT2:ROBO1 increases RHOA activity / RHO GTPases Activate Rhotekin and Rhophilins / Sema4D mediated inhibition of cell attachment and migration / RHO GTPases Activate ROCKs / ERBB2 Regulates Cell Motility / RHO GTPases activate KTN1 / PI3K/AKT activation ...EPHA-mediated growth cone collapse / PCP/CE pathway / RHO GTPases activate PKNs / SLIT2:ROBO1 increases RHOA activity / RHO GTPases Activate Rhotekin and Rhophilins / Sema4D mediated inhibition of cell attachment and migration / RHO GTPases Activate ROCKs / ERBB2 Regulates Cell Motility / RHO GTPases activate KTN1 / PI3K/AKT activation / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / positive regulation of vascular associated smooth muscle contraction / Sema4D induced cell migration and growth-cone collapse / Ovarian tumor domain proteases / angiotensin-mediated vasoconstriction involved in regulation of systemic arterial blood pressure / negative regulation of motor neuron apoptotic process / Axonal growth inhibition (RHOA activation) / Axonal growth stimulation / VEGFA-VEGFR2 Pathway / spindle localization / GPVI-mediated activation cascade / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / RHO GTPases Activate Formins / regulation of neural precursor cell proliferation / G alpha (12/13) signalling events / negative regulation of intracellular steroid hormone receptor signaling pathway / negative regulation of synapse assembly / RHO GTPases activate CIT / cerebral cortex cell migration / polar body extrusion after meiotic divisions / establishment or maintenance of actin cytoskeleton polarity / RHOA GTPase cycle / regulation of actin polymerization or depolymerization / forebrain radial glial cell differentiation / cellular response to progesterone stimulus / regulation of dendrite development / positive regulation of podosome assembly / embryonic cleavage / alpha-beta T cell lineage commitment / regulation of systemic arterial blood pressure by endothelin / aortic valve formation / beta selection / endothelial tube lumen extension / skeletal muscle satellite cell migration / bone trabecula morphogenesis / Roundabout signaling pathway / cleavage furrow formation / negative regulation of cell size / positive regulation of smooth muscle contraction / regulation of osteoblast proliferation / regulation of modification of postsynaptic actin cytoskeleton / mitotic cleavage furrow formation / apical junction assembly / negative regulation of cell migration involved in sprouting angiogenesis / androgen receptor signaling pathway / establishment of epithelial cell apical/basal polarity / EPHB-mediated forward signaling / positive regulation of alpha-beta T cell differentiation / cell junction assembly / cellular response to chemokine / negative regulation of oxidative phosphorylation / regulation of modification of postsynaptic structure / odontogenesis / G beta:gamma signalling through PI3Kgamma / meiotic spindle organization / positive regulation of actin filament polymerization / apolipoprotein A-I-mediated signaling pathway / meiotic spindle / wound healing, spreading of cells / stress fiber assembly / GTP metabolic process / positive regulation of leukocyte adhesion to vascular endothelial cell / negative regulation of neuron differentiation / microtubule depolymerization / regulation of neuron projection development / stress-activated protein kinase signaling cascade / Neutrophil degranulation / skeletal muscle tissue development / ossification involved in bone maturation / positive regulation of protein serine/threonine kinase activity / negative chemotaxis / apical junction complex / Rho GDP-dissociation inhibitor binding / myosin binding / negative regulation of vascular associated smooth muscle cell migration / positive regulation of cytokinesis / cellular response to cytokine stimulus / regulation of calcium ion transport / cleavage furrow / response to amino acid / semaphorin-plexin signaling pathway / negative regulation of vascular associated smooth muscle cell proliferation / negative regulation of cell-substrate adhesion / response to glucose / mitotic spindle assembly / Rho protein signal transduction / positive regulation of vasoconstriction / response to mechanical stimulus / endothelial cell migration / positive regulation of stress fiber assembly
Similarity search - Function
Small GTPase Rho / Small GTPase Rho 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 Rho / Small GTPase Rho 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
5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / Transforming protein RhoA
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.989 Å
AuthorsSwaminathan, K. / Pal, K. / Jobichen, C.
CitationJournal: J.Struct.Funct.Genom. / Year: 2012
Title: Crystal structure of mouse RhoA:GTPgammaS complex in a centered lattice.
Authors: Jobichen, C. / Pal, K. / Swaminathan, K.
History
DepositionSep 20, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Nov 1, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transforming protein RhoA
B: Transforming protein RhoA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7536
Polymers43,6262
Non-polymers1,1274
Water61334
1
A: Transforming protein RhoA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3773
Polymers21,8131
Non-polymers5642
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Transforming protein RhoA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3773
Polymers21,8131
Non-polymers5642
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.813, 122.652, 91.276
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 6:181 )
211CHAIN B AND (RESSEQ 6:181 )

-
Components

#1: Protein Transforming protein RhoA


Mass: 21813.186 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Arha, Arha2, Rhoa / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P61589
#2: Chemical ChemComp-GSP / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE


Mass: 539.246 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3S
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.59 Å3/Da / Density % sol: 52.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.2M Ammonium acetate, 0.1M Sodium acetate (pH4.6), 30% Polyethylene glycol 4000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Mar 21, 2011 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.989→29 Å / Num. all: 8595 / Num. obs: 8595 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Rsym value: 0.16
Reflection shellResolution: 3→3.15 Å / Redundancy: 4.9 % / Rsym value: 0.34 / % possible all: 99

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FTN

1ftn


Resolution: 2.989→14.999 Å / SU ML: 0.6 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 25.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2825 853 9.92 %RANDOM
Rwork0.2226 ---
all0.2284 8595 --
obs0.2284 8595 91.27 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 10.69 Å2 / ksol: 0.34 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--10.3504 Å2-0 Å20 Å2
2---0.7651 Å20 Å2
3---11.1155 Å2
Refinement stepCycle: LAST / Resolution: 2.989→14.999 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2840 0 66 34 2940
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092972
X-RAY DIFFRACTIONf_angle_d1.134041
X-RAY DIFFRACTIONf_dihedral_angle_d19.4261139
X-RAY DIFFRACTIONf_chiral_restr0.072446
X-RAY DIFFRACTIONf_plane_restr0.004519
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1398X-RAY DIFFRACTIONPOSITIONAL
12B1398X-RAY DIFFRACTIONPOSITIONAL0.051
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.9895-3.17510.39531340.2956122688
3.1751-3.41760.30791290.2594119686
3.4176-3.75660.36361350.2921122287
3.7566-4.2890.27761400.2052126690
4.289-5.36240.23461540.172136696
5.3624-14.99870.18951610.176146699

+
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