[English] 日本語
Yorodumi
- PDB-2q3h: The crystal structure of RhouA in the GDP-bound state. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2q3h
TitleThe crystal structure of RhouA in the GDP-bound state.
ComponentsRas homolog gene family, member U
KeywordsSTRUCTURAL GENOMICS / GTPase / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


regulation of small GTPase mediated signal transduction / podosome / positive regulation of protein targeting to mitochondrion / establishment of cell polarity / Rac protein signal transduction / RHOU GTPase cycle / cytoskeleton organization / guanyl-nucleotide exchange factor activity / actin filament organization / cell projection ...regulation of small GTPase mediated signal transduction / podosome / positive regulation of protein targeting to mitochondrion / establishment of cell polarity / Rac protein signal transduction / RHOU GTPase cycle / cytoskeleton organization / guanyl-nucleotide exchange factor activity / actin filament organization / cell projection / G1/S transition of mitotic cell cycle / endocytosis / regulation of cell shape / Interleukin-4 and Interleukin-13 signaling / endosome membrane / Golgi membrane / focal adhesion / GTPase activity / protein kinase binding / GTP binding / signal transduction / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Small GTPase Rho / small GTPase Rho family 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 Rho / small GTPase Rho family 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 / Rho-related GTP-binding protein RhoU / :
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsGileadi, C. / Yang, X. / Papagrigoriou, E. / Elkins, J. / Zhao, Y. / Bray, J. / Gileadi, O. / Umeano, C. / Ugochukwu, E. / Uppenberg, J. ...Gileadi, C. / Yang, X. / Papagrigoriou, E. / Elkins, J. / Zhao, Y. / Bray, J. / Gileadi, O. / Umeano, C. / Ugochukwu, E. / Uppenberg, J. / Bunkoczi, G. / von Delft, F. / Pike, A.C.W. / Phillips, C. / Savitsky, P. / Fedorov, O. / Edwards, A. / Weigelt, J. / Arrowsmith, C.H. / Sundstrom, M. / Doyle, D.A. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: The crystal structure of RhouA in the GDP-bound state.
Authors: Gileadi, C. / Yang, X. / Papagrigoriou, E. / Elkins, J. / Zhao, Y. / Bray, J. / Gileadi, O. / Umeano, C. / Ugochukwu, E. / Uppenberg, J. / Bunkoczi, G. / von Delft, F. / Pike, A.C.W. / ...Authors: Gileadi, C. / Yang, X. / Papagrigoriou, E. / Elkins, J. / Zhao, Y. / Bray, J. / Gileadi, O. / Umeano, C. / Ugochukwu, E. / Uppenberg, J. / Bunkoczi, G. / von Delft, F. / Pike, A.C.W. / Phillips, C. / Savitsky, P. / Fedorov, O. / Edwards, A. / Weigelt, J. / Arrowsmith, C.H. / Sundstrom, M. / Doyle, D.A.
History
DepositionMay 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Apr 3, 2024Group: 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 / 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.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 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ras homolog gene family, member U
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1543
Polymers21,6871
Non-polymers4682
Water2,234124
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.068, 53.600, 54.128
Angle α, β, γ (deg.)90.00, 118.80, 90.00
Int Tables number5
Space group name H-MC121
Detailsthe monomer in the asu represents a biological unit

-
Components

#1: Protein Ras homolog gene family, member U / Ras-like gene family member U / Wrch-1 / Ryu GTPase / CDC42-like GTPase / Rho GTPase-like protein ...Ras-like gene family member U / Wrch-1 / Ryu GTPase / CDC42-like GTPase / Rho GTPase-like protein ARHU / GTP-binding protein like 1


Mass: 21686.646 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RHOU / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli)
Strain (production host): BL21(DE3) with with pRARE plasmid encoding rare codon tRNAs,(chloramphenicol-resistant)
References: UniProt: Q9NPY5, UniProt: Q7L0Q8*PLUS
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M MgCl2; 0.1M TRIS; 25% PEG 3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.03315 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 16, 2007 / Details: Si(111)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03315 Å / Relative weight: 1
ReflectionResolution: 1.73→47.46 Å / Num. all: 21616 / Num. obs: 21530 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.033 / Rsym value: 0.049
Reflection shellResolution: 1.73→1.79 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.49 / Num. unique all: 2077 / Rsym value: 0.387 / % possible all: 98

-
Processing

Software
NameVersionClassification
REFMAC5.3.0034refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: homology based model

Resolution: 1.73→47.46 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.621 / SU ML: 0.083 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.101 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22198 1107 5.1 %RANDOM
Rwork0.18276 ---
all0.18276 21616 --
obs0.18474 20423 99.56 %-
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: 35.051 Å2
Baniso -1Baniso -2Baniso -3
1--1.62 Å20 Å2-2.01 Å2
2--1.5 Å20 Å2
3----1.82 Å2
Refinement stepCycle: LAST / Resolution: 1.73→47.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1276 0 29 124 1429
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221336
X-RAY DIFFRACTIONr_bond_other_d0.0030.02861
X-RAY DIFFRACTIONr_angle_refined_deg1.6862.0011828
X-RAY DIFFRACTIONr_angle_other_deg0.97732131
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4765171
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.69925.30649
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.93415213
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.968155
X-RAY DIFFRACTIONr_chiral_restr0.1020.2224
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021458
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02246
X-RAY DIFFRACTIONr_nbd_refined0.2280.2280
X-RAY DIFFRACTIONr_nbd_other0.1970.2913
X-RAY DIFFRACTIONr_nbtor_refined0.1820.2669
X-RAY DIFFRACTIONr_nbtor_other0.0870.2682
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2113
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.3350.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.5330.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2740.213
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0820.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.423879
X-RAY DIFFRACTIONr_mcbond_other1.0453341
X-RAY DIFFRACTIONr_mcangle_it4.29951398
X-RAY DIFFRACTIONr_scbond_it6.7528521
X-RAY DIFFRACTIONr_scangle_it8.10611429
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.73→1.775 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 84 -
Rwork0.238 1441 -
obs--97.13 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
15.2441-4.0615-0.57199.68580.46152.17110.58620.6493-0.16-0.3367-0.55960.5989-0.2604-0.523-0.0266-0.16790.1276-0.0609-0.0132-0.0479-0.10449.0861-3.230314.6322
24.3903-3.4276-0.73494.98590.94442.66070.78730.9580.2871-0.8143-0.83360.1182-0.3171-0.42680.0463-0.04470.19770.01470.00130.0535-0.112214.28950.004110.8588
35.7783-1.6892-1.55866.9632-0.04124.99180.22590.62-0.5824-0.3066-0.2541-0.01710.62670.00640.0282-0.14130.0241-0.0693-0.2069-0.0543-0.118426.5595-18.647617.144
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA49 - 7120 - 42
2X-RAY DIFFRACTION2AA80 - 16351 - 134
3X-RAY DIFFRACTION2AA164 - 184135 - 155
4X-RAY DIFFRACTION3AA185 - 227156 - 198

+
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