[English] 日本語
Yorodumi
- PDB-1gwn: The crystal structure of the core domain of RhoE/Rnd3 - a constit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1gwn
TitleThe crystal structure of the core domain of RhoE/Rnd3 - a constitutively activated small G protein
ComponentsRho-related GTP-binding protein RhoE
KeywordsGTPASE / INACTIVE GTPASE / SIGNAL TRANSDUCTION
Function / homology
Function and homology information


cortical cytoskeleton organization / establishment or maintenance of cell polarity / small GTPase-mediated signal transduction / cell projection / regulation of actin cytoskeleton organization / actin filament organization / cell migration / cell cortex / regulation of cell shape / cytoplasmic vesicle ...cortical cytoskeleton organization / establishment or maintenance of cell polarity / small GTPase-mediated signal transduction / cell projection / regulation of actin cytoskeleton organization / actin filament organization / cell migration / cell cortex / regulation of cell shape / cytoplasmic vesicle / actin cytoskeleton organization / vesicle / cytoskeleton / Golgi membrane / intracellular membrane-bounded organelle / GTPase activity / GTP binding / protein kinase binding / plasma membrane / cytoplasm
Similarity search - Function
Rho-related GTP-binding protein RhoE / Small GTPase Rho / small GTPase Rho family profile. / Small GTPase / Ras family / 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'-TRIPHOSPHATE / Rho-related GTP-binding protein RhoE
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGaravini, H. / Riento, K. / Phelan, J.P. / McAlister, M.S.B. / Ridley, A.J. / Keep, N.H.
CitationJournal: Biochemistry / Year: 2002
Title: Crystal Structure of the Core Domain of Rhoe/Rnd3: A Constitutively Activated Small G Protein
Authors: Garavini, H. / Riento, K. / Phelan, J.P. / McAlister, M.S.B. / Ridley, A.J. / Keep, N.H.
History
DepositionMar 19, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 5, 2002Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jun 20, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _audit_author.name / _citation.page_last ..._audit_author.name / _citation.page_last / _citation_author.name / _entity.pdbx_description / _entity_name_com.name / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_seq_type
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Rho-related GTP-binding protein RhoE
C: Rho-related GTP-binding protein RhoE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8206
Polymers45,7252
Non-polymers1,0954
Water3,549197
1
A: Rho-related GTP-binding protein RhoE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4103
Polymers22,8631
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: Rho-related GTP-binding protein RhoE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4103
Polymers22,8631
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)59.454, 59.454, 233.024
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.978372, -0.026484, 0.205153), (-0.01144, -0.999393, -0.027627), (0.20576, 0.022671, -0.978339)
Vector: -6.938, 113.0113, 72.5454)

-
Components

#1: Protein Rho-related GTP-binding protein RhoE / Rho family GTPase 3 / Rnd3


Mass: 22862.746 Da / Num. of mol.: 2 / Fragment: CORE DOMAIN, RESIDUES 16-200
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rnd3, Arhe, Rhoe / Plasmid: PET28A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61588
#2: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#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.: 197 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 1-15 AND 201 ONWARDS HAVE BEEN DELETED. THE N-TERMINUS INCLUDES AN UNCLEAVED HIS-TAG.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 44 %
Crystal growpH: 7.5 / Details: 0.1M HEPES PH 7.5, 10% PROPAN-2-OL, 20% PEG 4000
Crystal grow
*PLUS
Temperature: 16 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
130 mg/mlprotein1drop
20.1 MHEPES1reservoirpH7.5
310 %propanol-di-ol1reservoir
420 %(w/v)PEG40001reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.1→18.8 Å / Num. obs: 25276 / % possible obs: 99.8 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 6.4
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 2.2 / % possible all: 100
Reflection
*PLUS
Num. measured all: 115552
Reflection shell
*PLUS
% possible obs: 100 % / Num. unique obs: 3592 / Num. measured obs: 15240 / Mean I/σ(I) obs: 3.5

-
Processing

Software
NameVersionClassification
REFMAC5refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CXZ CHAIN A

1cxz


Resolution: 2.1→18.8 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.943 / SU B: 5.871 / SU ML: 0.158 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.198 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE ELECTRON DENSITY IN THE REGION OF RESIDUE 23 IS AMBIGUOUS AND THE CIS-CONFORMATION OF LYS23 MAY BE DUE TO THE POOR DEFINITION OF THE ENCLOSING DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.212 1260 4.9 %RANDOM
Rwork0.183 ---
obs0.185 24265 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Refinement stepCycle: LAST / Resolution: 2.1→18.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2780 0 66 197 3043
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0212933
X-RAY DIFFRACTIONr_bond_other_d0.0010.022536
X-RAY DIFFRACTIONr_angle_refined_deg
X-RAY DIFFRACTIONr_angle_other_deg1.9281.984013
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg0.90635941
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1370.2462
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023219
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02557
X-RAY DIFFRACTIONr_nbd_refined0.2410.3728
X-RAY DIFFRACTIONr_nbd_other0.2120.32622
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2240.5239
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.37703
X-RAY DIFFRACTIONr_metal_ion_refined0.06201
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.240.320
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1620.352
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2750.516
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9651.51799
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.79322935
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.91131134
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.6664.51078
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.254 81
Rwork0.218 1758
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)
11.2102-0.1609-0.19793.32541.04672.4926-0.1093-0.0587-0.01350.30190.07990.07360.1908-0.030.02940.1959-0.01550.0220.00630.02960.197734.57247.1451.517
21.3152-0.14460.15282.2910.40772.3641-0.0234-0.1628-0.0211-0.11480.0313-0.00770.0023-0.1093-0.00790.072-0.0028-0.00530.01990.03950.21146.70522.83930.348
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A22 - 200
2X-RAY DIFFRACTION2C23 - 200
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 22.3 Å / Rfactor obs: 0.183 / Rfactor Rfree: 0.212 / Rfactor Rwork: 0.183
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.021
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.92
LS refinement shell
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 2.15 Å / Rfactor obs: 0.218

+
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://pdbjlvh1.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