[English] 日本語
Yorodumi
- PDB-3iug: Crystal structure of the RhoGAP domain of RICS -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3iug
TitleCrystal structure of the RhoGAP domain of RICS
ComponentsRho/Cdc42/Rac GTPase-activating protein RICS
KeywordsSPLICING / Structural Genomics Consortium (SGC) / GAP / Alternative splicing / Cell junction / Cell membrane / Cell projection / Cytoplasm / Endoplasmic reticulum / Endosome / Golgi apparatus / GTPase activation / Membrane / Phosphoprotein / Postsynaptic cell membrane / SH3 domain / Synapse
Function / homology
Function and homology information


: / phosphatidylinositol phosphate binding / regulation of small GTPase mediated signal transduction / small GTPase-mediated signal transduction / GTPase activator activity / fibrillar center / actin cytoskeleton / cell cortex / dendritic spine / postsynaptic density ...: / phosphatidylinositol phosphate binding / regulation of small GTPase mediated signal transduction / small GTPase-mediated signal transduction / GTPase activator activity / fibrillar center / actin cytoskeleton / cell cortex / dendritic spine / postsynaptic density / endosome membrane / Golgi membrane / endoplasmic reticulum membrane / Golgi apparatus / nucleoplasm / cytosol
Similarity search - Function
Rho GTPase-activating protein 32, PX domain / Phosphatidylinositol 3-kinase; Chain A / Rho GTPase activation protein / PX domain superfamily / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Variant SH3 domain / Rho GTPase activation protein ...Rho GTPase-activating protein 32, PX domain / Phosphatidylinositol 3-kinase; Chain A / Rho GTPase activation protein / PX domain superfamily / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Variant SH3 domain / Rho GTPase activation protein / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Rho GTPase-activating protein 32
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.77 Å
AuthorsNedyalkova, L. / Tempel, W. / Tong, Y. / Li, Y. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Crystal structure of the RhoGAP domain of RICS
Authors: Nedyalkova, L. / Tempel, W. / Tong, Y. / Li, Y. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H.
History
DepositionAug 31, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Rho/Cdc42/Rac GTPase-activating protein RICS
B: Rho/Cdc42/Rac GTPase-activating protein RICS


Theoretical massNumber of molelcules
Total (without water)52,60013
Polymers52,6002
Non-polymers011
Water5,549308
1
A: Rho/Cdc42/Rac GTPase-activating protein RICS


Theoretical massNumber of molelcules
Total (without water)26,3003
Polymers26,3001
Non-polymers02
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Rho/Cdc42/Rac GTPase-activating protein RICS


Theoretical massNumber of molelcules
Total (without water)26,30010
Polymers26,3001
Non-polymers09
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.264, 117.369, 37.717
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
DetailsThe biological unit was not determined.

-
Components

#1: Protein Rho/Cdc42/Rac GTPase-activating protein RICS / p200RhoGAP / p250GAP / RhoGAP involved in the beta-catenin-N-cadherin and NMDA receptor signaling / ...p200RhoGAP / p250GAP / RhoGAP involved in the beta-catenin-N-cadherin and NMDA receptor signaling / Brain-specific Rho GTPase-activating protein / GAB-associated Cdc42/Rac GTPase-activating protein / GC-GAP / GTPase regulator interacting with TrkA


Mass: 26300.014 Da / Num. of mol.: 2 / Fragment: Rho-GAP domain: UNP residues 367-577
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GI:134105571, GRIT, KIAA0712, RICS / Plasmid: pET28-mhl / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2 / References: UniProt: A7KAX9
#2: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 11 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 308 / 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: 2.15 Å3/Da / Density % sol: 42.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30% PEG 5000 MME, 0.2M Ammonium sulfate, 0.1M MES, 1:100 w/w subtilisin, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jun 15, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. obs: 45281 / % possible obs: 99.7 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.064 / Χ2: 1.463 / Net I/σ(I): 11
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.77-1.836.60.70243591.18197.9
1.83-1.916.90.55444881.33100
1.91-1.9970.38344791.476100
1.99-2.17.10.23644831.592100
2.1-2.237.20.17744791.534100
2.23-2.47.20.12544861.602100
2.4-2.647.30.08545251.476100
2.64-3.037.30.05845561.47100
3.03-3.817.30.03746191.469100
3.81-5070.03248071.46599.6

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.5.0102refinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2OSA

2osa


Resolution: 1.77→20 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.922 / WRfactor Rfree: 0.237 / WRfactor Rwork: 0.19 / SU B: 2.22 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. U VALUES: REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1027 2.273 %Thin shells (sftools)
Rwork0.199 ---
obs0.2 45184 99.912 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 18.231 Å2
Baniso -1Baniso -2Baniso -3
1-0.734 Å20 Å20 Å2
2---1.457 Å20 Å2
3---0.723 Å2
Refinement stepCycle: LAST / Resolution: 1.77→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2995 0 11 309 3315
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223079
X-RAY DIFFRACTIONr_bond_other_d0.0010.022028
X-RAY DIFFRACTIONr_angle_refined_deg1.5631.9654216
X-RAY DIFFRACTIONr_angle_other_deg1.00434972
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1875396
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.35723.819144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.66715504
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1791518
X-RAY DIFFRACTIONr_chiral_restr0.0950.2490
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213443
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02633
X-RAY DIFFRACTIONr_mcbond_it1.0481.51893
X-RAY DIFFRACTIONr_mcbond_other0.2871.5751
X-RAY DIFFRACTIONr_mcangle_it1.83823081
X-RAY DIFFRACTIONr_scbond_it2.731186
X-RAY DIFFRACTIONr_scangle_it4.34.51120
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.77-1.8160.311700.3623183328599.026
1.816-1.8650.351630.331043167100
1.865-1.9190.28560.24530483104100
1.919-1.9770.267560.21429723028100
1.977-2.0410.2461100.19127832893100
2.041-2.1120.225530.17628022855100
2.112-2.1910.192330.18227372770100
2.191-2.2790.236520.17625702622100
2.279-2.3790.242930.17424622555100
2.379-2.4930.246290.16424232452100
2.493-2.6260.189710.1732236230899.957
2.626-2.7820.239390.17521682207100
2.782-2.970.228560.1882030208799.952
2.97-3.2020.224690.2041884195499.949
3.202-3.4990.183330.2141774181099.834
3.499-3.8970.274310.20216171648100
3.897-4.4720.215480.1631423147299.932
4.472-5.410.323370.1841262130099.923
5.41-7.3850.387170.25110101027100
7.385-200.266110.261669680100

+
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