[English] 日本語
Yorodumi
- PDB-8k70: Structural basis for the distinct roles of non-conserved Pro116 a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8k70
TitleStructural basis for the distinct roles of non-conserved Pro116 and conserved Tyr124 of BCH domain of yeast p50RhoGAP
ComponentsPutative Rho GTPase-activating protein C1565.02c
KeywordsLIPID BINDING PROTEIN / GTPase-activating protein / Rho / Scaffold
Function / homology
Function and homology information


: / phospholipid transfer activity / intermembrane phospholipid transfer / GTPase activator activity / Golgi apparatus / signal transduction
Similarity search - Function
Divergent CRAL/TRIO domain / CRAL-TRIO lipid binding domain / CRAL-TRIO lipid binding domain superfamily / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Rho GTPase activation protein
Similarity search - Domain/homology
Putative Rho GTPase-activating protein C1565.02c
Similarity search - Component
Biological speciesSchizosaccharomyces pombe 972h- (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å
AuthorsShankar, S. / Sivaraman, J.
Funding support Singapore, 2items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore)R154-000-C07-114 Singapore
Ministry of Education (MoE, Singapore)A-8000477-00-00 Singapore
CitationJournal: Cell.Mol.Life Sci. / Year: 2024
Title: Structural basis for the distinct roles of non-conserved Pro116 and conserved Tyr124 of BCH domain of yeast p50RhoGAP.
Authors: Shankar, S. / Chew, T.W. / Chichili, V.P.R. / Low, B.C. / Sivaraman, J.
History
DepositionJul 26, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 29, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative Rho GTPase-activating protein C1565.02c
B: Putative Rho GTPase-activating protein C1565.02c
C: Putative Rho GTPase-activating protein C1565.02c
D: Putative Rho GTPase-activating protein C1565.02c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,4088
Polymers71,6314
Non-polymers7774
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.110, 108.110, 250.803
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

-
Components

#1: Protein
Putative Rho GTPase-activating protein C1565.02c


Mass: 17907.658 Da / Num. of mol.: 4 / Mutation: P116A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe 972h- (yeast)
Strain: 972 / Gene: SPAC1565.02c
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9P3B1
#2: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.88 Å3/Da / Density % sol: 79.08 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Bis-Tris propane pH 7.0 and 2.1 M NaCl

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.8→49.64 Å / Num. obs: 37961 / % possible obs: 93.83 % / Redundancy: 5 % / Biso Wilson estimate: 79.17 Å2 / Rsym value: 0.14 / Net I/σ(I): 19.7
Reflection shellResolution: 2.8→2.87 Å / Rmerge(I) obs: 0.23 / Num. unique obs: 2084

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
PDB_EXTRACTdata extraction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.81→46.81 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.45 / Phase error: 30.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2395 1994 5.25 %
Rwork0.211 --
obs0.2125 37945 93.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.81→46.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4999 0 0 0 4999
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01
X-RAY DIFFRACTIONf_angle_d1.212
X-RAY DIFFRACTIONf_dihedral_angle_d8.195695
X-RAY DIFFRACTIONf_chiral_restr0.062766
X-RAY DIFFRACTIONf_plane_restr0.009844
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.81-2.880.40011110.36032015X-RAY DIFFRACTION74
2.88-2.950.36821380.35592304X-RAY DIFFRACTION85
2.95-3.040.3591290.34332416X-RAY DIFFRACTION88
3.04-3.140.36141350.32542465X-RAY DIFFRACTION90
3.14-3.250.3161420.29242560X-RAY DIFFRACTION93
3.25-3.380.28431450.2732539X-RAY DIFFRACTION93
3.38-3.530.29141400.24772609X-RAY DIFFRACTION95
3.54-3.720.28361500.23882686X-RAY DIFFRACTION98
3.72-3.950.27721490.20062694X-RAY DIFFRACTION99
3.95-4.260.23571470.18552705X-RAY DIFFRACTION99
4.26-4.690.20391500.17922740X-RAY DIFFRACTION99
4.69-5.360.20641540.18122716X-RAY DIFFRACTION100
5.37-6.760.26391510.22632754X-RAY DIFFRACTION100
6.76-46.810.16241530.15692748X-RAY DIFFRACTION100

+
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