[English] 日本語
Yorodumi
- PDB-4mt6: Crystal structure of closed inactive collybistin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4mt6
TitleCrystal structure of closed inactive collybistin
ComponentsRho guanine nucleotide exchange factor 9
KeywordsPROTEIN BINDING / closed conformation
Function / homology
Function and homology information


CDC42 GTPase cycle / GABA receptor activation / regulation of postsynaptic specialization assembly / NRAGE signals death through JNK / G alpha (12/13) signalling events / RHOQ GTPase cycle / postsynaptic specialization / glycinergic synapse / receptor clustering / GABA-ergic synapse ...CDC42 GTPase cycle / GABA receptor activation / regulation of postsynaptic specialization assembly / NRAGE signals death through JNK / G alpha (12/13) signalling events / RHOQ GTPase cycle / postsynaptic specialization / glycinergic synapse / receptor clustering / GABA-ergic synapse / guanyl-nucleotide exchange factor activity / cell cortex / postsynaptic density / plasma membrane / cytosol
Similarity search - Function
Rho guanine nucleotide exchange factor 9, SH3 domain / Variant SH3 domain / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / PH domain / PH domain profile. / Pleckstrin homology domain. ...Rho guanine nucleotide exchange factor 9, SH3 domain / Variant SH3 domain / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily
Similarity search - Domain/homology
Rho guanine nucleotide exchange factor 9
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 5.501 Å
AuthorsSchneeberger, D. / Schindelin, H.
CitationJournal: Embo J. / Year: 2014
Title: A conformational switch in collybistin determines the differentiation of inhibitory postsynapses.
Authors: Soykan, T. / Schneeberger, D. / Tria, G. / Buechner, C. / Bader, N. / Svergun, D. / Tessmer, I. / Poulopoulos, A. / Papadopoulos, T. / Varoqueaux, F. / Schindelin, H. / Brose, N.
History
DepositionSep 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 guanine nucleotide exchange factor 9


Theoretical massNumber of molelcules
Total (without water)54,0781
Polymers54,0781
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)217.259, 217.259, 217.259
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213

-
Components

#1: Protein Rho guanine nucleotide exchange factor 9 / Collybistin / Rac/Cdc42 guanine nucleotide exchange factor 9


Mass: 54078.262 Da / Num. of mol.: 1 / Mutation: G33E, V34L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Arhgef9 / Plasmid: pTYB12 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9QX73

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 7.9 Å3/Da / Density % sol: 84.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20mM Na-cacodylate, 5mM Co(III)hexamine chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 23, 2012
RadiationMonochromator: horizontally diffracting Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 5.501→153.625 Å / Num. all: 5698 / Num. obs: 5698 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11 % / Biso Wilson estimate: 300.13 Å2 / Rsym value: 0.155 / Net I/σ(I): 10.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
5.5-5.811.20.0160.51.5691100
5.8-6.1511.20.0160.61.2431100
6.15-6.5711.20.0160.90.8381100
6.57-7.111.10.0161.50.5131100
7.1-7.7811.10.0162.90.2611100
7.78-8.7110.0165.90.1251100
8.7-10.04110.0167.40.091100
10.04-12.310.80.0166.10.1071100
12.3-17.3910.50.01611.20.0541100
17.39-108.6299.30.0165.50.055199.7

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.18 Å19.83 Å
Translation5.18 Å19.83 Å

-
Processing

Software
NameVersionClassificationNB
SCALA3.3.15data scaling
PHASER2.3.0phasing
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
DNAdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 5.501→108.629 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.91 / σ(F): 1.35 / Phase error: 38.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.282 268 4.71 %
Rwork0.2367 --
obs0.2389 5694 99.93 %
all-5694 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 177.0586 Å2
Refinement stepCycle: LAST / Resolution: 5.501→108.629 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3292 0 0 0 3292
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043372
X-RAY DIFFRACTIONf_angle_d0.6824536
X-RAY DIFFRACTIONf_dihedral_angle_d15.5311278
X-RAY DIFFRACTIONf_chiral_restr0.047462
X-RAY DIFFRACTIONf_plane_restr0.003589
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
5.5007-6.93010.3581370.31992674X-RAY DIFFRACTION100
6.9301-108.65060.26141310.21512752X-RAY DIFFRACTION100
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)
11.0237-0.0116-0.67081.06440.34360.5848-0.8403-0.4057-0.8757-0.09860.0332-0.08220.5749-0.11280.46511.6140.75230.74292.63570.28870.2029-22.4396-35.0715-6.6584
22.96490.1515-0.19812.66560.26832.6673-0.45240.4546-1.1471-1.12040.1639-0.3783-0.3838-0.8042-0.23490.38960.3592-0.17821.41530.4671.6232-42.6989-24.1394-9.78
35.423-0.508-0.5540.78531.25422.9333-1.0936-0.3532-2.0853-0.0270.49150.42271.3769-1.35640.54721.4607-0.28620.1181.7060.42181.4207-23.9646-59.07114.986
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resseq 18:72
2X-RAY DIFFRACTION2chain A and resseq 106:293
3X-RAY DIFFRACTION3chain A and resseq 294:439

+
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