[English] 日本語
Yorodumi
- PDB-3fk2: Crystal structure of the RhoGAP domain of human glucocorticoid re... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3fk2
TitleCrystal structure of the RhoGAP domain of human glucocorticoid receptor DNA-binding factor 1
ComponentsGlucocorticoid receptor DNA-binding factor 1
KeywordsSIGNALING PROTEIN / HYDROLASE ACTIVATOR / Structural Genomics Consortium / GTPase-activating protein / SGC / Alternative splicing / Anti-oncogene / Cell cycle / Cytoplasm / DNA-binding / GTPase activation / Nucleus / Phosphoprotein / Repressor / Transcription / Transcription regulation
Function / homology
Function and homology information


neuron projection guidance / central nervous system neuron axonogenesis / establishment or maintenance of actin cytoskeleton polarity / regulation of actin polymerization or depolymerization / : / positive regulation of cilium assembly / mammary gland development / camera-type eye development / RHOD GTPase cycle / negative regulation of vascular permeability ...neuron projection guidance / central nervous system neuron axonogenesis / establishment or maintenance of actin cytoskeleton polarity / regulation of actin polymerization or depolymerization / : / positive regulation of cilium assembly / mammary gland development / camera-type eye development / RHOD GTPase cycle / negative regulation of vascular permeability / axonal fasciculation / GTPase activating protein binding / regulation of small GTPase mediated signal transduction / Sema4D mediated inhibition of cell attachment and migration / RND1 GTPase cycle / wound healing, spreading of cells / RND2 GTPase cycle / RND3 GTPase cycle / negative regulation of Rho protein signal transduction / regulation of cell size / RHOB GTPase cycle / regulation of axonogenesis / RHOJ GTPase cycle / RHOC GTPase cycle / RHOQ GTPase cycle / CDC42 GTPase cycle / Rho protein signal transduction / RHOG GTPase cycle / RHOA GTPase cycle / RAC3 GTPase cycle / RAC2 GTPase cycle / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / forebrain development / RAC1 GTPase cycle / GTPase activator activity / ciliary basal body / neural tube closure / axon guidance / regulation of actin cytoskeleton organization / phospholipid binding / positive regulation of neuron projection development / cell migration / actin cytoskeleton / regulation of cell shape / GTPase activity / protein-containing complex binding / GTP binding / DNA binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Rho GTPase-activating protein, pG1 and pG2 domain / p190RhoGAP, pG1 and pG2 domains / Rho GTPase-activating protein, FF domain / Rho GTPase-activating protein, pG2 domain / Rho GTPase-activating protein, pG1 domain / p190-A and -B Rho GAPs FF domain / pG1 pseudoGTPase domain profile. / pG2 pseudoGTPase domain profile. / Phosphatidylinositol 3-kinase; Chain A / Rho GTPase activation protein ...Rho GTPase-activating protein, pG1 and pG2 domain / p190RhoGAP, pG1 and pG2 domains / Rho GTPase-activating protein, FF domain / Rho GTPase-activating protein, pG2 domain / Rho GTPase-activating protein, pG1 domain / p190-A and -B Rho GAPs FF domain / pG1 pseudoGTPase domain profile. / pG2 pseudoGTPase domain profile. / Phosphatidylinositol 3-kinase; Chain A / Rho GTPase activation protein / FF domain / FF domain superfamily / FF domain profile. / Contains two conserved F residues / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Rho GTPase activation protein / Small GTPase / Ras family / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Rho GTPase-activating protein 35
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsNedyalkova, L. / Tong, Y. / Tempel, W. / Loppnau, P. / 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 human glucocorticoid receptor DNA-binding factor 1
Authors: Nedyalkova, L. / Tong, Y. / Tempel, W. / Loppnau, P. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H.
History
DepositionDec 15, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: 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 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glucocorticoid receptor DNA-binding factor 1
B: Glucocorticoid receptor DNA-binding factor 1
C: Glucocorticoid receptor DNA-binding factor 1
D: Glucocorticoid receptor DNA-binding factor 1


Theoretical massNumber of molelcules
Total (without water)115,52012
Polymers115,5204
Non-polymers08
Water0
1
A: Glucocorticoid receptor DNA-binding factor 1


Theoretical massNumber of molelcules
Total (without water)28,8803
Polymers28,8801
Non-polymers02
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glucocorticoid receptor DNA-binding factor 1


Theoretical massNumber of molelcules
Total (without water)28,8803
Polymers28,8801
Non-polymers02
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Glucocorticoid receptor DNA-binding factor 1


Theoretical massNumber of molelcules
Total (without water)28,8803
Polymers28,8801
Non-polymers02
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Glucocorticoid receptor DNA-binding factor 1


Theoretical massNumber of molelcules
Total (without water)28,8803
Polymers28,8801
Non-polymers02
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)165.025, 72.408, 72.863
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
12
22
13
23

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain C and (resseq 1244:1437 )
211chain D and (resseq 1244:1437 )
311chain A and (resseq 1244:1437 )
112chain A and (resseq 1244:1407 )
212chain B and (resseq 1244:1407 )
113chain A and (resseq 1418:1437 )
213chain B and (resseq 1418:1437 )

NCS ensembles :
ID
1
2
3

-
Components

#1: Protein
Glucocorticoid receptor DNA-binding factor 1 / Glucocorticoid receptor repression factor 1 / GRF-1 / Rho GAP p190A / p190-A


Mass: 28880.037 Da / Num. of mol.: 4 / Fragment: UNP residues 1212-1439
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: The authors suspect that the sample was truncated by in-situ proteolysis.
Gene: GRLF1, GRF1, KIAA1722 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R-pRARE2 / References: UniProt: Q9NRY4
#2: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 8 / Source method: obtained synthetically

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 26% PEG 3350, 0.1M Bis-Tris, 0.2M lithium sulfate, 0.001M DTT, 1:100 (w/w) trypsin, pH 6.0, vapor diffusion, sitting drop, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97883 Å
DetectorType: ADSC Q315 / Detector: CCD / Date: Nov 28, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97883 Å / Relative weight: 1
ReflectionResolution: 2.8→40 Å / Num. obs: 21961 / % possible obs: 98.1 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.157 / Χ2: 1.255 / Net I/σ(I): 5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.8-2.93.50.59819551.1289
2.9-3.024.10.51420981.13295.2
3.02-3.154.70.4421421.12698.6
3.15-3.325.20.36822111.24499.6
3.32-3.535.50.28421881.50899.8
3.53-3.85.70.21222441.227100
3.8-4.185.70.15422141.402100
4.18-4.795.70.12422501.44299.9
4.79-6.035.50.1322751.1599.7
6.03-405.40.05723841.06899

-
Phasing

PhasingMethod: molecular replacement

-
Processing

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

2osa


Resolution: 2.8→36.431 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1878 4.7 %Thin shells (SFTOOLS)
Rwork0.223 ---
obs0.226 21824 96.15 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.711 Å2
Baniso -1Baniso -2Baniso -3
1-5.775 Å2-0 Å2-0 Å2
2---0.526 Å20 Å2
3----6.284 Å2
Refinement stepCycle: LAST / Resolution: 2.8→36.431 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6157 0 8 0 6165
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066315
X-RAY DIFFRACTIONf_angle_d1.0058597
X-RAY DIFFRACTIONf_chiral_restr0.074973
X-RAY DIFFRACTIONf_plane_restr0.0031111
X-RAY DIFFRACTIONf_dihedral_angle_d18.8712230
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11C1504X-RAY DIFFRACTIONPOSITIONAL
12D1504X-RAY DIFFRACTIONPOSITIONAL0.03
13A1515X-RAY DIFFRACTIONPOSITIONAL0.033
21A1297X-RAY DIFFRACTIONPOSITIONAL
22B1297X-RAY DIFFRACTIONPOSITIONAL0.035
31A175X-RAY DIFFRACTIONPOSITIONAL
32B175X-RAY DIFFRACTIONPOSITIONAL0.038
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.87580.30752499X-RAY DIFFRACTION79
2.8758-2.96040.38212520.31172528X-RAY DIFFRACTION87
2.9604-3.05590.28053024X-RAY DIFFRACTION94
3.0559-3.16510.35412520.27992874X-RAY DIFFRACTION97
3.1651-3.29170.29971810.23472984X-RAY DIFFRACTION99
3.2917-3.44140.3097650.2223073X-RAY DIFFRACTION99
3.4414-3.62270.2511780.21442986X-RAY DIFFRACTION99
3.6227-3.84950.22112020.19592959X-RAY DIFFRACTION100
3.8495-4.14630.26521380.16713026X-RAY DIFFRACTION99
4.1463-4.56280.18091300.16413052X-RAY DIFFRACTION99
4.5628-5.22140.22291950.16122988X-RAY DIFFRACTION100
5.2214-6.57210.26981330.22753049X-RAY DIFFRACTION100
6.5721-36.43460.27371520.22563011X-RAY DIFFRACTION99

+
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