[English] 日本語
Yorodumi
- PDB-1htj: STRUCTURE OF THE RGS-LIKE DOMAIN FROM PDZ-RHOGEF -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1htj
TitleSTRUCTURE OF THE RGS-LIKE DOMAIN FROM PDZ-RHOGEF
ComponentsKIAA0380
KeywordsSIGNALING PROTEIN / RGS-like / Regulator of G protein signaling / GEF / Guanine nucleotide exchange factor
Function / homology
Function and homology information


Sema4D induced cell migration and growth-cone collapse / regulation of small GTPase mediated signal transduction / RHOB GTPase cycle / NRAGE signals death through JNK / RHOC GTPase cycle / Rho protein signal transduction / RHOA GTPase cycle / striated muscle contraction / CDC42 GTPase cycle / establishment of cell polarity ...Sema4D induced cell migration and growth-cone collapse / regulation of small GTPase mediated signal transduction / RHOB GTPase cycle / NRAGE signals death through JNK / RHOC GTPase cycle / Rho protein signal transduction / RHOA GTPase cycle / striated muscle contraction / CDC42 GTPase cycle / establishment of cell polarity / RAC1 GTPase cycle / GTPase activator activity / guanyl-nucleotide exchange factor activity / G alpha (12/13) signalling events / regulation of cell growth / G protein-coupled receptor binding / actin cytoskeleton organization / G protein-coupled receptor signaling pathway / positive regulation of DNA-templated transcription / nucleoplasm / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Rho guanine nucleotide exchange factor 11 / Rho guanine nucleotide exchange factor 11, PH domain / Rho guanine nucleotide exchange factor 11, RGS domain / Regulator of G protein signalling-like domain / Regulator of G protein signalling-like domain / ARHGEF1-like, PH domain / PH domain / Regulator of G-protein Signalling 4, domain 2 / Regulator of G-protein Signalling 4; domain 2 / RGS, subdomain 2 ...Rho guanine nucleotide exchange factor 11 / Rho guanine nucleotide exchange factor 11, PH domain / Rho guanine nucleotide exchange factor 11, RGS domain / Regulator of G protein signalling-like domain / Regulator of G protein signalling-like domain / ARHGEF1-like, PH domain / PH domain / Regulator of G-protein Signalling 4, domain 2 / Regulator of G-protein Signalling 4; domain 2 / RGS, subdomain 2 / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS domain superfamily / 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 profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / PH-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Rho guanine nucleotide exchange factor 11
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsLongenecker, K.L. / Lewis, M.E. / Chikumi, H. / Gutkind, J.S. / Derewenda, Z.S.
CitationJournal: Structure / Year: 2001
Title: Structure of the RGS-like domain from PDZ-RhoGEF: linking heterotrimeric g protein-coupled signaling to Rho GTPases.
Authors: Longenecker, K.L. / Lewis, M.E. / Chikumi, H. / Gutkind, J.S. / Derewenda, Z.S.
History
DepositionDec 29, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
F: KIAA0380


Theoretical massNumber of molelcules
Total (without water)23,9011
Polymers23,9011
Non-polymers00
Water1,51384
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.61, 61.61, 201.91
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
DetailsThe assymetric unit contains a protein fragment that is a single domain isolated from a multi-domain protein, and is not known to organize into multimers.

-
Components

#1: Protein KIAA0380


Mass: 23901.242 Da / Num. of mol.: 1 / Fragment: RGS-LIKE DOMAIN (RESIDUES 281-490) / Mutation: K463A, E465A, E466A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIAA0380 / Plasmid details: BASED ON PET22B / Plasmid: PHIS-PARALLEL / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: O15085
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.3 Å3/Da / Density % sol: 46.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: Ammonium Sulfate, PEG 400, Tris-HCl, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112 mg/mlprotein1drop
220 mMTris-HCl1drop
35 mMdithiothreitol1drop
440-42 %satammonium sulfate1reservoir
52 %PEG4001reservoir
6100 mMTris-HCl1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.9717 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 1, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9717 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 12161 / Num. obs: 12161 / % possible obs: 98.7 % / Redundancy: 4.8 % / Biso Wilson estimate: 38 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 12.1
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 4.4 / Num. unique all: 1160 / % possible all: 98.6
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 57934
Reflection shell
*PLUS
% possible obs: 99 %

-
Processing

Software
NameVersionClassification
SOLVEphasing
MLPHAREphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.258 799 6.5 %RANDOM
Rwork0.223 ---
obs0.226 11167 91 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--10.212 Å2-8.331 Å20 Å2
2---10.212 Å20 Å2
3---20.423 Å2
Refine analyze
ObsFree
Luzzati d res low5 Å-
Luzzati sigma a0.35 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1445 0 0 84 1529
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0078
X-RAY DIFFRACTIONc_angle_deg1.257
X-RAY DIFFRACTIONc_dihedral_angle_d19.34
X-RAY DIFFRACTIONc_improper_angle_d0.7427
LS refinement shellResolution: 2.2→2.28 Å
RfactorNum. reflection% reflection
Rfree0.381 69 -
Rwork0.36 820 -
obs-889 76 %
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 6.5 % / Rfactor all: 0.226 / Rfactor obs: 0.223
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.34
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.7427
LS refinement shell
*PLUS
Rfactor Rfree: 0.381 / Rfactor Rwork: 0.36

+
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