[English] 日本語
Yorodumi
- PDB-2row: The C1 domain of ROCK II -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2row
TitleThe C1 domain of ROCK II
ComponentsRho-associated protein kinase 2
KeywordsTRANSFERASE / protein / ATP-binding / Coiled coil / Cytoplasm / Kinase / Membrane / Metal-binding / Nucleotide-binding / Phorbol-ester binding / Phosphoprotein / Serine/threonine-protein kinase / Zinc / Zinc-finger
Function / homology
Function and homology information


RHOBTB1 GTPase cycle / RHO GTPases Activate ROCKs / Sema4D induced cell migration and growth-cone collapse / VEGFA-VEGFR2 Pathway / RHOB GTPase cycle / negative regulation of protein localization to lysosome / RHOC GTPase cycle / cellular response to acetylcholine / regulation of cellular response to hypoxia / RHOH GTPase cycle ...RHOBTB1 GTPase cycle / RHO GTPases Activate ROCKs / Sema4D induced cell migration and growth-cone collapse / VEGFA-VEGFR2 Pathway / RHOB GTPase cycle / negative regulation of protein localization to lysosome / RHOC GTPase cycle / cellular response to acetylcholine / regulation of cellular response to hypoxia / RHOH GTPase cycle / G alpha (12/13) signalling events / positive regulation of amyloid precursor protein catabolic process / positive regulation of connective tissue growth factor production / positive regulation of centrosome duplication / RHOA GTPase cycle / regulation of angiotensin-activated signaling pathway / Rho-dependent protein serine/threonine kinase activity / regulation of keratinocyte differentiation / positive regulation of connective tissue replacement / postsynaptic actin cytoskeleton organization / positive regulation of fibroblast growth factor production / regulation of nervous system process / negative regulation of bicellular tight junction assembly / negative regulation of myosin-light-chain-phosphatase activity / regulation of cell junction assembly / response to transforming growth factor beta / negative regulation of nitric oxide biosynthetic process / positive regulation of protein localization to early endosome / response to angiotensin / embryonic morphogenesis / EPHB-mediated forward signaling / cellular response to testosterone stimulus / regulation of protein metabolic process / actomyosin structure organization / spindle pole centrosome / regulation of establishment of endothelial barrier / positive regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process / dendrite morphogenesis / chromosome condensation / smooth muscle contraction / cortical actin cytoskeleton organization / mRNA destabilization / positive regulation of cardiac muscle hypertrophy / Rho protein signal transduction / positive regulation of amyloid-beta formation / blood vessel diameter maintenance / mitotic cytokinesis / centrosome duplication / extrinsic apoptotic signaling pathway via death domain receptors / epithelial to mesenchymal transition / positive regulation of stress fiber assembly / response to ischemia / negative regulation of angiogenesis / I-kappaB kinase/NF-kappaB signaling / Schaffer collateral - CA1 synapse / positive regulation of endothelial cell migration / protein localization to plasma membrane / neural tube closure / cytoplasmic ribonucleoprotein granule / regulation of circadian rhythm / small GTPase binding / actin cytoskeleton organization / rhythmic process / kinase activity / peptidyl-threonine phosphorylation / positive regulation of MAPK cascade / cytoskeleton / non-specific serine/threonine protein kinase / peptidyl-serine phosphorylation / positive regulation of cell migration / protein kinase activity / viral RNA genome replication / positive regulation of protein phosphorylation / centrosome / glutamatergic synapse / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of gene expression / protein phosphorylation / ATP binding / metal ion binding / plasma membrane / nucleus / cytoplasm
Similarity search - Function
Rho-associated protein kinase 2, HR1 domain / Rho Binding / ROCK, Rho binding domain / Rho-binding (RhoBD) domain profile. / Rho-associated protein kinase 1/2 / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #20 / HR1 rho-binding domain / REM-1 domain profile. / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) ...Rho-associated protein kinase 2, HR1 domain / Rho Binding / ROCK, Rho binding domain / Rho-binding (RhoBD) domain profile. / Rho-associated protein kinase 1/2 / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #20 / HR1 rho-binding domain / REM-1 domain profile. / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / C1-like domain superfamily / Extension to Ser/Thr-type protein kinases / AGC-kinase C-terminal domain profile. / AGC-kinase, C-terminal / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Rho-associated protein kinase 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / simulated annealing
AuthorsWen, W. / Zhang, M.
CitationJournal: To be Published
Title: The C1 domain of ROCK II
Authors: Wen, W. / Liu, W. / Yan, J. / Zhang, M.
History
DepositionApr 25, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jun 24, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / 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: Rho-associated protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,1373
Polymers10,0061
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Rho-associated protein kinase 2 / Rho-associated / coiled-coil-containing protein kinase 2 / p164 ROCK-2 / RhoA-binding kinase 2 / ...Rho-associated / coiled-coil-containing protein kinase 2 / p164 ROCK-2 / RhoA-binding kinase 2 / p150 ROK-alpha / ROKalpha


Mass: 10005.706 Da / Num. of mol.: 1 / Fragment: C1 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Rock2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q62868, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1223D 1H-13C NOESY
1333D CBCA(CO)NH
1433D HN(CA)CB

-
Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 15N] protein, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-100% 13C] protein, 100% D2O100% D2O
31 mM [U-100% 13C; U-100% 15N] protein, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMprotein[U-100% 15N]1
1 mMprotein[U-100% 13C]2
1 mMprotein[U-100% 13C; U-100% 15N]3
Sample conditionsIonic strength: 0.5 / pH: 5.5 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 750 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
CNS1.1refinement
CYANAGuntert, Mumenthaler and Wuthrichprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1

+
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