[English] 日本語
Yorodumi
- PDB-2kap: Solution structure of DLC1-SAM -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2kap
TitleSolution structure of DLC1-SAM
ComponentsRho GTPase-activating protein 7
KeywordsSIGNALING PROTEIN / Solution Structure / SAM domain / DLC-1 / Cytoplasm / GTPase activation / Phosphoprotein / Polymorphism
Function / homology
Function and homology information


hindbrain morphogenesis / negative regulation of focal adhesion assembly / regulation of Rho protein signal transduction / focal adhesion assembly / regulation of small GTPase mediated signal transduction / negative regulation of stress fiber assembly / negative regulation of Rho protein signal transduction / cortical actin cytoskeleton / RHOB GTPase cycle / RHOC GTPase cycle ...hindbrain morphogenesis / negative regulation of focal adhesion assembly / regulation of Rho protein signal transduction / focal adhesion assembly / regulation of small GTPase mediated signal transduction / negative regulation of stress fiber assembly / negative regulation of Rho protein signal transduction / cortical actin cytoskeleton / RHOB GTPase cycle / RHOC GTPase cycle / RHOQ GTPase cycle / positive regulation of execution phase of apoptosis / CDC42 GTPase cycle / RHOA GTPase cycle / heart morphogenesis / positive regulation of protein dephosphorylation / forebrain development / RAC1 GTPase cycle / SH2 domain binding / negative regulation of cell migration / GTPase activator activity / neural tube closure / caveola / regulation of actin cytoskeleton organization / ruffle membrane / activation of cysteine-type endopeptidase activity involved in apoptotic process / regulation of cell shape / actin cytoskeleton organization / membrane raft / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / focal adhesion / lipid binding / apoptotic process / endoplasmic reticulum / signal transduction / nucleus / cytoplasm / cytosol
Similarity search - Function
Helix Hairpins - #2070 / in StAR and phosphatidylcholine transfer protein / START domain / START domain / START domain profile. / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Rho GTPase activation protein ...Helix Hairpins - #2070 / in StAR and phosphatidylcholine transfer protein / START domain / START domain / START domain profile. / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Rho GTPase activation protein / START-like domain superfamily / SAM domain (Sterile alpha motif) / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Rho GTPase-activating protein 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsYang, S. / Yang, D.
CitationJournal: Biochemistry / Year: 2009
Title: Characterization of DLC1-SAM equilibrium unfolding at the amino acid residue level
Authors: Yang, S. / Noble, C.G. / Yang, D.
History
DepositionNov 12, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Rho GTPase-activating protein 7


Theoretical massNumber of molelcules
Total (without water)7,1021
Polymers7,1021
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Rho GTPase-activating protein 7 / Rho-type GTPase-activating protein 7 / Deleted in liver cancer 1 protein / Dlc-1 / StAR-related ...Rho-type GTPase-activating protein 7 / Deleted in liver cancer 1 protein / Dlc-1 / StAR-related lipid transfer protein 12 / START domain-containing protein 12 / StARD12 / HP protein


Mass: 7102.202 Da / Num. of mol.: 1
Fragment: sterile alpha motif (SAM) domain, UNP residues 17-76
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DLC1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q96QB1

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1111D 1H SPECTRUM
1222D 1H-15N HSQC
1332D 1H-13C HSQC
1442D DQF-COSY
1542D 1H-1H NOESY
1642D 1H-1H TOCSY
1733D CBCA(CO)NH
1833D HN(CA)CB
1933D (H)CCH-TOCSY
11023D 1H-15N NOESY
11123D 1H-15N TOCSY
11253D 1H-13C NOESY
11333D H(CCO)NH
11433D CC(CO)NH

-
Sample preparation

Details
Solution-IDContentsSolvent system
11mM DLC1-SAM, 50mM sodium phosphate, 3mM DTT, 5% [U-100% 2H] D2O, 95% H2O/5% D2O95% H2O/5% D2O
21mM [U-100% 15N] DLC1-SAM, 50mM sodium phosphate, 3mM DTT, 5% [U-100% 2H] D2O, 95% H2O/5% D2O95% H2O/5% D2O
31mM [U-100% 13C; U-100% 15N] DLC1-SAM, 50mM sodium phosphate, 3mM DTT, 5% [U-100% 2H] D2O, 95% H2O/5% D2O95% H2O/5% D2O
41mM DLC1-SAM, 50mM sodium phosphate, 3mM DTT, 100 % D2O, 100% D2O100% D2O
51mM [U-100% 13C; U-100% 15N] DLC1-SAM, 50mM sodium phosphate, 3mM DTT, 100% D2O, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMDLC1-SAM1
50 mMsodium phosphate1
3 mMDTT1
5 %D2O[U-100% 2H]1
1 mMDLC1-SAM[U-100% 15N]2
50 mMsodium phosphate2
3 mMDTT2
5 %D2O[U-100% 2H]2
1 mMDLC1-SAM[U-100% 13C; U-100% 15N]3
50 mMsodium phosphate3
3 mMDTT3
5 %D2O[U-100% 2H]3
1 mMDLC1-SAM4
50 mMsodium phosphate4
3 mMDTT4
100 %D2O4
1 mMDLC1-SAM[U-100% 13C; U-100% 15N]5
50 mMsodium phosphate5
3 mMDTT5
100 %D2O5
Sample conditionspH: 6.8 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz

-
Processing

NMR software
NameDeveloperClassification
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmgeometry optimization
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
MOLMOLKoradi, Billeter and Wuthrichgraphic display
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificchemical shift calculation
NMRViewJohnson, One Moon Scientificdata analysis
NMRViewJohnson, One Moon Scientificpeak picking
ProcheckNMRLaskowski and MacArthurstructure validation
TALOSCornilescu, Delaglio and Baxrefinement
XwinNMRBruker Biospincollection
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10 / 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://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