[English] 日本語
Yorodumi
- PDB-2jm3: Solution structure of the THAP domain from C. elegans C-terminal ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2jm3
TitleSolution structure of the THAP domain from C. elegans C-terminal binding protein (CtBP)
ComponentsHypothetical protein
KeywordsMETAL BINDING PROTEIN / protein / zinc finger
Function / homology
Function and homology information


Repression of WNT target genes / Deactivation of the beta-catenin transactivating complex / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / transcription corepressor activity / NAD binding / DNA binding / nucleus / metal ion binding
Similarity search - Function
THAP / THAP-type zinc finger superfamily / THAP-type zinc finger / THAP domain / Zinc finger THAP-type profile / C-terminal binding protein / D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain ...THAP / THAP-type zinc finger superfamily / THAP-type zinc finger / THAP domain / Zinc finger THAP-type profile / C-terminal binding protein / D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
C-terminal-binding protein 1
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsLiew, C.K. / Crossley, M. / Mackay, J.P. / Nicholas, H.R.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Solution structure of the THAP domain from Caenorhabditis elegans C-terminal binding protein (CtBP).
Authors: Liew, C.K. / Crossley, M. / Mackay, J.P. / Nicholas, H.R.
History
DepositionSep 21, 2006Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / 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 / _pdbx_nmr_software.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5932
Polymers10,5271
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 500lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Hypothetical protein


Mass: 10527.181 Da / Num. of mol.: 1
Fragment: C-terminal binding protein THAP domain, residues 1-89
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: F49E10.5 / Plasmid: pGEX-2T / Production host: Escherichia coli (E. coli) / References: UniProt: Q20595
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1133D HNCO
1233D HNCA
1333D HN(CA)CB
1433D HN(CO)CA
1533D CBCA(CO)NH
2643D (H)CCH-TOCSY
2743D (H)CCH-COSY
1823D 1H-15N NOESY
2943D 1H-13C NOESY
11012D NOESY
1113C(CO)NH-TOCSY
1123H(CCO)NH-TOCSY
11323D HNHA
11433D HN(CA)CO
NMR detailsText: The structure was determined using a combination of NOE and coupling constant data.

-
Sample preparation

Details
Solution-IDContentsSolvent system
11 mM CtBP THAP domain, 20 mM sodium phosphate, 100 mM sodium chloride, 1 mM DTT, 0.1 mM DSS, 93% H2O, 7% D2O93% H2O/7% D2O
20.45 mM [U-99% 15N] CtBP THAP domain, 20 mM sodium phosphate, 100 mM sodium chloride, 1 mM DTT, 0.1 mM DSS, 93% H2O, 7% D2O93% H2O/7% D2O
30.6 mM [U-98% 13C, U-98% 15N] CtBP THAP domain, 20 mM sodium phosphate, 100 mM sodium chloride, 1 mM DTT, 0.1 mM DSS, 93% H2O, 7% D2O93% H2O/7% D2O
40.6 mM [U-98% 13C, U-98% 15N] CtBP THAP domain, 20 mM sodium phosphate, 100 mM sodium chloride, 1 mM DTT, 0.1 mM DSS, 99% D2O99% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMCtBP THAP domain1
20 mMsodium phosphate1
100 mMsodium chloride1
1 mMDTT1
0.1 mMDSS1
0.4 mMCtBP THAP domain[U-99% 15N]2
20 mMsodium phosphate2
100 mMsodium chloride2
1 mMDTT2
0.1 mMDSS2
0.6 mMCtBP THAP domain[U-98% 13C; U-98% 15N]3
20 mMsodium phosphate3
100 mMsodium chloride3
1 mMDTT3
0.1 mMDSS3
0.6 mMCtBP THAP domain[U-98% 13C; U-98% 15N]4
20 mMsodium phosphate4
100 mMsodium chloride4
1 mMDTT4
0.1 mMDSS4
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.12 6.5 ambient 298 K
20.12 6.9 ambient 298 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX6001
Bruker AMXBrukerAMX6002

-
Processing

NMR software
NameDeveloperClassification
SparkyT Goddarddata analysis
XwinNMRBruker Biospincollection
ARIAJ Linge, S O'Donoghue and M Nilgesstructure solution
TALOSG Cornilescu, F Delaglio and A Baxstructure solution
CNSrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: ARIA/CNS was used for structure calculation and refinement
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: lowest energy / Conformers calculated total number: 500 / Conformers submitted total number: 20

+
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