[English] 日本語
Yorodumi
- PDB-2gcc: SOLUTION STRUCTURE OF THE GCC-BOX BINDING DOMAIN, NMR, MINIMIZED ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2gcc
TitleSOLUTION STRUCTURE OF THE GCC-BOX BINDING DOMAIN, NMR, MINIMIZED MEAN STRUCTURE
ComponentsATERF1
KeywordsTRANSCRIPTION FACTOR / ETHLENE INDUCIBLE
Function / homology
Function and homology information


phloem or xylem histogenesis / ethylene-activated signaling pathway / response to nematode / defense response / transcription cis-regulatory region binding / DNA-binding transcription factor activity / cell division / nucleus
Similarity search - Function
AP2/ERF domain / Ethylene-responsive transcription factor / GCC-box Binding Domain / AP2/ERF domain superfamily / AP2/ERF domain profile. / DNA-binding domain in plant proteins such as APETALA2 and EREBPs / AP2 domain / AP2/ERF domain / DNA-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ethylene-responsive transcription factor 1A
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodSOLUTION NMR / SIMULATED ANEALING PROTOCOL IN X-PLOR 3.1 WAS CARRIED OUT TO OBTAIN 46 STRUCTURES.
AuthorsAllen, M.D. / Yamasaki, K. / Ohme-Takagi, M. / Tateno, M. / Suzuki, M.
CitationJournal: EMBO J. / Year: 1998
Title: A novel mode of DNA recognition by a beta-sheet revealed by the solution structure of the GCC-box binding domain in complex with DNA.
Authors: Allen, M.D. / Yamasaki, K. / Ohme-Takagi, M. / Tateno, M. / Suzuki, M.
History
DepositionMar 13, 1998Processing site: BNL
Revision 1.0Mar 23, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
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: ATERF1


Theoretical massNumber of molelcules
Total (without water)7,8921
Polymers7,8921
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)1 / 1NO NOE VIOLATIONS
Representative

-
Components

#1: Protein ATERF1


Mass: 7891.974 Da / Num. of mol.: 1 / Fragment: GCC-BOX BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Description: DNA-BINDING DOMAIN OF ATERF1 / Cell line: BL21 / Gene: ATERF1 / Plasmid: PAF104 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: O80337

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121TOCSY
131DQF-COSY
1411H-15N HSQC
1513D 1H-15N NOESY-HMQC
1613D 1H-15N TOCSY-HMQC
17113C
18115N-FILTERED NOESY
NMR detailsText: SIGNALS DUE TO PROTEINS WERE OBTAINED BY NOESY, TOCSY, DQF-COSY FOR UNLABELED SAMPLE AND 1H-15N HSQC, 3D 1H-15N NOESY-HMQC AND 3D 1H-15N TOCSY-HMQC FOR THE SAMPLE WITH 15N-LABELED PROTEIN.

-
Sample preparation

DetailsContents: POTASIUM PHOSPHATE
Sample conditionsIonic strength: 90 mM / pH: 6 / Pressure: 1 ATMOSPHERE / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMX750BrukerDMX7507501
Bruker DMX500BrukerDMX5005002

-
Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
X-PLOR3.1structure solution
RefinementMethod: SIMULATED ANEALING PROTOCOL IN X-PLOR 3.1 WAS CARRIED OUT TO OBTAIN 46 STRUCTURES.
Software ordinal: 1 / Details: SEE REMARK 210
NMR ensembleConformer selection criteria: NO NOE VIOLATIONS / Conformers calculated total number: 1 / Conformers submitted total number: 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