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- PDB-2gcc: SOLUTION STRUCTURE OF THE GCC-BOX BINDING DOMAIN, NMR, MINIMIZED ... -

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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/ERF domain / AP2 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATERF1


Theoretical massNumber of molelcules
Total (without water)7,8921
Polymers7,8921
Non-polymers00
Water0
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

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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

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Experimental details

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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.

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Sample preparation

DetailsContents: POTASIUM PHOSPHATE
Sample conditionsIonic strength: 90 mM / pH: 6.0 / Pressure: 1 ATMOSPHERE / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

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

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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

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