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- PDB-2hdc: STRUCTURE OF TRANSCRIPTION FACTOR GENESIS/DNA COMPLEX -

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Basic information

Entry
Database: PDB / ID: 2hdc
TitleSTRUCTURE OF TRANSCRIPTION FACTOR GENESIS/DNA COMPLEX
Components
  • DNA (5'-D(P*GP*CP*TP*TP*AP*AP*AP*AP*TP*AP*AP*CP*AP*AP*TP*AP*C)-3')
  • DNA (5'-D(P*GP*TP*AP*TP*TP*GP*TP*TP*AP*TP*TP*TP*TP*AP*AP*GP*C)-3')
  • PROTEIN (TRANSCRIPTION FACTOR)
KeywordsPROTEIN/DNA / DYANAMICS / GENESIS / WINGED HELIX PROTEIN / PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


trophectodermal cell differentiation / embryonic placenta development / cellular response to leukemia inhibitory factor / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding / double-stranded DNA binding / in utero embryonic development / transcription cis-regulatory region binding / DNA-binding transcription factor activity ...trophectodermal cell differentiation / embryonic placenta development / cellular response to leukemia inhibitory factor / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding / double-stranded DNA binding / in utero embryonic development / transcription cis-regulatory region binding / DNA-binding transcription factor activity / chromatin / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus
Similarity search - Function
: / Fork head domain conserved site1 / Fork head domain signature 1. / Fork head domain / Forkhead domain / Fork head domain profile. / FORKHEAD / Fork head domain conserved site 2 / Fork head domain signature 2. / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain ...: / Fork head domain conserved site1 / Fork head domain signature 1. / Fork head domain / Forkhead domain / Fork head domain profile. / FORKHEAD / Fork head domain conserved site 2 / Fork head domain signature 2. / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Forkhead box protein D3
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / distance geometry
AuthorsJin, C. / Marsden, I. / Chen, X. / Liao, X.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Dynamic DNA contacts observed in the NMR structure of winged helix protein-DNA complex.
Authors: Jin, C. / Marsden, I. / Chen, X. / Liao, X.
History
DepositionMay 5, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jul 5, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DNA (5'-D(P*GP*CP*TP*TP*AP*AP*AP*AP*TP*AP*AP*CP*AP*AP*TP*AP*C)-3')
C: DNA (5'-D(P*GP*TP*AP*TP*TP*GP*TP*TP*AP*TP*TP*TP*TP*AP*AP*GP*C)-3')
A: PROTEIN (TRANSCRIPTION FACTOR)


Theoretical massNumber of molelcules
Total (without water)21,8243
Polymers21,8243
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)20 / 200LEAST RESTRAINT VIOLATION
RepresentativeModel #1

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Components

#1: DNA chain DNA (5'-D(P*GP*CP*TP*TP*AP*AP*AP*AP*TP*AP*AP*CP*AP*AP*TP*AP*C)-3')


Mass: 5187.426 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(P*GP*TP*AP*TP*TP*GP*TP*TP*AP*TP*TP*TP*TP*AP*AP*GP*C)-3')


Mass: 5222.404 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein PROTEIN (TRANSCRIPTION FACTOR)


Mass: 11414.109 Da / Num. of mol.: 1 / Fragment: DNA BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: GENESIS / Organelle: NUCLEUSCell nucleus / References: UniProt: Q63245

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121HNCA
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N (AND 2H)-LABELED SAMPLE

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Sample preparation

DetailsContents: 90% WATER/10% D2O
Sample conditionspH: 6.5 / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX7502

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5GUNTERT, PETER, ET ALrefinement
DYANAstructure solution
RefinementMethod: distance geometry / Software ordinal: 1
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 200 / Conformers submitted total number: 20

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