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- PDB-2bby: DNA-BINDING DOMAIN FROM HUMAN RAP30, NMR, 30 STRUCTURES -

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Basic information

Entry
Database: PDB / ID: 2bby
TitleDNA-BINDING DOMAIN FROM HUMAN RAP30, NMR, 30 STRUCTURES
ComponentsRAP30
KeywordsTRANSCRIPTION REGULATION / RAP30 / DNA-BINDING DOMAIN
Function / homology
Function and homology information


transcription factor TFIIF complex / Abortive elongation of HIV-1 transcript in the absence of Tat / FGFR2 alternative splicing / Signaling by FGFR2 IIIa TM / Viral Messenger RNA Synthesis / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / RNA polymerase II general transcription initiation factor activity ...transcription factor TFIIF complex / Abortive elongation of HIV-1 transcript in the absence of Tat / FGFR2 alternative splicing / Signaling by FGFR2 IIIa TM / Viral Messenger RNA Synthesis / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / RNA polymerase II general transcription initiation factor activity / mRNA Capping / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / mRNA Splicing - Minor Pathway / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / Processing of Capped Intron-Containing Pre-mRNA / RNA polymerase II transcribes snRNA genes / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / mRNA Splicing - Major Pathway / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / microtubule cytoskeleton / Estrogen-dependent gene expression / transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus
Similarity search - Function
Transcription initiation factor IIF, beta subunit / TFIIF beta subunit, HTH domain / TFIIF, beta subunit, N-terminal / TFIIF, beta subunit HTH domain / TFIIF, beta subunit N-terminus / Transcription Factor IIF, Rap30/Rap74, interaction / 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 ...Transcription initiation factor IIF, beta subunit / TFIIF beta subunit, HTH domain / TFIIF, beta subunit, N-terminal / TFIIF, beta subunit HTH domain / TFIIF, beta subunit N-terminus / Transcription Factor IIF, Rap30/Rap74, interaction / 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
General transcription factor IIF subunit 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DYNAMICAL SIMULATED ANNEALING
AuthorsGroft, C.M. / Uljon, S.N. / Wang, R. / Werner, M.H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: Structural homology between the Rap30 DNA-binding domain and linker histone H5: implications for preinitiation complex assembly.
Authors: Groft, C.M. / Uljon, S.N. / Wang, R. / Werner, M.H.
History
DepositionApr 27, 1998Processing site: BNL
Revision 1.0Nov 25, 1998Provider: 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 22, 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: RAP30


Theoretical massNumber of molelcules
Total (without water)8,3721
Polymers8,3721
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)30 / 150LEAST RESTRAINT AND ANGULAR VIOLATION
Representative

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Components

#1: Protein RAP30


Mass: 8371.669 Da / Num. of mol.: 1 / Fragment: DNA-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET11D / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174 (DE3) / References: UniProt: P13984

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 3D/4D HETERONUCLEAR NOESY/ROESY
NMR detailsText: STRUCTURE DETERMINED USING STANDARD MULTI-NUCLEAR 3D/4D SPECTROSCOPY

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Sample preparation

DetailsContents: AQUEOUS
Sample conditionsIonic strength: 10mM PHOSPHATE, 50mM NACL / pH: 7.2 / Pressure: 1 atm / Temperature: 297 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMX500BrukerDMX5005001
Bruker DMX600BrukerDMX6006002

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
X-PLOR3.851phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERrefinement
X-PLOR3.851structure solution
RefinementMethod: DYNAMICAL SIMULATED ANNEALING / Software ordinal: 1 / Details: REFINEMENT DETAILS CAN BE FOUND IN JRNL CITATION
NMR ensembleConformer selection criteria: LEAST RESTRAINT AND ANGULAR VIOLATION
Conformers calculated total number: 150 / Conformers submitted total number: 30

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