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- PDB-1gau: SOLUTION STRUCTURE OF THE SPECIFIC DNA COMPLEX OF THE ZINC CONTAI... -

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Basic information

Entry
Database: PDB / ID: 1gau
TitleSOLUTION STRUCTURE OF THE SPECIFIC DNA COMPLEX OF THE ZINC CONTAINING DNA BINDING DOMAIN OF THE ERYTHROID TRANSCRIPTION FACTOR GATA-1 BY MULTIDIMENSIONAL NMR
Components
  • DNA (5'-D(P*AP*GP*AP*TP*AP*AP*AP*C)-3')
  • DNA (5'-D(P*GP*TP*TP*TP*AP*TP*CP*T)-3')
  • ERYTHROID TRANSCRIPTION FACTOR GATA-1
KeywordsTRANSCRIPTION/DNA / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


cell fate commitment / transcription coactivator binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleus
Similarity search - Function
Transcription factor GATA / GATA-type zinc finger domain. / GATA-type zinc finger domain profile. / zinc finger binding to DNA consensus sequence [AT]GATA[AG] / GATA zinc finger / Zinc finger, GATA-type / Erythroid Transcription Factor GATA-1, subunit A / Erythroid Transcription Factor GATA-1; Chain A / Zinc finger, NHR/GATA-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / Erythroid transcription factor
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodSOLUTION NMR
AuthorsClore, G.M. / Omichinski, J.G. / Gronenborn, A.M.
CitationJournal: Science / Year: 1993
Title: NMR structure of a specific DNA complex of Zn-containing DNA binding domain of GATA-1.
Authors: Omichinski, J.G. / Clore, G.M. / Schaad, O. / Felsenfeld, G. / Trainor, C. / Appella, E. / Stahl, S.J. / Gronenborn, A.M.
History
DepositionJun 28, 1993Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 5, 2012Group: Database references
Revision 1.4May 1, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DNA (5'-D(P*AP*GP*AP*TP*AP*AP*AP*C)-3')
C: DNA (5'-D(P*GP*TP*TP*TP*AP*TP*CP*T)-3')
A: ERYTHROID TRANSCRIPTION FACTOR GATA-1


Theoretical massNumber of molelcules
Total (without water)11,6503
Polymers11,6503
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 / -
Representative

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Components

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


Mass: 2443.657 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(P*GP*TP*TP*TP*AP*TP*CP*T)-3')


Mass: 2407.601 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein ERYTHROID TRANSCRIPTION FACTOR GATA-1


Mass: 6798.865 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P17678

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

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Processing

RefinementSoftware ordinal: 1
Details: DETAILS OF THE STRUCTURE DETERMINATION AND ALL STRUCTURAL STATISTICS ARE GIVEN IN THE REFERENCE CITED ON THE *JRNL* RECORDS ABOVE (I.E. AGREEMENT WITH EXPERIMENTAL RESTRAINTS, DEVIATIONS ...Details: DETAILS OF THE STRUCTURE DETERMINATION AND ALL STRUCTURAL STATISTICS ARE GIVEN IN THE REFERENCE CITED ON THE *JRNL* RECORDS ABOVE (I.E. AGREEMENT WITH EXPERIMENTAL RESTRAINTS, DEVIATIONS FROM IDEALITY FOR BOND LENGTHS, ANGLES, PLANES AND CHIRALITY, NON-BONDED CONTACTS, ATOMIC RMS DIFFERENCES BETWEEN THE CALCULATED STRUCTURES). THE STRUCTURES ARE BASED ON A TOTAL OF 1740 EXPERIMENTAL NMR RESTRAINTS COMPRISING: 1444 INTERPROTON DISTANCE RESTRAINTS DERIVED FROM NOE MEASUREMENTS; AND 296 TORSION ANGLE RESTRAINTS. THE NOE RESTRAINTS ARE SUBDIVIDED AS FOLLOWS: (A) WITHIN THE PROTEIN: 242 INTERRESIDUE SEQUENTIAL (|I-J|=1); 161 INTERRESIDUE SHORT RANGE (1(LESS THAN)|I-J|(LESS THAN)=5); 182 INTERRESIDUE LONG RANGE (|I-J|(GREATER THAN)5); AND 334 INTRARESIDUE. (B) WITHIN THE DNA: 157 INTRARESIDUE; 180 SEQUENTIAL INTRASTRAND; 34 INTERSTRAND; AND 37 H-BONDS (C) BETWEEN PROTEIN AND DNA: 117. THE TORSION ANGLE RESTRAINTS ARE SUBDIVIDED AS FOLLOWS: 144 ANGLES FOR THE PROTEIN (58 PHI, 56 PSI, 26 CHI1 AND 4 CHI2) AND 152 FOR THE DNA. THE TORSION ANGLE RESTRAINTS FOR THE DNA COMPRISE LOOSE RESTRAINTS ON THE BACKBONE TORSION ANGLES ALPHA, BETA, GAMMA, EPSILON AND ZETA TO PREVENT PROBLEMS ASSOCIATED WITH LOCAL MIRROR IMAGES. THE METHOD USED TO DETERMINE THE STRUCTURES IS THE HYBRID METRIC MATRIX DISTANCE GEOMETRY-DYNAMICAL SIMULATED ANNEALING METHOD [M.NILGES, G.M.CLORE, AND A.M.GRONENBORN FEBS LETT. 229, 317-324 (1988)]. A TOTAL OF 30 STRUCTURES WERE CALCULATED. THE ATOMIC RMS DISTRIBUTION ABOUT THE MEAN COORDINATE POSITIONS FOR RESIDUES 2 - 59 OF THE PROTEIN AND BASE PAIRS 6 - 13 OF THE DNA IS 0.70 (+/-0.13) A FOR THE BACKBONE ATOMS OF THE PROTEIN AND ALL ATOMS OF THE DNA, AND 1.13 (+/-0.08) A FOR ALL ATOMS OF THE PROTEIN AND DNA. THE N-TERMINUS (RESIDUE 1) AND C-TERMINUS (RESIDUES 60 - 66) ARE DISORDERED. THE ORIENTATION OF THE FIRST 5 AND LAST 3 BASE PAIRS OF THE 16MER DNA DUPLEX, WHICH ARE NOT IN CONTACT WITH THE DNA, IS POORLY DEFINED WITH RESPECT TO THE CORE OF THE COMPLEX. CONSEQUENTLY, ONLY THE COORDINATES OF THE COMPLEX PROPER HAVE BEEN DEPOSITED: I.E. RESIDUES 1 - 60 OF THE PROTEIN AND BASE PAIRS 6 - 13 OF THE DNA. THE COORDINATES OF THE 30 INDIVIDUAL SA STRUCTURES ARE PRESENTED AS MODELS 1 TO 30. THE QUANTITY IN COLUMNS 61 - OF THESE MODELS HAS NO MEANING. THE COORDINATES OF THE RESTRAINED MINIMIZED STRUCTURE ARE PRESENTED IN PROTEIN DATA BANK ENTRY 1GAT. THE (SA)R RESTRAINED MINIMIZED MEAN STRUCTURE WAS DERIVED BY AVERAGING THE COORDINATES OF THE INDIVIDUAL SA STRUCTURES (BEST FITTED TO RESIDUES 2 - 59 OF THE PROTEIN AND BASE PAIRS 6 - 13 OF THE DNA), AND SUBJECTING THE RESULTING COORDINATES TO RESTRAINED MINIMIZATION. THE QUANTITY PRESENTED IN COLUMNS 61 - 66 OF MEAN STRUCTURE, PRESENTED IN PROTEIN DATA BANK ENTRY 1GAT, REPRESENTS THE ATOMIC RMS DEVIATIONS OF THE 30 INDIVIDUAL SA STRUCTURES ABOUT THE MEAN STRUCTURE.
NMR ensembleConformers submitted total number: 30

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