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- PDB-2gat: SOLUTION STRUCTURE OF THE C-TERMINAL DOMAIN OF CHICKEN GATA-1 BOU... -

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Basic information

Entry
Database: PDB / ID: 2gat
TitleSOLUTION STRUCTURE OF THE C-TERMINAL DOMAIN OF CHICKEN GATA-1 BOUND TO DNA, NMR, REGULARIZED MEAN STRUCTURE
Components
  • DNA (5'-D(*AP*AP*TP*GP*TP*TP*TP*AP*TP*CP*TP*GP*CP*AP*AP*C)-3')
  • DNA (5'-D(*GP*TP*TP*GP*CP*AP*GP*AP*TP*AP*AP*AP*CP*AP*TP*T)-3')
  • ERYTHROID TRANSCRIPTION FACTOR GATA-1
KeywordsTRANSCRIPTION/DNA / DNA BINDING PROTEIN / TRANSCRIPTION FACTOR / ZINC BINDING DOMAIN / COMPLEX (TRANSCRIPTION REGULATION-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 / DNA (> 10) / Erythroid transcription factor
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodSOLUTION NMR / simulated annealing
AuthorsClore, G.M. / Tjandra, N. / Starich, M. / Omichinski, J.G. / Gronenborn, A.M.
Citation
Journal: Nat.Struct.Biol. / Year: 1997
Title: Use of dipolar 1H-15N and 1H-13C couplings in the structure determination of magnetically oriented macromolecules in solution.
Authors: Tjandra, N. / Omichinski, J.G. / Gronenborn, A.M. / Clore, G.M. / Bax, A.
#1: Journal: J.Mol.Biol. / Year: 1998
Title: The solution structure of the Leu22-->Val mutant AREA DNA binding domain complexed with a TGATAG core element defines a role for hydrophobic packing in the determination of specificity
Authors: Starich, M.R. / Wikstrom, M. / Shumacher, S. / Arst, H.N. / Gronenborn, A.M. / Clore, G.M.
#2: Journal: 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
DepositionNov 7, 1997Processing site: BNL
Revision 1.0Jan 28, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)17,4174
Polymers17,3513
Non-polymers651
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 / 34REGULARIZED MEAN STRUCTURE
Representative

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Components

#1: DNA chain DNA (5'-D(*GP*TP*TP*GP*CP*AP*GP*AP*TP*AP*AP*AP*CP*AP*TP*T)-3')


Mass: 4921.228 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*AP*AP*TP*GP*TP*TP*TP*AP*TP*CP*TP*GP*CP*AP*AP*C)-3')


Mass: 4872.190 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein ERYTHROID TRANSCRIPTION FACTOR GATA-1


Mass: 7557.844 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Production host: Escherichia coli (E. coli) / References: UniProt: P17678
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: DATA WERE RECORDED ON A 1:1 COMPLEX OF 1 MOLECULE OF DNA.

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Sample preparation

Sample conditionspH: 6.1 / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AM360BrukerAM3606001
Bruker DMX500BrukerDMX5005002
Bruker AMX600BrukerAMX6003603
Bruker DMX750BrukerDMX7507504

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
X-PLOR MODIFIEDMODIFIEDstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: THE STRUCTURES WERE CALCULATED USING THE SIMULATED ANNEALING PROTOCOL OF NILGES ET AL. (1988) FEBS LETT. 229, 129 - 136 AND PROTEIN ENGINEERING 2, 27 - 38 USING THE PROGRAM X-PLOR MODIFIED ...Details: THE STRUCTURES WERE CALCULATED USING THE SIMULATED ANNEALING PROTOCOL OF NILGES ET AL. (1988) FEBS LETT. 229, 129 - 136 AND PROTEIN ENGINEERING 2, 27 - 38 USING THE PROGRAM X-PLOR MODIFIED TO INCORPORATE DIPOLAR COUPLING RESTRAINTS (TJANDRA ET AL. (1997) NATURE STRUCT BIOL 4, 732-738) AND A CONFORMATIONAL DATABASE POTENTIAL FOR PROTEINS AND NUCLEIC ACIDS (KUSZEWSKI ET AL. (1996) PROTEIN SCI 5, 1067 - 1080 AND (1997) J. MAGN. RESON. 125, 171-177). THE EXPERIMENTAL RESTRAINTS ARE GIVEN IN R2GATMR. THE STRUCTURES ARE BASED ON A TOTAL OF 1830 EXPERIMENTAL NMR RESTRAINTS COMPRISING: 1444 INTERPROTON DISTANCE RESTRAINTS DERIVED FROM NOE MEASUREMENTS; 296 TORSION ANGLE RESTRAINTS; 90 RESIDUAL DIPOLAR COUPLINGS (52 N-H AND 38 C-H). 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 STRUCTURE IN THIS ENTRY IS THE RESTRAINED REGULARIZED MEAN STRUCTURE AND THE LAST NUMERIC COLUMN REPRESENTS THE RMS OF THE 34 INDIVIDUAL SIMULATED ANNEALING STRUCTURES FOUND IN PDB ENTRY 3GAT ABOUT THE MEAN COORDINATE POSITIONS. THE LAST NUMERIC COLUMN IN THE INDIVIDUAL SA STRUCTURES HAS NO MEANING. THE FOLLOWING TWO SETS OF COORDINATES DEFINE THE PRINCIPAL AXIS OF THE MAGNETIC SUSCEPTIBILITY TENSOR: POINT 1 50.250 -27.763 2.413 POINT 2 50.328 -26.611 3.418
NMR ensembleConformer selection criteria: REGULARIZED MEAN STRUCTURE / Conformers calculated total number: 34 / Conformers submitted total number: 1

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