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- PDB-3gat: SOLUTION NMR STRUCTURE OF THE C-TERMINAL DOMAIN OF CHICKEN GATA-1... -

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Basic information

Entry
Database: PDB / ID: 3gat
TitleSOLUTION NMR STRUCTURE OF THE C-TERMINAL DOMAIN OF CHICKEN GATA-1 BOUND TO DNA, 34 STRUCTURES
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 / TCOMPLEX (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 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 16, 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
Revision 1.4May 22, 2024Group: 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(*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
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)34 / 34
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 FOLLOWING TWO SETS OF COORDINATES DEFINE THE PRINCIPAL AXIS OF THE MAGNETIC SUSCEPTIBILITY TENSOR: MODEL 1 POINT 1 0.378 -50.982 -38.862 POINT 2 0.472 -49.836 -37.853 MODEL 2 POINT 1 9.054 -65.114 92.057 POINT 2 9.125 -63.952 93.051 MODEL 3 POINT 1 159.392 0.215 -60.612 POINT 2 159.391 1.382 -59.623 MODEL 4 POINT 1 1.446 -13.082 18.709 POINT 2 1.560 -11.891 19.663 MODEL 5 POINT 1 36.350 -69.900 58.948 POINT 2 36.375 -68.721 59.923 MODEL 6 POINT 1 126.484 -20.411 -50.611 POINT 2 126.594 -19.266 -49.602 MODEL 7 POINT 1 88.897 -14.889 116.035 POINT 2 89.009 -13.746 117.045 MODEL 8 POINT 1 33.575 14.467 0.174 POINT 2 33.645 15.627 1.168 MODEL 9 POINT 1 83.455-111.061-109.708 POINT 2 83.524-109.891-108.724 MODEL 10 POINT 1 54.992 12.813 -1.197 POINT 2 55.119 13.958 -0.188 MODEL 11 POINT 1 -5.927 -98.366 8.457 POINT 2 -5.849 -97.197 9.441 MODEL 12 POINT 1 -16.731 -79.619 -28.952 POINT 2 -16.693 -78.486 -27.923 MODEL 13 POINT 1 69.885 -59.142 22.056 POINT 2 69.992 -57.968 23.033 MODEL 14 POINT 1 60.771 80.864 -67.242 POINT 2 60.765 82.035 -66.258 MODEL 15 POINT 1 88.367-100.303 26.657 POINT 2 88.485 -99.179 27.688 MODEL 16 POINT 1 71.362 19.714 75.498 POINT 2 71.461 20.908 76.450 MODEL 17 POINT 1 55.206 36.123 129.402 POINT 2 55.272 37.358 130.301 MODEL 18 POINT 1 -0.207 63.643 9.656 POINT 2 -0.119 64.869 10.566 MODEL 19 POINT 1 50.329 42.850 -53.654 POINT 2 50.424 44.067 -52.731 MODEL 20 POINT 1 51.532 -39.600 87.552 POINT 2 51.620 -38.437 88.540 MODEL 21 POINT 1 9.452 -38.136 23.088 POINT 2 9.459 -36.990 24.103 MODEL 22 POINT 1 52.844 16.158 -59.776 POINT 2 52.863 17.351 -58.818 MODEL 23 POINT 1 55.060 6.778 -32.793 POINT 2 55.121 7.966 -31.831 MODEL 24 POINT 1 63.527 -10.417 -15.482 POINT 2 63.570 -9.300 -14.436 MODEL 25 POINT 1 43.182 -28.794 21.016 POINT 2 43.233 -27.638 22.017 MODEL 26 POINT 1 93.739 -3.416 28.751 POINT 2 93.856 -2.334 29.826 MODEL 27 POINT 1 106.589 5.146 33.748 POINT 2 106.637 6.346 34.695 MODEL 28 POINT 1 51.597 -15.726 20.577 POINT 2 51.712 -14.540 21.538 MODEL 29 POINT 1 63.361 -27.745 -32.153 POINT 2 63.448 -26.576 -31.169 MODEL 30 POINT 1 -59.343 5.979 38.193 POINT 2 -59.203 7.083 39.244 MODEL 31 POINT 1 -4.120-119.412 -63.274 POINT 2 -4.040-118.211 -62.331 MODEL 32 POINT 1 38.468 -28.280 -19.797 POINT 2 38.602 -27.192 -18.729 MODEL 33 POINT 1 139.677-206.067 -84.072 POINT 2 139.702-204.924 -83.054 MODEL 34 POINT 1 35.819 -48.400 -10.080 POINT 2 35.876 -47.237 -9.088
NMR ensembleConformers calculated total number: 34 / Conformers submitted total number: 34

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