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- PDB-5gat: SOLUTION NMR STRUCTURE OF THE WILD TYPE DNA BINDING DOMAIN OF ARE... -

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Entry
Database: PDB / ID: 5gat
TitleSOLUTION NMR STRUCTURE OF THE WILD TYPE DNA BINDING DOMAIN OF AREA COMPLEXED TO A 13BP DNA CONTAINING A CGATA SITE, 35 STRUCTURES
Components
  • DNA (5'-D(*CP*AP*GP*CP*GP*AP*TP*AP*GP*AP*GP*AP*C)-3')
  • DNA (5'-D(*GP*TP*CP*TP*CP*TP*AP*TP*CP*GP*CP*TP*G)-3')
  • NITROGEN REGULATORY PROTEIN AREA
KeywordsTRANSCRIPTION/DNA / DNA BINDING PROTEIN / TRANSCRIPTION FACTOR / ZINC BINDING DOMAIN / COMPLEX (TRANSCRIPTION REGULATION-DNA) / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


regulation of amide catabolic process / regulation of arginine metabolic process / regulation of nitrogen utilization / nitrate assimilation / regulation of gene expression / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of transcription by RNA polymerase II ...regulation of amide catabolic process / regulation of arginine metabolic process / regulation of nitrogen utilization / nitrate assimilation / regulation of gene expression / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin remodeling / 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
Nitrogen regulatory AreA, N-terminal / Nitrogen regulatory protein AreA N terminus / Nitrogen regulatory protein areA, GATA-like domain / Fungal protein of unknown function (DUF1752) / 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 ...Nitrogen regulatory AreA, N-terminal / Nitrogen regulatory protein AreA N terminus / Nitrogen regulatory protein areA, GATA-like domain / Fungal protein of unknown function (DUF1752) / 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) / Nitrogen regulatory protein areA
Similarity search - Component
Biological speciesEmericella nidulans (mold)
MethodSOLUTION NMR / simulated annealing
AuthorsClore, G.M. / Starich, M. / Wikstrom, M. / Gronenborn, A.M.
CitationJournal: J.Mol.Biol. / Year: 1998
Title: The solution structure of a fungal AREA protein-DNA complex: an alternative binding mode for the basic carboxyl tail of GATA factors.
Authors: Starich, M.R. / Wikstrom, M. / Arst Jr., H.N. / Clore, G.M. / 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_ref_seq_dif / 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_ref_seq_dif.details / _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(*CP*AP*GP*CP*GP*AP*TP*AP*GP*AP*GP*AP*C)-3')
C: DNA (5'-D(*GP*TP*CP*TP*CP*TP*AP*TP*CP*GP*CP*TP*G)-3')
A: NITROGEN REGULATORY PROTEIN AREA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3764
Polymers15,3113
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)35 / 35
Representative

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Components

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


Mass: 4009.637 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*GP*TP*CP*TP*CP*TP*AP*TP*CP*GP*CP*TP*G)-3')


Mass: 3933.558 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein NITROGEN REGULATORY PROTEIN AREA


Mass: 7367.480 Da / Num. of mol.: 1 / Fragment: DNA BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Emericella nidulans (mold) / Gene: POTENTIAL / Organ: TAIL / Production host: Escherichia coli (E. coli) / References: UniProt: P17429
#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

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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 AM360BrukerAM3603601
Bruker AMX500BrukerAMX5005002
Bruker DMX500BrukerDMX5005003
Bruker AMX600BrukerAMX6006004
Bruker DMX600BrukerDMX6006005
Bruker DMX750BrukerDMX7507506

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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 COUPLING CONSTANT RESTRAINTS (GARRETT ET AL. (1994) J. MAGN RESON. SERIES B 104, 99 - 103), CARBON CHEMICAL SHIFT RESTRAINTS (KUSZEWSKI ET AL. (1995) J. MAGN. RESON. SERIES B 106, 92 - 96) RESTRAINTS, 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 3D STRUCTURE OF THE COMPLEX OF THE WILD TYPE AREA DBD-DNA COMPLEX WAS SOLVED BY MULTI-DIMENSIONAL HETERONUCLEAR-EDITED AND -FILTERED NMR IS BASED ON THE FOLLOWING 1098 EXPERIMENTAL RESTRAINTS (A) PROTEIN: 119 SEQUENTIAL (|I-J|=1), 49 SHORT RANGE (1 < |I-J| >=5), 68 LONG RANGE (|I-J|>5), AND 64 INTRARESIDUE APPROXIMATE INTERPROTON DISTANCE RESTRAINTS; NULL 124 TORSION ANGLE RESTRAINTS (61 PHI, 8 PSI, 39 CHI1, 15 CHI2, AND 1 CHI3), 41 THREE-BOND HN-HA COUPLING CONSTANT RESTRAINTS; NULL 77 (41 CALPHA AND 36 CBETA) 13C CHEMICAL SHIFT RESTRAINTS; NULL 48 RESIDUAL N-H DIPOLAR COUPLING RESTRAINTS; 20 DISTANCE RESTRAINTS FOR 10 BACKBONE HYDROGEN BONDS. (B) DNA: 75 INTRARESIDUE, 115 SEQUENTIAL INTRASTRAND AND 20 INTERSTRAND INTERPROTON DISTANCE RESTRAINTS; 66 DISTANCES FOR WATSON-CRICK BASE PAIR HYDROGEN BONDS; 170 TORSION ANGLE RESTRAINTS FOR THE DNA BACKBONE COVERING VALUES CHARACTERISTIC OF BOTH A AND B DNA. (C) 48 INTERMOLECULAR INTERPROTON DISTANCE RESTRAINTS (D) 2 INTERMOLECULAR DISTANCE RESTRAINTS TO PHOSPHATES (E) 8 'REPULSIVE' RESTRAINTS (F) 4 DISTANCE RESTRAINTS FOR 2 INTERMOLECULAR H-BONDS BETWEEN ARG 24 AND BASE OF GUA5. THE FOLLOWING TWO SETS OF COORDINATES DEFINE THE PRINCIPAL AXIS OF THE MAGNETIC SUSCEPTIBILITY TENSOR: MODEL 1 POINT 1 102.092-193.887-255.981 POINT 2 102.732-192.538-255.651 MODEL 2 POINT 1 86.136-234.098 -40.447 POINT 2 86.796-232.777 -40.050 MODEL 3 POINT 1 134.979-162.786-132.132 POINT 2 135.695-161.464-131.850 MODEL 4 POINT 1 -70.103 -54.685 51.419 POINT 2 -69.500 -53.313 51.726 MODEL 5 POINT 1 135.883-100.066-174.175 POINT 2 136.516 -98.700-173.898 MODEL 6 POINT 1 76.125-132.662-107.324 POINT 2 76.655-131.248-107.078 MODEL 7 POINT 1 149.063-111.077 -36.611 POINT 2 149.663-109.715 -36.255 MODEL 8 POINT 1 122.564 -99.258 13.431 POINT 2 123.265 -97.930 13.723 MODEL 9 POINT 1 89.110 -79.702 -46.597 POINT 2 89.824 -78.392 -46.258 MODEL 10 POINT 1 142.398 -66.526 -89.227 POINT 2 143.080 -65.195 -88.905 MODEL 11 POINT 1 131.492-187.153 13.577 POINT 2 132.170-185.854 14.018 MODEL 12 POINT 1 210.687-129.261-129.735 POINT 2 211.314-127.906-129.402 MODEL 13 POINT 1 115.833-147.381-125.532 POINT 2 116.493-146.040-125.205 MODEL 14 POINT 1 213.481 -97.161 -62.866 POINT 2 214.099 -95.785 -62.612 MODEL 15 POINT 1 47.875-239.077 -96.187 POINT 2 48.454-237.709 -95.820 MODEL 16 POINT 1 123.077-156.502-154.067 POINT 2 123.774-155.182-153.731 MODEL 17 POINT 1 89.571 -78.309 3.456 POINT 2 90.142 -76.928 3.784 MODEL 18 POINT 1 35.762-246.462 -37.437 POINT 2 36.440-245.133 -37.101 MODEL 19 POINT 1 121.519-157.548 -7.594 POINT 2 122.144-156.197 -7.236 MODEL 20 POINT 1 113.586 -86.299-148.635 POINT 2 114.193 -84.935-148.298 MODEL 21 POINT 1 91.562-134.645 -78.697 POINT 2 92.233-133.317 -78.335 MODEL 22 POINT 1 118.977-218.365-122.566 POINT 2 119.576-217.008-122.192 MODEL 23 POINT 1 80.952-182.035 -80.709 POINT 2 81.615-180.694 -80.392 MODEL 24 POINT 1 188.361-123.949-146.548 POINT 2 189.022-122.608-146.225 MODEL 25 POINT 1 114.771-280.049 -48.411 POINT 2 115.463-278.730 -48.065 MODEL 26 POINT 1 161.250-143.808 74.628 POINT 2 161.956-142.504 75.004 MODEL 27 POINT 1 143.106-116.338 -57.993 POINT 2 143.761-114.989 -57.690 MODEL 28 POINT 1 114.944-162.825 -21.630 POINT 2 115.575-161.468 -21.310 MODEL 29 POINT 1 89.010-134.313-122.747 POINT 2 89.573-132.932-122.407 MODEL 30 POINT 1 81.718-198.065 -81.738 POINT 2 82.448-196.759 -81.416 MODEL 31 POINT 1 177.911-171.893 -37.695 POINT 2 178.512-170.518 -37.399 MODEL 32 POINT 1 100.216-159.685-185.688 POINT 2 100.906-158.386-185.268 MODEL 33 POINT 1 64.235-177.747 -56.722 POINT 2 64.894-176.431 -56.302 MODEL 34 POINT 1 237.150 -92.701 -2.650 POINT 2 237.781 -91.352 -2.296 MODEL 35 POINT 1 91.957-116.106 -54.093 POINT 2 92.589-114.744 -53.797
NMR ensembleConformers calculated total number: 35 / Conformers submitted total number: 35

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