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- PDB-1yui: SOLUTION NMR STRUCTURE OF THE GAGA FACTOR/DNA COMPLEX, REGULARIZE... -

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Basic information

Entry
Database: PDB / ID: 1yui
TitleSOLUTION NMR STRUCTURE OF THE GAGA FACTOR/DNA COMPLEX, REGULARIZED MEAN STRUCTURE
Components
  • DNA (5'-D(*GP*CP*CP*GP*AP*GP*AP*GP*TP*AP*C)-3')
  • DNA (5'-D(*GP*TP*AP*CP*TP*CP*TP*CP*GP*GP*C)-3')
  • GAGA-FACTOR
KeywordsDNA BINDING PROTEIN/DNA / COMPLEX (DNA-BINDING PROTEIN-DNA) / CHROMATIN REMODELING / DNA BINDING PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


maternal-to-zygotic transition of gene expression / response to ecdysone / syncytial blastoderm mitotic cell cycle / POZ domain binding / imaginal disc-derived wing morphogenesis / nuclear division / sex-chromosome dosage compensation / polytene chromosome / nucleosome organization / DNA-binding transcription activator activity ...maternal-to-zygotic transition of gene expression / response to ecdysone / syncytial blastoderm mitotic cell cycle / POZ domain binding / imaginal disc-derived wing morphogenesis / nuclear division / sex-chromosome dosage compensation / polytene chromosome / nucleosome organization / DNA-binding transcription activator activity / oogenesis / transcription factor binding / pericentric heterochromatin / heterochromatin formation / core promoter sequence-specific DNA binding / molecular function activator activity / euchromatin / chromatin organization / spermatogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / amyloid fibril formation / sequence-specific DNA binding / nucleic acid binding / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin remodeling / protein heterodimerization activity / DNA-binding transcription factor activity / cell division / negative regulation of DNA-templated transcription / chromatin binding / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / zinc ion binding / identical protein binding / nucleus
Similarity search - Function
Zinc finger, GAGA-binding factor / GAGA factor / Classic Zinc Finger / BTB/POZ domain / BTB domain profile. / Double Stranded RNA Binding Domain / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / SKP1/BTB/POZ domain superfamily / Zinc finger C2H2 type domain signature. ...Zinc finger, GAGA-binding factor / GAGA factor / Classic Zinc Finger / BTB/POZ domain / BTB domain profile. / Double Stranded RNA Binding Domain / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / SKP1/BTB/POZ domain superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Transcription activator GAGA
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodSOLUTION NMR / simulated annealing
AuthorsClore, G.M. / Omichinski, J.G. / Gronenborn, A.M.
CitationJournal: Nat.Struct.Biol. / Year: 1997
Title: The solution structure of a specific GAGA factor-DNA complex reveals a modular binding mode.
Authors: Omichinski, J.G. / Pedone, P.V. / Felsenfeld, G. / Gronenborn, A.M. / Clore, G.M.
History
DepositionDec 31, 1996Processing site: BNL
Revision 1.0Dec 31, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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*CP*CP*GP*AP*GP*AP*GP*TP*AP*C)-3')
C: DNA (5'-D(*GP*TP*AP*CP*TP*CP*TP*CP*GP*GP*C)-3')
A: GAGA-FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9764
Polymers12,9113
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)1 / -REGULARIZED MEAN STRUCTURE
Representative

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Components

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


Mass: 3383.224 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*GP*TP*AP*CP*TP*CP*TP*CP*GP*GP*C)-3')


Mass: 3325.172 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein GAGA-FACTOR


Mass: 6202.233 Da / Num. of mol.: 1 / Fragment: DNA BINDING DOMAIN, RESIDUES 310 - 372 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q08605
#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 experimentType: TRIPLE RESONANCE
NMR detailsText: TRIPLE RESONANCE FOR ASSIGNMENT OF PROTEIN 12C- FILTERED NOE, 12C-FILTERED HOHAHA AND 1H-1H NOE FOR DNA. QUANTITATIVE J CORRELATION FOR COUPLING CONSTANTS 3D 15N- SEPARATED, 3D 13C-SEPARATED, ...Text: TRIPLE RESONANCE FOR ASSIGNMENT OF PROTEIN 12C- FILTERED NOE, 12C-FILTERED HOHAHA AND 1H-1H NOE FOR DNA. QUANTITATIVE J CORRELATION FOR COUPLING CONSTANTS 3D 15N- SEPARATED, 3D 13C-SEPARATED, 3D 12C-FILTERED 3D 13C- SEPARATED/12C-FILTERED, AND 2D 1H-1H NOE EXPERIMENTS.

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Sample preparation

Sample conditionspH: 6.00 / Temperature: 303.50 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMX500BrukerAMX5005001
Bruker AMX600BrukerAMX6006002

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameClassification
X-PLOR (SEE ABOVE)structure solution
X-PLOR (SEE ABOVE)refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: THE 3D STRUCTURE OF THE GAGA FACTOR/DNA COMPLEX WAS SOLVED BY MULTI-DIMENSIONAL HETERONUCLEAR-EDITED AND -FILTERED NMR AND IS BASED ON 1475 EXPERIMENTAL NMR RESTRAINTS: (A) INTRAPROTEIN: 188 ...Details: THE 3D STRUCTURE OF THE GAGA FACTOR/DNA COMPLEX WAS SOLVED BY MULTI-DIMENSIONAL HETERONUCLEAR-EDITED AND -FILTERED NMR AND IS BASED ON 1475 EXPERIMENTAL NMR RESTRAINTS: (A) INTRAPROTEIN: 188 SEQUENTIAL (|I- J|=1), 134 MEDIUM RANGE (1 < |I-J| <=5) AND 95 LONG RANGE (|I-J| >5) INTERRESIDUES AND 275 INTRARESIDUE APPROXIMATE INTERPROTON DISTANCE RESTRAINTS; 140 TORSION ANGLE RESTRAINTS; 33 THREE-BOND HN-HA COUPLING CONSTANT RESTRAINTS; AND 94 (48 CALPHA AND 46 CBETA) 13C SHIFT RESTRAINTS. (NUMBERS OF RESIDUES 10 - 61) (B) INTRA-DNA: 124 INTRARESIDUE, 112 SEQUENTIAL INTRASTRAND, 21 INTERSTRAND INTERPROTON DISTANCE RESTRAINTS; 102 TORSION ANGLE RESTRAINTS (FOR ALPHA, BETA, GAMMA, DELTA, EPSILON AND AND ZETA BACKBONE TORSION ANGLES). (C) INTERMOLECULAR: 75 INTERPROTON DISTANCE RESTRAINTS. THE EXPERIMENTAL NMR RESTRAINTS ARE SUPPLEMENTED BY HYDROGEN BONDING RESTRAINTS: 24 DISTANCES FOR 12 BACKBONE HYDROGEN BONDS WITHIN THE PROTEIN, 58 DISTANCES FOR WATSON-CRICK BASE-PAIRING WITHIN THE DNA, AND 10 AMBIGUOUS DISTANCE RESTRAINTS BETWEEN THE PROTEIN AND THE DNA. THE RESTRAINTS HAVE BEEN DEPOSITED. THE STRUCTURES WERE CALCULATED USING THE SIMULATED ANNEALING PROTOCOL OF NILGES ET AL. (1988) FEBS LETT. 229, 129-136 USING THE PROGRAM X-PLOR 3.1 (BRUNGER) MODIFIED TO INCORPORATE COUPLING CONSTANT (GARRETT ET AL. (1984) J. MAGN. RESON. SERIES B 104, 99-103) AND CARBON CHEMICAL SHIFT (KUSZEWSKI ET AL. (1995) J. MAGN. RESON. SERIES B 106, 92-96) RESTRAINTS, AND A CONFORMATIONAL DATABASE POTENTIAL (KUSZEWSKI ET AL.(1996) PROTEIN SCI. 5, 1067-1080 THE RESTRAINED REGULARIZED MEAN STRUCTURE IS PRESENTED IN THIS ENTRY AND 50 STRUCTURES ARE PRESENTED IN ENTRY 1YUJ. IN THE RESTRAINED REGULARIZED MEAN COORDINATES THE LAST COLUMN REPRESENTS THE AVERAGE RMS DIFFERENCE BETWEEN THE INDIVIDUAL SIMULATED ANNEALING STRUCTURES AND THE MEAN COORDINATE POSITIONS. THE LAST COLUMN IN THE INDIVIDUAL SA STRUCTURES HAS NO MEANING. BEST FITTING TO GENERATE THE AVERAGE STRUCTURE IS WITH RESPECT TO RESIDUES 14 - 58 OF THE PROTEIN AND BASE PAIRS 1 - 11 OF THE DNA (RESIDUES 10 - 13 AND 59 - 61 ARE DISORDERED IN SOLUTION). RESIDUE 10 CORRESPONDS TO RESIDUE 319 OF THE NATURAL SEQUENCE. NOTE THE OCCUPANCY FIELD HAS NO MEANING.
NMR ensembleConformer selection criteria: REGULARIZED MEAN STRUCTURE / Conformers submitted total number: 1

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