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- PDB-1hbw: Solution nmr structure of the dimerization domain of the yeast tr... -

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Basic information

Entry
Database: PDB / ID: 1hbw
TitleSolution nmr structure of the dimerization domain of the yeast transcriptional activator Gal4 (residues 50-106)
ComponentsREGULATORY PROTEIN GAL4
KeywordsTRANSCRIPTIONAL ACTIVATOR / GALACTOSE AND MELIBIOSE METABOLISM / DIMERIZATION DOMAIN / COILED-COIL DIMERIC
Function / homology
Function and homology information


regulation of transcription from RNA polymerase II promoter by galactose / galactose metabolic process / positive regulation of transcription from RNA polymerase II promoter by galactose / transcription repressor complex / DNA-binding transcription activator activity, RNA polymerase II-specific / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-templated transcription / zinc ion binding ...regulation of transcription from RNA polymerase II promoter by galactose / galactose metabolic process / positive regulation of transcription from RNA polymerase II promoter by galactose / transcription repressor complex / DNA-binding transcription activator activity, RNA polymerase II-specific / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-templated transcription / zinc ion binding / identical protein binding / nucleus
Similarity search - Function
Gal4 dimerisation domain / Gal4-like dimerisation domain / Fungal specific transcription factor domain / Transcription factor domain, fungi / Fungal specific transcription factor domain / Zn(2)-C6 fungal-type DNA-binding domain signature. / Fungal Zn(2)-Cys(6) binuclear cluster domain / Zn(2)-C6 fungal-type DNA-binding domain superfamily / Zn(2)-C6 fungal-type DNA-binding domain profile. / GAL4-like Zn(II)2Cys6 (or C6 zinc) binuclear cluster DNA-binding domain ...Gal4 dimerisation domain / Gal4-like dimerisation domain / Fungal specific transcription factor domain / Transcription factor domain, fungi / Fungal specific transcription factor domain / Zn(2)-C6 fungal-type DNA-binding domain signature. / Fungal Zn(2)-Cys(6) binuclear cluster domain / Zn(2)-C6 fungal-type DNA-binding domain superfamily / Zn(2)-C6 fungal-type DNA-binding domain profile. / GAL4-like Zn(II)2Cys6 (or C6 zinc) binuclear cluster DNA-binding domain / Zn(2)-C6 fungal-type DNA-binding domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Basic-leucine zipper domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Regulatory protein GAL4
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodSOLUTION NMR / SIMULATED ANNEALING PROTOCOL
AuthorsHidalgo, P. / Ansari, A.Z. / Schmidt, P. / Hare, B. / Simkovic, N. / Farrell, S. / Shin, E.J. / Ptashne, M. / Wagner, G.
CitationJournal: Genes Dev. / Year: 2001
Title: Recruitment of the Transcriptional Machinery Through Gal11P: Structure and Interactions of the GAL4 Dimerization Domain
Authors: Hidalgo, P. / Ansari, A.Z. / Schmidt, P. / Hare, B. / Simkovich, N. / Farrell, S. / Shin, E.J. / Ptashne, M. / Wagner, G.
History
DepositionApr 20, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 10, 2001Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jan 15, 2020Group: Atomic model / Data collection / Other
Category: atom_site / pdbx_database_status ...atom_site / pdbx_database_status / pdbx_nmr_representative / pdbx_validate_torsion
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_nmr_representative.conformer_id / _pdbx_validate_torsion.PDB_model_num / _pdbx_validate_torsion.auth_asym_id / _pdbx_validate_torsion.auth_comp_id / _pdbx_validate_torsion.auth_seq_id / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi
Revision 2.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: REGULATORY PROTEIN GAL4
B: REGULATORY PROTEIN GAL4


Theoretical massNumber of molelcules
Total (without water)13,3872
Polymers13,3872
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)17 / 300LOWEST ENERGY AND MINIMAL NOE DERIVED DISTANCE RESTRAINTS VIOLATIONS
RepresentativeModel #1

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Components

#1: Protein REGULATORY PROTEIN GAL4


Mass: 6693.702 Da / Num. of mol.: 2 / Fragment: DIMERIZATION DOMAIN RESIDUES 50-106 / Mutation: YES / Source method: obtained synthetically / Source: (synth.) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P04386
Compound detailsCHAIN A, B ENGINEERED MUTATION GLN87ARG, LYS90GLU GAL4 IS A POSITIVE REGULATOR FOR THE GALACTOSE-INDUCED GENES

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY (1H
12113C
13115N)
141HNHA
151HNHB
161HNCA
171HN(CO)CA

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Sample preparation

Sample conditionsIonic strength: 50 MM SODIUM PHOSPHATE / pH: 7.4 / Temperature: 308 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UP 750VarianUP 7507501
Bruker UP 400BrukerUP 4006002
Bruker AMXBrukerAMX5003
Bruker AMXBrukerAMX4004
Varian INOVAVarianINOVA5005

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Processing

NMR software
NameDeveloperClassification
CNSBRUNGER,ADAMS,CLORE,DELANO,GROS, GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ, RICE,SIMONSON,WARRENrefinement
CNSstructure solution
RefinementMethod: SIMULATED ANNEALING PROTOCOL / Software ordinal: 1
Details: C2 SYMMETRY WAS ENFORCED IN THE STRUCTURE CALCULATIONS.
NMR ensembleConformer selection criteria: LOWEST ENERGY AND MINIMAL NOE DERIVED DISTANCE RESTRAINTS VIOLATIONS
Conformers calculated total number: 300 / Conformers submitted total number: 17

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