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- PDB-1zw8: Solution structure of a ZAP1 zinc-responsive domain provides insi... -

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Basic information

Entry
Database: PDB / ID: 1zw8
TitleSolution structure of a ZAP1 zinc-responsive domain provides insights into metalloregulatory transcriptional repression in Saccharomyces cerevisiae
ComponentsZinc-responsive transcriptional regulator ZAP1
KeywordsTRANSCRIPTION / ZAP1 / interacting C2H2 zinc fingers / beta-beta-alpha / NMR solution structure
Function / homology
Function and homology information


RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleus
Similarity search - Function
Helix Hairpins - #370 / Zap1, zinc finger 2 / Zap1 zinc finger 2 / Helix Hairpins / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type ...Helix Hairpins - #370 / Zap1, zinc finger 2 / Zap1 zinc finger 2 / Helix Hairpins / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / Helix non-globular / Special
Similarity search - Domain/homology
Zinc-responsive transcriptional regulator ZAP1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / torsion angle dynamics, cartesian refinement
AuthorsWang, Z. / Feng, L.S. / Venkataraman, K. / Matskevich, V.A. / Parasuram, P. / Laity, J.H.
Citation
Journal: J.Mol.Biol. / Year: 2006
Title: Solution structure of a Zap1 zinc-responsive domain provides insights into metalloregulatory transcriptional repression in Saccharomyces cerevisiae.
Authors: Wang, Z. / Feng, L.S. / Matskevich, V. / Venkataraman, K. / Parasuram, P. / Laity, J.H.
#1: Journal: Embo J. / Year: 2003
Title: Zinc fingers can act as Zn(II) sensors to regulate transcriptional activation domain function
Authors: Bird, A.J. / McCal, K. / Kramer, M. / Blankman, E. / Winge, D.R. / Eid, D.J.
#2: Journal: Mol.Cell / Year: 1997
Title: Zap1p, a metalloregulatory protein involved in zinc-responsive transcriptional regulation in Saccharomyces cerevisiae
Authors: Zhao, H. / Eide, D.J.
History
DepositionJun 3, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_conn_angle / 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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

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Assembly

Deposited unit
A: Zinc-responsive transcriptional regulator ZAP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,5503
Polymers7,4191
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Zinc-responsive transcriptional regulator ZAP1


Mass: 7419.285 Da / Num. of mol.: 1 / Fragment: two interacting zinc fingers
Mutation: three non-canonical cyteines converted to alanines due to oxidative instability
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Description: Zap1 gene derived from pYeF2ZAP1. (Gift from D.J. Eide, University of Wisconsin-Madison). ZZF1-2 portion of gene cloned into pET-21a plasmid (Novagen). Further details can be found in entry citation.
Gene: ZAP1 / Plasmid: p21a-zzf1-2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P47043
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
NMR detailsText: pulse squences were from the Varian BioPack software package add-on within VNMR two 3D 13C-NOESY-HSQC spectra were recorded in 99% (v/v)D2O with carrier centered on aliphatic (43 ppm) and ...Text: pulse squences were from the Varian BioPack software package add-on within VNMR two 3D 13C-NOESY-HSQC spectra were recorded in 99% (v/v)D2O with carrier centered on aliphatic (43 ppm) and aromatic (125 ppm) regions, respectiviely.

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Sample preparation

DetailsContents: 0.7 mM protein, 1.5 mM Zn(II), 20 mM MES, 0.2 mM DSS, 1 mM NaN2, 5 mM Beta-mercaptoethanol
Solvent system: 90% H2O, 10% D2O or 99% D2O
Sample conditionsIonic strength: no salt / pH: 6.9 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR softwareName: CNS / Version: 1.1
Developer: A.T.Brunger, P.D.Adams, G.M.Clore, W.L.Delano, P.Gros, R.W.Grosse-Kunstleve, J.-S.Jiang, J.Kuszewski, M.Nilges, N.S.Pannu, R.J.Read, L.M.Rice, T.Simonson, G.L.Warren
Classification: refinement
RefinementMethod: torsion angle dynamics, cartesian refinement / Software ordinal: 1
Details: 1443 NOE-derived distance restraints, and 98 dihedral angle restraints.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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