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- PDB-2zta: X-RAY STRUCTURE OF THE GCN4 LEUCINE ZIPPER, A TWO-STRANDED, PARAL... -

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Basic information

Entry
Database: PDB / ID: 2zta
TitleX-RAY STRUCTURE OF THE GCN4 LEUCINE ZIPPER, A TWO-STRANDED, PARALLEL COILED COIL
ComponentsGCN4 LEUCINE ZIPPER
KeywordsLEUCINE ZIPPER
Function / homology
Function and homology information


nitrogen catabolite activation of transcription from RNA polymerase II promoter / FCERI mediated MAPK activation / protein localization to nuclear periphery / Activation of the AP-1 family of transcription factors / response to amino acid starvation / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / mediator complex binding / Oxidative Stress Induced Senescence / TFIID-class transcription factor complex binding ...nitrogen catabolite activation of transcription from RNA polymerase II promoter / FCERI mediated MAPK activation / protein localization to nuclear periphery / Activation of the AP-1 family of transcription factors / response to amino acid starvation / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / mediator complex binding / Oxidative Stress Induced Senescence / TFIID-class transcription factor complex binding / amino acid biosynthetic process / positive regulation of RNA polymerase II transcription preinitiation complex assembly / positive regulation of transcription initiation by RNA polymerase II / cellular response to nutrient levels / cellular response to amino acid starvation / RNA polymerase II transcription regulator complex / DNA-binding transcription activator activity, RNA polymerase II-specific / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / transcription regulator complex / DNA-binding transcription factor activity, RNA polymerase II-specific / intracellular signal transduction / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus
Similarity search - Function
: / Basic region leucine zipper / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain / Basic-leucine zipper domain superfamily
Similarity search - Domain/homology
General control transcription factor GCN4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsO'Shea, E.K. / Klemm, J.D. / Kim, P.S. / Alber, T.
Citation
Journal: Science / Year: 1991
Title: X-ray structure of the GCN4 leucine zipper, a two-stranded, parallel coiled coil.
Authors: O'Shea, E.K. / Klemm, J.D. / Kim, P.S. / Alber, T.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1991
Title: X-Ray Scattering Indicates that the Leucine Zipper is a Coiled Coil
Authors: Rasmussen, R. / Benvegnu, D. / O'Shea, E.K. / Kim, P.S. / Alber, T.
#2: Journal: Science / Year: 1989
Title: Evidence that the Leucine Zipper is a Coiled Coil
Authors: O'Shea, E.K. / Rutkowski, R. / Kim, P.S.
History
DepositionJul 5, 1991Processing site: BNL
Revision 1.0Oct 15, 1992Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn
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.pdbx_leaving_atom_flag
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GCN4 LEUCINE ZIPPER
B: GCN4 LEUCINE ZIPPER


Theoretical massNumber of molelcules
Total (without water)8,0632
Polymers8,0632
Non-polymers00
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-21 kcal/mol
Surface area4900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.630, 30.350, 21.860
Angle α, β, γ (deg.)90.00, 94.70, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein/peptide GCN4 LEUCINE ZIPPER


Mass: 4031.701 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P03069
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.98 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion / Details: took 5 from original paper
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlpeptide1drop
210 mM1dropNaPO4
30.15 M1dropNaCl
40.02 %1dropNaN3
550 %(w/v)ammonium sulfate1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 1.8 Å / Num. obs: 5790 / % possible obs: 92 % / Num. measured all: 11527 / Rmerge(I) obs: 0.043

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementRfactor Rwork: 0.179 / Highest resolution: 1.8 Å
Refinement stepCycle: LAST / Highest resolution: 1.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms524 0 0 52 576
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Lowest resolution: 6 Å / σ(I): 2 / Rfactor obs: 0.179
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 2.5

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