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- PDB-1zil: GCN4-LEUCINE ZIPPER CORE MUTANT ASN16GLN IN THE DIMERIC STATE -

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Basic information

Entry
Database: PDB / ID: 1zil
TitleGCN4-LEUCINE ZIPPER CORE MUTANT ASN16GLN IN THE DIMERIC STATE
ComponentsGENERAL CONTROL PROTEIN GCN4
KeywordsLEUCINE ZIPPER / AMINO-ACID BIOSYNTHESIS / TRANSCRIPTION REGULATION / ACTIVATOR / DNA-BINDING / NUCLEAR PROTEIN / COILED COIL
Function / homology
Function and homology information


protein localization to nuclear periphery / Activation of the AP-1 family of transcription factors / response to amino acid starvation / mediator complex binding / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / nitrogen catabolite activation of transcription from RNA polymerase II promoter / TFIID-class transcription factor complex binding / amino acid biosynthetic process / positive regulation of transcription initiation by RNA polymerase II ...protein localization to nuclear periphery / Activation of the AP-1 family of transcription factors / response to amino acid starvation / mediator complex binding / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / nitrogen catabolite activation of transcription from RNA polymerase II promoter / TFIID-class transcription factor complex binding / amino acid biosynthetic process / positive regulation of transcription initiation by RNA polymerase II / positive regulation of RNA polymerase II transcription preinitiation complex assembly / cellular response to amino acid starvation / RNA polymerase II transcription regulator complex / : / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / intracellular signal transduction / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / 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 superfamily / Basic-leucine zipper domain
Similarity search - Domain/homology
General control transcription factor GCN4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 2.25 Å
AuthorsGonzalez Junior, L. / Woolfson, D.N. / Alber, T.
Citation
Journal: Nat.Struct.Biol. / Year: 1996
Title: Buried polar residues and structural specificity in the GCN4 leucine zipper.
Authors: Gonzalez Jr., L. / Woolfson, D.N. / Alber, T.
#1: Journal: Nat.Struct.Biol. / Year: 1996
Title: An Engineered Allosteric Switch in Leucine-Zipper Oligomerization
Authors: Gonzalez Junior, L. / Plecs, J.J. / Alber, T.
#2: Journal: Nature / Year: 1994
Title: Crystal Structure of an Isoleucine-Zipper Trimer
Authors: Harbury, P.B. / Kim, P.S. / Alber, T.
#3: Journal: Science / Year: 1993
Title: A Switch between Two-, Three-, and Four-Stranded Coiled Coils in GCN4 Leucine Zipper Mutants
Authors: Harbury, P.B. / Zhang, T. / Kim, P.S. / Alber, T.
#4: 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.
History
DepositionOct 30, 1996Processing site: BNL
Revision 1.0Jul 7, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Other
Category: database_2 / pdbx_database_status / struct_ref_seq_dif
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_ref_seq_dif.details
Revision 1.4Feb 14, 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: GENERAL CONTROL PROTEIN GCN4
B: GENERAL CONTROL PROTEIN GCN4


Theoretical massNumber of molelcules
Total (without water)8,0392
Polymers8,0392
Non-polymers00
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-19 kcal/mol
Surface area4670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.250, 30.790, 22.020
Angle α, β, γ (deg.)90.00, 95.57, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein/peptide GENERAL CONTROL PROTEIN GCN4 / GCN4


Mass: 4019.690 Da / Num. of mol.: 2 / Mutation: N16Q
Source method: isolated from a genetically manipulated source
Details: THIS STRUCTURE IS IN THE DIMERIC STATE
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P03069
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 44 %
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlpeptide1drop
250 mM1reservoirNaPO4
30.4 M1reservoirNaBr
42.5 %PEG14501reservoir

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Data collection

Diffraction sourceSource: SEALED TUBE / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Sep 1, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 2627 / % possible obs: 65 % / Observed criterion σ(I): 2 / Redundancy: 1.8 % / Rmerge(I) obs: 0.086
Reflection
*PLUS
Highest resolution: 2.25 Å / Lowest resolution: 6 Å / Num. measured all: 4794

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Processing

Software
NameClassification
TNTrefinement
R-AXISdata reduction
R-AXISdata scaling
RefinementResolution: 2.25→6 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.174 -
obs-2627
Refinement stepCycle: LAST / Resolution: 2.25→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms512 0 0 32 544
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.01
X-RAY DIFFRACTIONt_angle_deg1.7
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.174
Solvent computation
*PLUS
Displacement parameters
*PLUS

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