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- PDB-1gcl: GCN4 LEUCINE ZIPPER CORE MUTANT P-LI -

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Basic information

Entry
Database: PDB / ID: 1gcl
TitleGCN4 LEUCINE ZIPPER CORE MUTANT P-LI
ComponentsGCN4
KeywordsLEUCINE ZIPPER / HYDROPHOBIC CORE MUTANT
Function / homology
Function and homology information


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 ...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 / transcription regulator complex / sequence-specific DNA binding / RNA polymerase II-specific DNA-binding transcription factor 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 / 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: 2.1 Å
AuthorsHarbury, P.B. / Zhang, T. / Kim, P.S. / Alber, T.
Citation
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.
#1: Journal: Science / Year: 1991
Title: X-Ray Structure of the GCN4 Leucine Zipper, a Two-Stranded, Parallel Coiled Coil
Authors: Shea, E.K. / Klemm, J.D. / Kim, P.S. / Alber, T.
#2: Journal: Science / Year: 1989
Title: Evidence that the Leucine Zipper is a Coiled Coil
Authors: Shea, E.K. / Rutkowski, R. / Kim, P.S.
History
DepositionOct 20, 1993Processing site: BNL
Revision 1.0Jun 3, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 24, 2013Group: Other
Revision 1.4Jun 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 / 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_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 23, 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
B: GCN4
C: GCN4
D: GCN4


Theoretical massNumber of molelcules
Total (without water)16,2914
Polymers16,2914
Non-polymers00
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6970 Å2
ΔGint-59 kcal/mol
Surface area7480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.432, 48.634, 51.765
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide
GCN4


Mass: 4072.837 Da / Num. of mol.: 4 / Mutation: L5I,V9L,L12I,N16L,L19I,V23L,L26I,V30L
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.: 77 / 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: 1.83 Å3/Da / Density % sol: 32.89 %
Crystal grow
*PLUS
pH: 3 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlpeptide1drop
2100 mMsodium acetate1drop
385 mMammonium sulfate1drop
410 %PEG14001drop
510 %isopropanol1drop
6100 mMsodium acetate1reservoir

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Data collection

Diffraction sourceWavelength: 1.54
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: 1992
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionNum. obs: 5643 / % possible obs: 73 % / Observed criterion σ(I): 2
Reflection
*PLUS
Highest resolution: 2.1 Å / Rmerge(I) obs: 0.07

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Processing

Software
NameClassification
X-PLORmodel building
TNTrefinement
X-PLORrefinement
R-AXISdata reduction
X-PLORphasing
RefinementHighest resolution: 2.1 Å / σ(F): 5 /
RfactorNum. reflection
obs0.152 5266
Displacement parametersBiso mean: 40 Å2
Refinement stepCycle: LAST / Highest resolution: 2.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1060 0 0 77 1137
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.018
X-RAY DIFFRACTIONt_angle_deg2.9
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

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