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- PDB-3k7z: GCN4-Leucine zipper core mutant as N16A trigonal automatic solution -

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Basic information

Entry
Database: PDB / ID: 3k7z
TitleGCN4-Leucine zipper core mutant as N16A trigonal automatic solution
ComponentsGeneral control protein GCN4
KeywordsDNA BINDING PROTEIN / COILED COIL / LEUCINE ZIPPER / Structural Genomics / TB Structural Genomics Consortium / TBSGC / Activator / Amino-acid biosynthesis / DNA-binding / Nucleus / Phosphoprotein / Transcription / Transcription regulation
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
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsHolton, J. / Alber, T. / TB Structural Genomics Consortium (TBSGC)
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: Automated Protein Crystal Structure Determination Using Elves.
Authors: Holton, J. / Alber, T.
#1: Journal: Nat.Struct.Biol. / Year: 1996
Title: An Engineered Allosteric Switch in Leucine-Zipper Oligomerization
Authors: Gonzalez Jr., 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 13, 2009Deposition site: RCSB / Processing site: RCSB
SupersessionNov 24, 2009ID: 1RB1
Revision 1.0Nov 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: General control protein GCN4
B: General control protein GCN4
C: General control protein GCN4


Theoretical massNumber of molelcules
Total (without water)11,8883
Polymers11,8883
Non-polymers00
Water11,187621
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-37 kcal/mol
Surface area6130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.943, 89.943, 46.481
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein/peptide General control protein GCN4 / Amino acid biosynthesis regulatory protein


Mass: 3962.639 Da / Num. of mol.: 3 / Fragment: LEUCINE-ZIPPER (RESIDUES 249-281) / Mutation: N16A / Source method: obtained synthetically
Details: THE SEQUENCE OF THE PROTEIN IS NATURALLY FOUND IN SACCHAROMYCES CEREVISIAE. THE PROTEIN WAS SYNTHESIZED BY SOLID PHASE PEPTIDE SYNTHESIS.
References: UniProt: P03069
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 621 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.54 Å3/Da / Density % sol: 75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: 100MM BIS-TRIS buffer only, pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 1.0688, 0.9800, 0.9795, 0.9322
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 5, 1997
RadiationMonochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.06881
20.981
30.97951
40.93221
ReflectionResolution: 1.8→45 Å / Num. all: 23719 / Num. obs: 23195 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11 % / Rmerge(I) obs: 0.097
Reflection shellResolution: 1.8→1.9 Å / % possible all: 98.4

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Processing

Software
NameVersionClassification
SSRLBL1-5data collection
ELVESmodel building
REFMAC4refinement
MOSFLMdata reduction
SCALAdata scaling
ELVESphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→25.96 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: refmac
Details: THIS ENTRY WAS SOLVED USING AUTOMATED STRUCTURE WHILE RELATED ENTRTY 1RB5 WAS SOLVED USING NON-AUTOMATED STRUCTURE DETERMINATION METHOD. THE NUMBER OF CLOSE CONTACTS IN THIS STRUCTURE IS AN ...Details: THIS ENTRY WAS SOLVED USING AUTOMATED STRUCTURE WHILE RELATED ENTRTY 1RB5 WAS SOLVED USING NON-AUTOMATED STRUCTURE DETERMINATION METHOD. THE NUMBER OF CLOSE CONTACTS IN THIS STRUCTURE IS AN ARTIFACT OF THE CURRENT STATE-OF-THE-ART AUTOMATED MODEL BUILDING PROCEDURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.259 861 5.2 %RANDOM
Rwork0.202 ---
all0.204 17020 --
obs0.204 16998 --
Displacement parametersBiso mean: 44 Å2
Refinement stepCycle: LAST / Resolution: 1.9→25.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms719 0 0 621 1340

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