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- PDB-1rb4: ANTIPARALLEL TRIMER OF GCN4-LEUCINE ZIPPER CORE MUTANT AS N16A TE... -

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Basic information

Entry
Database: PDB / ID: 1rb4
TitleANTIPARALLEL TRIMER OF GCN4-LEUCINE ZIPPER CORE MUTANT AS N16A TETRAGONAL AUTOMATIC SOLUTION
ComponentsGeneral control protein GCN4
KeywordsDNA BINDING PROTEIN / COILED COIL / LEUCINE ZIPPER / AUTOMATION
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
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsHolton, J. / Alber, T.
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
DepositionNov 1, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 27, 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 1.5Feb 14, 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
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-39 kcal/mol
Surface area6170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.947, 64.947, 78.012
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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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 PEPTIDE IS NATURALLY FOUND IN SACCHAROMYCES CEREVISIAE. THE PEPTIDE WAS CHEMICALLY SYNTHESIZED.
References: UniProt: P03069
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 3.44 Å3/Da / Density % sol: 75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: 25 mM phosphate pH 7.3 400 mM NaCl 15% PEG8000, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mg/mlprotein1drop
225 mMphosphaye1reservoirpH7.0
312 %(w/v)PEG14501reservoir
4400 mM1reservoirNaBr

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 0.9795 / Wavelength: 1.0688, 0.9800, 0.9797, 0.9795, 0.9322
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 11, 1998
RadiationMonochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
21.06881
30.981
40.97971
50.93221
ReflectionResolution: 1.8→45 Å / Num. obs: 15956 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.8→1.9 Å / % possible all: 74.8
Reflection
*PLUS
% possible obs: 97 % / Redundancy: 17.7 % / Rmerge(I) obs: 0.081
Reflection shell
*PLUS
% possible obs: 82.8 % / Redundancy: 12 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 5.7

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
REFMAC26/11/99refinement
CCP4(SCALA)data scaling
ELVESphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→45 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.307 809 5.2 %RANDOM
Rwork0.202 ---
all0.206 13638 --
obs0.204 13638 --
Displacement parametersBiso mean: 44 Å2
Refinement stepCycle: LAST / Resolution: 1.9→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms762 0 0 157 919
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_angle_deg1.8
Software
*PLUS
Name: REFMAC / Version: 4 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.009
X-RAY DIFFRACTIONp_angle_deg0.9

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