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- PDB-5iiv: GCN4p pH 1.5 -

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Basic information

Entry
Database: PDB / ID: 5iiv
TitleGCN4p pH 1.5
ComponentsGeneral control protein GCN4
KeywordsTRANSCRIPTION / Supercoil parameters / leucine zipper / salt bridge / closely related NMR structures / conformational transition / electrostatics / knobs-into-holes / canonical alpha helix
Function / homology
Function and homology information


protein localization to nuclear periphery / FCERI mediated MAPK activation / 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 / Oxidative Stress Induced Senescence / TFIID-class transcription factor complex binding ...protein localization to nuclear periphery / FCERI mediated MAPK activation / 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 / Oxidative Stress Induced Senescence / TFIID-class transcription factor complex binding / positive regulation of transcription initiation by RNA polymerase II / positive regulation of RNA polymerase II transcription preinitiation complex assembly / amino acid biosynthetic process / 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 / transcription regulator complex / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of cell cycle / 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)
MethodSOLUTION NMR
AuthorsBrady, M.R. / Kaplan, A.R. / Alexandrescu, A.T.
CitationJournal: Biochemistry / Year: 2017
Title: Nuclear Magnetic Resonance Structures of GCN4p Are Largely Conserved When Ion Pairs Are Disrupted at Acidic pH but Show a Relaxation of the Coiled Coil Superhelix.
Authors: Kaplan, A.R. / Brady, M.R. / Maciejewski, M.W. / Kammerer, R.A. / Alexandrescu, A.T.
History
DepositionMar 1, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2017Group: Database references
Revision 1.2Apr 5, 2017Group: Database references
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)7,6712
Polymers7,6712
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1630 Å2
ΔGint-23 kcal/mol
Surface area5360 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / -
Representative

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Components

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


Mass: 3835.406 Da / Num. of mol.: 2 / Fragment: UNP residues 250-280
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: GCN4, AAS3, ARG9, YEL009C / Production host: Escherichia coli (E. coli) / References: UniProt: P03069

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
114isotropic13D HN(CA)CB
124isotropic12D 1H-15N HSQC
134isotropic13D 1H-15N NOESY
144isotropic13D 1H-13C NOESY
154isotropic13D HNCO
162isotropic12D 1H-15N HSQC
174isotropic12D 15N NOESY
283isotropic23D IF 1H-13C NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution41.5 mM [U-99% 13C; U-99% 15N] GCN4p, 90% H2O/10% D2O190% H2O/10% D2O
solution21.5 mM [U-99% 13C; U-99% 15N] GCN4p, 100% D2O13C, 15N100% D2O
solution31.5 mM 66% - 13C 33%- 12C GCN4p, 100% D2O3100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.5 mMGCN4p[U-99% 13C; U-99% 15N]4
1.5 mMGCN4p[U-99% 13C; U-99% 15N]2
1.5 mMGCN4p66% - 13C 33%- 12C3
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)Details
120 mM11.5 1 atm298 K
220 mMIF-mixed1.5 1 atm298 Ksample consists of mixed dimer where 66% is 13C labelled monomers and 33% is natural abundance (12C) labelled monomers

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Varian INOVAVarianINOVA6001cryogenic probe
Varian VNMRSVarianVNMRS8002cryogenic probe

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Processing

NMR software
NameDeveloperClassification
FelixAccelrys Software Inc.processing
CcpNMRCCPNchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
ARIALinge, O'Donoghue and Nilgesrefinement
NMR ensembleConformers submitted total number: 20

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