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- PDB-1fmh: NMR SOLUTION STRUCTURE OF A DESIGNED HETERODIMERIC LEUCINE ZIPPER -

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Basic information

Entry
Database: PDB / ID: 1fmh
TitleNMR SOLUTION STRUCTURE OF A DESIGNED HETERODIMERIC LEUCINE ZIPPER
Components(GENERAL CONTROL PROTEIN GCN4) x 2
KeywordsTRANSCRIPTION / COILED COIL / LEUCINE ZIPPER / INTER-HELICAL ION PAIRING
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
MethodSOLUTION NMR / 1. DISTANCE GEOMETRY, REGULARIZATION, 2. SIMULATED ANNEALING, 3. MOLECULAR DYNAMICS SIMULATION INCLUDING 8 ANGSTROMS WATER SHELL
AuthorsMarti, D.N. / Jelesarov, I. / Bosshard, H.R.
Citation
Journal: Biochemistry / Year: 2000
Title: Interhelical ion pairing in coiled coils: solution structure of a heterodimeric leucine zipper and determination of pKa values of Glu side chains.
Authors: Marti, D.N. / Jelesarov, I. / Bosshard, H.R.
#1: Journal: J.Mol.Biol. / Year: 1996
Title: Thermodynamic Characterization of the Coupled Folding and Association of Heterodimeric Coiled Coils (Leucine Zippers)
Authors: Jelesarov, I. / Bosshard, H.R.
#2: Journal: Biochemistry / Year: 1999
Title: Extremely Fast Folding of a Very Stable Leucine Zipper with a Strengthened Hydrophobic Core and Lacking Electrostatic Interactions between Helices
Authors: Durr, E. / Jelesarov, I. / Bosshard, H.R.
History
DepositionAug 17, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / 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_nmr_software.name / _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

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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)7,1112
Polymers7,1112
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 50structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #14closest to the average

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Components

#1: Protein/peptide GENERAL CONTROL PROTEIN GCN4


Mass: 3541.782 Da / Num. of mol.: 1 / Fragment: LEUCINE ZIPPER ACIDIC CHAIN
Mutation: R249E M250V K251A D255K K256E E258A E259Q L260A L261E S262A K263E H266Q N269Q R273Q K275E K276H L277E V278C
Source method: obtained synthetically
Details: SYNTHETIC PEPTIDE BASED ON THE SEQUENCE OF THE LEUCINE ZIPPER DOMAIN IN GCN4 (BAKER'S YEAST)
References: UniProt: P03069
#2: Protein/peptide GENERAL CONTROL PROTEIN GCN4


Mass: 3569.301 Da / Num. of mol.: 1 / Fragment: LEUCINE ZIPPER BASIC CHAIN
Mutation: R249E M250V K251Q Q252A E254K D255K K256R E258Q E259A L261K S262A K263R H266A L267A E268K N269Q E270K A272Q R273A K275R K276H L277K V278C
Source method: obtained synthetically
Details: SYNTHETIC PEPTIDE BASED ON THE SEQUENCE OF THE LEUCINE ZIPPER DOMAIN IN GCN4 (BAKER'S YEAST)
References: UniProt: P03069

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
1212D TOCSY
1312D NOESY
NMR detailsText: STRUCTURE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR TECHNIQUES

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Sample preparation

DetailsContents: 2.1 mM AB zipper; 90% H2O, 10% D2O / Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 10 mM / pH: 5.65 / Pressure: ambient / Temperature: 310 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX8002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6BRUKERcollection
Felix98Molecular Simulations, Inc.processing
X-PLOR3.851Brungerstructure solution
X-PLOR3.851Brungerrefinement
RefinementMethod: 1. DISTANCE GEOMETRY, REGULARIZATION, 2. SIMULATED ANNEALING, 3. MOLECULAR DYNAMICS SIMULATION INCLUDING 8 ANGSTROMS WATER SHELL
Software ordinal: 1
Details: STRUCTURES WERE CALCULATED ON THE BASIS OF 1494 NOE DERIVED DISTANCE CONSTRAINTS AND 52 PHI ANGLE RESTRAINTS
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 25

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