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- PDB-1u2u: Nmr solution structure of a designed heterodimeric leucine zipper -

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Basic information

Entry
Database: PDB / ID: 1u2u
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 / ELECTROSTATIC INTERACTIONS
MethodSOLUTION NMR / DISTANCE GEOMETRY, REGULARIZATION, SIMULATED ANNEALING, MOLECULAR DYNAMICS SIMULATION IN VACUO
AuthorsMarti, D.N. / Bosshard, H.R.
Citation
Journal: Biochemistry / Year: 2004
Title: Inverse electrostatic effect: electrostatic repulsion in the unfolded state stabilizes a leucine zipper.
Authors: Marti, D.N. / Bosshard, H.R.
#1: Journal: J.Mol.Biol. / Year: 2003
Title: Electrostatic interactions in leucine zippers: thermodynamic analysis of the contributions of Glu and His residues and the effect of mutating salt bridges
Authors: Marti, D.N. / Bosshard, H.R.
#2: 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.
History
DepositionJul 20, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 5, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: 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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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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)6,9892
Polymers6,9892
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)27 / 50structures with the least restraint violations, structures with the lowest energy, low deviation of experimental pKa values from pKa derived by continuum electrostatics calculations on structures
RepresentativeModel #25closest to the average

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Components

#1: Protein/peptide General control protein GCN4


Mass: 3480.719 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Synthetic peptide based on the sequence of the leucine zipper domain in GCN4 (baker's yeast)
#2: Protein/peptide General control protein GCN4


Mass: 3508.238 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: synthetic peptide based on the sequence of the leucine zipper domain in GCN4 (baker's yeast)
Has protein modificationY

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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
1412D 1H-15N HSQC
1512D 1H-13C HSQC
NMR detailsText: STRUCTURE WAS DETERMINED USING STANDARD 2D NMR TECHNIQUES

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Sample preparation

DetailsContents: 2.6mM, 90% H2O, 10% D2O / Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 10mM / pH: 5.7 / Pressure: AMBIENT / Temperature: 310.00 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3Brukercollection
Felix2000Accelrysdata analysis
CNS1.1structure solution
PROCHECK3.4.4Laskowskidata analysis
WHAT IF19991018Vrienddata analysis
CNS1.1refinement
RefinementMethod: DISTANCE GEOMETRY, REGULARIZATION, SIMULATED ANNEALING, MOLECULAR DYNAMICS SIMULATION IN VACUO
Software ordinal: 1
Details: STRUCTURES WERE CALCULATED ON THE BASIS OF 1246 NOE DERIVED DISTANCE CONSTRAINTS AND 44 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, low deviation of experimental pKa values from pKa derived by continuum electrostatics ...Conformer selection criteria: structures with the least restraint violations, structures with the lowest energy, low deviation of experimental pKa values from pKa derived by continuum electrostatics calculations on structures
Conformers calculated total number: 50 / Conformers submitted total number: 27

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