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- PDB-1ce9: HELIX CAPPING IN THE GCN4 LEUCINE ZIPPER -

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Basic information

Entry
Database: PDB / ID: 1ce9
TitleHELIX CAPPING IN THE GCN4 LEUCINE ZIPPER
ComponentsPROTEIN (GCN4-PMSE)
KeywordsHELIX CAPPING / LEUCINE ZIPPER / HYDROGEN BONDING / THERMAL STABILITY / PROTEIN FOLDING
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 / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLu, M. / Shu, W. / Ji, H. / Spek, E. / Wang, L.-Y. / Kallenbach, N.R.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: Helix capping in the GCN4 leucine zipper.
Authors: Lu, M. / Shu, W. / Ji, H. / Spek, E. / Wang, L. / Kallenbach, N.R.
#1: 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
DepositionMar 18, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Mar 25, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: PROTEIN (GCN4-PMSE)
B: PROTEIN (GCN4-PMSE)
C: PROTEIN (GCN4-PMSE)
D: PROTEIN (GCN4-PMSE)


Theoretical massNumber of molelcules
Total (without water)16,1434
Polymers16,1434
Non-polymers00
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: PROTEIN (GCN4-PMSE)
D: PROTEIN (GCN4-PMSE)


Theoretical massNumber of molelcules
Total (without water)8,0712
Polymers8,0712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-18 kcal/mol
Surface area5200 Å2
MethodPISA
3
A: PROTEIN (GCN4-PMSE)
B: PROTEIN (GCN4-PMSE)


Theoretical massNumber of molelcules
Total (without water)8,0712
Polymers8,0712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-18 kcal/mol
Surface area5360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.304, 30.769, 42.884
Angle α, β, γ (deg.)75.41, 79.76, 90.08
Int Tables number1
Space group name H-MP1

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Components

#1: Protein/peptide
PROTEIN (GCN4-PMSE)


Mass: 4035.663 Da / Num. of mol.: 4 / Mutation: R2S,M3V,Q5E / Source method: obtained synthetically / References: UniProt: P03069
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.5 Å3/Da / Density % sol: 50 %
Crystal growpH: 4.6 / Details: SEE REFERENCE, pH 4.6
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlpeptide1drop
20.2 Mammonium acetate1reservoir
30.1 Msodium acetate1reservoir
420 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 1, 1998 / Details: MIRRORS
RadiationMonochromator: SUPPER DOUBLE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 11776 / % possible obs: 92.3 % / Observed criterion σ(I): 3 / Redundancy: 2 % / Rmerge(I) obs: 0.034 / Rsym value: 0.034 / Net I/σ(I): 13.6
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.059 / Mean I/σ(I) obs: 12 / Rsym value: 0.059 / % possible all: 88.7
Reflection
*PLUS
Num. measured all: 23475

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZTA

2zta


Resolution: 1.8→15 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.283 553 5 %RANDOM
Rwork0.214 ---
obs-11523 90.3 %-
Displacement parametersBiso mean: 20.1 Å2
Refinement stepCycle: LAST / Resolution: 1.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1128 0 0 150 1278
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.004
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg0.782
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.77
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.464
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.214
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.77
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.464

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