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- PDB-9z1p: Backbone Modification in the GCN4 Leucine Zipper: Prototype -

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Basic information

Entry
Database: PDB / ID: 9z1p
TitleBackbone Modification in the GCN4 Leucine Zipper: Prototype
ComponentsGeneral control transcription factor GCN4
KeywordsTRANSCRIPTION / coiled coil / backbone modification
Function / homology
Function and homology information


FCERI mediated MAPK activation / protein localization to nuclear periphery / Activation of the AP-1 family of transcription factors / negative regulation of ribosomal protein gene transcription by RNA polymerase II / response to amino acid starvation / positive regulation of cellular response to amino acid starvation / mediator complex binding / Oxidative Stress Induced Senescence / TFIID-class transcription factor complex binding / amino acid biosynthetic process ...FCERI mediated MAPK activation / protein localization to nuclear periphery / Activation of the AP-1 family of transcription factors / negative regulation of ribosomal protein gene transcription by RNA polymerase II / response to amino acid starvation / positive regulation of cellular response to amino acid starvation / mediator complex binding / Oxidative Stress Induced Senescence / TFIID-class transcription factor complex binding / amino acid biosynthetic process / positive regulation of RNA polymerase II transcription preinitiation complex assembly / positive regulation of transcription initiation by RNA polymerase II / cellular response to nutrient levels / cellular response to amino acid starvation / RNA polymerase II transcription regulator complex / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / sequence-specific DNA binding / RNA polymerase II-specific DNA-binding transcription factor 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 / Basic-leucine zipper domain superfamily
Similarity search - Domain/homology
General control transcription factor GCN4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsPage, G.E. / Lin, Y. / Horne, W.S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM149220 United States
National Science Foundation (NSF, United States)CHE 2216178 United States
Citation
Journal: Biochemistry / Year: 2026
Title: Manipulating the Unfolded State of a Folded Protein through Site-Specific Backbone Modification.
Authors: Page, G.E. / Lin, Y. / Horne, W.S.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionNov 4, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2026Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: General control transcription factor GCN4
B: General control transcription factor GCN4


Theoretical massNumber of molelcules
Total (without water)8,0412
Polymers8,0412
Non-polymers00
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-17 kcal/mol
Surface area5080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.178, 30.434, 27.824
Angle α, β, γ (deg.)90.000, 96.931, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11B-138-

HOH

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Components

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


Mass: 4020.680 Da / Num. of mol.: 2 / Fragment: leucine zipper domain / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P03069
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.04 Å3/Da / Density % sol: 39.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.2 M sodium acetate pH 4.5, 0.1 M sodium citrate pH 5.6, 10% w/v PEG 3350
PH range: 4.5-5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER IMUS 3.0 MICROFOCUS / Wavelength: 1.54184 Å
DetectorType: Bruker PHOTON III / Detector: PIXEL / Date: Mar 28, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 8725 / % possible obs: 99.8 % / Redundancy: 6.3 % / Biso Wilson estimate: 14.79 Å2 / Rrim(I) all: 0.053 / Net I/σ(I): 26.1
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 3.5 / Num. unique obs: 1389 / Rrim(I) all: 0.442 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→23.91 Å / SU ML: 0.217 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.1941
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2295 873 10.01 %
Rwork0.1881 7850 -
obs0.1922 8723 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.84 Å2
Refinement stepCycle: LAST / Resolution: 1.6→23.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms545 0 0 77 622
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084580
X-RAY DIFFRACTIONf_angle_d0.9326782
X-RAY DIFFRACTIONf_chiral_restr0.048987
X-RAY DIFFRACTIONf_plane_restr0.0073101
X-RAY DIFFRACTIONf_dihedral_angle_d14.7222242
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.70.26321440.22551299X-RAY DIFFRACTION99.59
1.7-1.830.28161430.22291286X-RAY DIFFRACTION99.93
1.83-2.020.27241450.19311298X-RAY DIFFRACTION100
2.02-2.310.21021450.1751314X-RAY DIFFRACTION99.93
2.31-2.910.21391450.18251298X-RAY DIFFRACTION100
2.91-23.910.21861510.18211355X-RAY DIFFRACTION99.6

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