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- PDB-1gd2: CRYSTAL STRUCTURE OF BZIP TRANSCRIPTION FACTOR PAP1 BOUND TO DNA -

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Basic information

Entry
Database: PDB / ID: 1gd2
TitleCRYSTAL STRUCTURE OF BZIP TRANSCRIPTION FACTOR PAP1 BOUND TO DNA
Components
  • DNA (5'-D(*AP*GP*GP*TP*TP*AP*CP*GP*TP*AP*AP*CP*C)-3')
  • TRANSCRIPTION FACTOR PAP1
Keywordstranscription/DNA / basic leucine zipper / protein-DNA complex / transcription-DNA COMPLEX
Function / homology
Function and homology information


: / chromatin-protein adaptor activity / chromatin => GO:0000785 / DNA binding, bending / RNA polymerase II transcription regulator complex / cellular response to oxidative stress / DNA-binding transcription activator activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II ...: / chromatin-protein adaptor activity / chromatin => GO:0000785 / DNA binding, bending / RNA polymerase II transcription regulator complex / cellular response to oxidative stress / DNA-binding transcription activator activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus / cytosol / cytoplasm
Similarity search - Function
Transcription factor PAP1 / Yap1 redox domain superfamily / Transcription factor PAP1 / bZIP transcription factor / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces ...Transcription factor PAP1 / Yap1 redox domain superfamily / Transcription factor PAP1 / bZIP transcription factor / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / AP-1-like transcription factor
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsFujii, Y. / Shimizu, T. / Toda, T. / Yanagida, M. / Hakoshima, T.
Citation
Journal: Nat.Struct.Biol. / Year: 2000
Title: Structural basis for the diversity of DNA recognition by bZIP transcription factors.
Authors: Fujii, Y. / Shimizu, T. / Toda, T. / Yanagida, M. / Hakoshima, T.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Crystallographic characterization of Pap1-DNA complex
Authors: Fujii, Y. / Ohira, T. / Kyogoku, Y. / Toda, T. / Yanagida, M. / Hakoshima, T.
History
DepositionAug 25, 2000Deposition site: PDBJ / Processing site: NDB
Revision 1.0Oct 2, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: 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: DNA (5'-D(*AP*GP*GP*TP*TP*AP*CP*GP*TP*AP*AP*CP*C)-3')
B: DNA (5'-D(*AP*GP*GP*TP*TP*AP*CP*GP*TP*AP*AP*CP*C)-3')
C: DNA (5'-D(*AP*GP*GP*TP*TP*AP*CP*GP*TP*AP*AP*CP*C)-3')
D: DNA (5'-D(*AP*GP*GP*TP*TP*AP*CP*GP*TP*AP*AP*CP*C)-3')
E: TRANSCRIPTION FACTOR PAP1
F: TRANSCRIPTION FACTOR PAP1
G: TRANSCRIPTION FACTOR PAP1
H: TRANSCRIPTION FACTOR PAP1
I: TRANSCRIPTION FACTOR PAP1
J: TRANSCRIPTION FACTOR PAP1


Theoretical massNumber of molelcules
Total (without water)66,04710
Polymers66,04710
Non-polymers00
Water14,970831
1
A: DNA (5'-D(*AP*GP*GP*TP*TP*AP*CP*GP*TP*AP*AP*CP*C)-3')
B: DNA (5'-D(*AP*GP*GP*TP*TP*AP*CP*GP*TP*AP*AP*CP*C)-3')
E: TRANSCRIPTION FACTOR PAP1
F: TRANSCRIPTION FACTOR PAP1


Theoretical massNumber of molelcules
Total (without water)24,6664
Polymers24,6664
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: DNA (5'-D(*AP*GP*GP*TP*TP*AP*CP*GP*TP*AP*AP*CP*C)-3')
D: DNA (5'-D(*AP*GP*GP*TP*TP*AP*CP*GP*TP*AP*AP*CP*C)-3')
G: TRANSCRIPTION FACTOR PAP1
H: TRANSCRIPTION FACTOR PAP1


Theoretical massNumber of molelcules
Total (without water)24,6664
Polymers24,6664
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
I: TRANSCRIPTION FACTOR PAP1
J: TRANSCRIPTION FACTOR PAP1


Theoretical massNumber of molelcules
Total (without water)16,7152
Polymers16,7152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)240.910, 240.910, 43.870
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Cell settingrhombohedral
Space group name H-MH3
DetailsThe biological assmbly is a dimer constructed from chain E and F, chain G and H, and chain I and J.

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Components

#1: DNA chain
DNA (5'-D(*AP*GP*GP*TP*TP*AP*CP*GP*TP*AP*AP*CP*C)-3')


Mass: 3975.611 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: Protein
TRANSCRIPTION FACTOR PAP1 / AP-1-LIKE TRANSCRIPTION FACTOR


Mass: 8357.505 Da / Num. of mol.: 6 / Fragment: LEUCINE ZIPPER DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Plasmid: PET3A / Production host: Escherichia coli (E. coli) / References: UniProt: Q01663
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 831 / 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: 3.67 Å3/Da / Density % sol: 66.52 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: PEG 6000, KCl, MES, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1MES11
2KCl11
3PEG 600011
4PEG 600012
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDCrystal-ID
11
21
31
41

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-C / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 12, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→45.6 Å / Num. all: 127588 / Num. obs: 53501 / % possible obs: 83.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 2.4 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 10.3
Reflection shellResolution: 2→2.07 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.244 / Num. unique all: 3856 / % possible all: 60.2
Reflection shell
*PLUS
% possible obs: 60.2 %

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Processing

Software
NameVersionClassification
MLPHAREphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.253 5430 10 %RANDOM
Rwork0.23 ---
obs-53446 83.3 %-
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2400 1056 0 831 4287
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1
X-RAY DIFFRACTIONx_torsion_deg18.88
X-RAY DIFFRACTIONx_torsion_impr_deg1.277
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 42.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.28

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