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- PDB-1ysa: THE GCN4 BASIC REGION LEUCINE ZIPPER BINDS DNA AS A DIMER OF UNIN... -

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Basic information

Entry
Database: PDB / ID: 1ysa
TitleTHE GCN4 BASIC REGION LEUCINE ZIPPER BINDS DNA AS A DIMER OF UNINTERRUPTED ALPHA HELICES: CRYSTAL STRUCTURE OF THE PROTEIN-DNA COMPLEX
Components
  • DNA (5'-D(*AP*AP*AP*CP*TP*GP*GP*AP*TP*GP*AP*GP*TP*CP*AP*TP*A P*GP*GP*A)-3')
  • DNA (5'-D(*TP*TP*CP*CP*TP*AP*TP*GP*AP*CP*TP*CP*AP*TP*CP*CP*A P*GP*TP*T)-3')
  • PROTEIN (GCN4)
KeywordsTRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / DOUBLE HELIX / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


FCERI mediated MAPK activation / protein localization to nuclear periphery / Activation of the AP-1 family of transcription factors / response to amino acid starvation / negative regulation of ribosomal protein gene transcription by RNA polymerase II / 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 / response to amino acid starvation / negative regulation of ribosomal protein gene transcription by RNA polymerase II / 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 / Classic Zinc Finger / 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 / Double Stranded RNA Binding Domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / General control transcription factor GCN4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 2.9 Å
AuthorsEllenberger, T.E. / Brandl, C.J. / Struhl, K. / Harrison, S.C.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 1992
Title: The GCN4 basic region leucine zipper binds DNA as a dimer of uninterrupted alpha helices: crystal structure of the protein-DNA complex.
Authors: Ellenberger, T.E. / Brandl, C.J. / Struhl, K. / Harrison, S.C.
#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
DepositionAug 9, 1993Deposition site: BNL / Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*TP*TP*CP*CP*TP*AP*TP*GP*AP*CP*TP*CP*AP*TP*CP*CP*A P*GP*TP*T)-3')
B: DNA (5'-D(*AP*AP*AP*CP*TP*GP*GP*AP*TP*GP*AP*GP*TP*CP*AP*TP*A P*GP*GP*A)-3')
C: PROTEIN (GCN4)
D: PROTEIN (GCN4)


Theoretical massNumber of molelcules
Total (without water)26,0504
Polymers26,0504
Non-polymers00
Water30617
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.130, 88.540, 59.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: TWO ADENINES, B 22 AND B 23, ARE NEAR THE 5-PRIME END OF DNA CHAIN B AND ARE LOOPED OUT OF THE DNA HELIX. THIS CONFORMATION IS PRESENT IN CRYSTALS THAT WERE SOAKED IN 35% (VOL/VOL) POLYETHYLENE ...1: TWO ADENINES, B 22 AND B 23, ARE NEAR THE 5-PRIME END OF DNA CHAIN B AND ARE LOOPED OUT OF THE DNA HELIX. THIS CONFORMATION IS PRESENT IN CRYSTALS THAT WERE SOAKED IN 35% (VOL/VOL) POLYETHYLENE GLYCOL MW 400, FOLLOWED BY RAPID FREEZING AND X-RAY DATA COLLECTION AT -155 DEGREES CENTIGRADE.

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Components

#1: DNA chain DNA (5'-D(*TP*TP*CP*CP*TP*AP*TP*GP*AP*CP*TP*CP*AP*TP*CP*CP*A P*GP*TP*T)-3')


Mass: 6034.915 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*AP*AP*AP*CP*TP*GP*GP*AP*TP*GP*AP*GP*TP*CP*AP*TP*A P*GP*GP*A)-3')


Mass: 6231.067 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein PROTEIN (GCN4)


Mass: 6892.072 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P03069
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.4 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.75
Details: pH 5.75, VAPOR DIFFUSION, HANGING DROP, temperature 295.00K TWO ADENINES, B22 AND B23, WHICH ARE NEAR THE 5-PRIME END OF DNA CHAIN B ARE LOOPED OUT OF THE DNA HELIX. THIS CONFORMATION IS ...Details: pH 5.75, VAPOR DIFFUSION, HANGING DROP, temperature 295.00K TWO ADENINES, B22 AND B23, WHICH ARE NEAR THE 5-PRIME END OF DNA CHAIN B ARE LOOPED OUT OF THE DNA HELIX. THIS CONFORMATION IS PRESENT IN CRYSTALS THAT WERE SOAKED IN 35% (VOL/VOL) POLYETHYLENE GLYCOL MW 400, FOLLOWED BY RAPID FREEZING AND X-RAY DATA COLLECTION AT -155 DEG. CENTIGRADE.
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2PEG 40011
3NACL11
4MGCL211
5MES11
6SPERMINE_HCL11
7WATER12
8PEG 40012
9WATER13
10PEG 40013
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion
Details: well solution contains twice the concentrations of salts and PEG400
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.95 mMpGCNK58 monomer1drop
20.57 mMDNA1drop
30.15 M1dropNaCl
40.03 M1dropMgCl2
50.025 M1drop
61 mMspermine-HCL1drop
712 %(v/v)PEG4001drop
81
91
101

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Data collection

DiffractionMean temperature: 118 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-13
DetectorType: SIEMENS-NICOLET / Detector: AREA DETECTOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.9→8 Å / Num. obs: 5289 / % possible obs: 96 % / Observed criterion σ(F): 1.5 / Rmerge(I) obs: 0.099
Reflection
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 8 Å / Observed criterion σ(F): 1.5 / Num. measured all: 21237 / Rmerge(I) obs: 0.099

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Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 2.9→8 Å / σ(F): 1.5 /
RfactorNum. reflection
obs0.23 5289
Refinement stepCycle: LAST / Resolution: 2.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms941 814 0 17 1772
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.023
X-RAY DIFFRACTIONt_angle_deg3.3
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Refinement
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 8 Å / Num. reflection obs: 5289 / Rfactor obs: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg3.3

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