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- PDB-1dgc: THE X-RAY STRUCTURE OF THE GCN4-BZIP BOUND TO ATF/CREB SITE DNA S... -

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Basic information

Entry
Database: PDB / ID: 1dgc
TitleTHE X-RAY STRUCTURE OF THE GCN4-BZIP BOUND TO ATF/CREB SITE DNA SHOWS THE COMPLEX DEPENDS ON DNA FLEXIBILITY
Components
  • DNA (5'-D(*TP*GP*GP*AP*GP*AP*TP*GP*AP*CP*GP*TP*CP*AP*TP*CP*T P*CP*C)-3')
  • PROTEIN (GCN4)
KeywordsTRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / DOUBLE HELIX / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


protein localization to nuclear periphery / FCERI mediated MAPK activation / 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 / Oxidative Stress Induced Senescence / TFIID-class transcription factor complex binding ...protein localization to nuclear periphery / FCERI mediated MAPK activation / 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 / Oxidative Stress Induced Senescence / TFIID-class transcription factor complex binding / positive regulation of RNA polymerase II transcription preinitiation complex assembly / positive regulation of transcription initiation by RNA polymerase II / amino acid biosynthetic process / 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 / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / 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 / Classic Zinc Finger / 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 / 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: 3 Å
AuthorsKoenig, P. / Richmond, T.J.
CitationJournal: J.Mol.Biol. / Year: 1993
Title: The X-ray structure of the GCN4-bZIP bound to ATF/CREB site DNA shows the complex depends on DNA flexibility.
Authors: Konig, P. / Richmond, T.J.
History
DepositionJul 15, 1993Deposition site: BNL / Processing site: BNL
Revision 1.0Jun 22, 1994Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)13,0652
Polymers13,0652
Non-polymers00
Water00
1
B: DNA (5'-D(*TP*GP*GP*AP*GP*AP*TP*GP*AP*CP*GP*TP*CP*AP*TP*CP*T P*CP*C)-3')
A: PROTEIN (GCN4)

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


Theoretical massNumber of molelcules
Total (without water)26,1304
Polymers26,1304
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_775-y+2,-x+2,-z+1/21
Unit cell
Length a, b, c (Å)58.660, 58.660, 86.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsTHE ASYMMETRIC UNIT CONTAINS ONE HALF OF PROTEIN/DNA COMPLEX PER ASYMMETRIC UNIT. MOLECULAR DYAD AXIS OF PROTEIN DIMER AND PALINDROMIC HALF SITES OF THE DNA COINCIDES WITH CRYSTALLOGRAPHIC TWO-FOLD AXIS. THE FULL PROTEIN/DNA COMPLEX CAN BE OBTAINED BY APPLYING THE FOLLOWING TRANSFORMATION MATRIX AND TRANSLATION VECTOR TO THE COORDINATES X Y Z: 0 -1 0 X 117.32 X SYMM -1 0 0 Y + 117.32 = Y SYMM 0 0 -1 Z 43.33 Z SYMM

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Components

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


Mass: 5820.771 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Protein PROTEIN (GCN4)


Mass: 7244.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P03069
Sequence detailsAMINO ACIDS NUMBERING (RESIDUE NUMBER) CORRESPONDS TO THE 281 AMINO ACIDS OF INTACT GCN4.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density meas: 1.28 Mg/m3 / Density % sol: 56.14 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.25
Details: pH 5.25, VAPOR DIFFUSION, HANGING DROP, temperature 277.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2PEG 600011
3NA CITRATE11
4CACL211
5WATER12
6PEG 600012
7NA CITRATE12
8CACL212
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.2-0.4 mMprotein1drop
2oligonucleotide1drop
315 mMsodium citrate1drop
415 mM1dropCaCl2
59 %(w/v)PEG60001drop
630 mMsodium citrate1reservoir
730 mM1reservoirCaCl2
818 %PEG60001reservoir

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Data collection

ReflectionResolution: 3→20 Å
Reflection
*PLUS
Highest resolution: 3 Å / Lowest resolution: 20 Å / % possible obs: 99 % / Rmerge(I) obs: 0.09

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 3→10 Å / σ(F): 3
RfactorNum. reflection% reflection
Rwork0.216 --
obs0.216 3296 98.2 %
Refinement stepCycle: LAST / Resolution: 3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms456 386 0 0 842
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
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_deg3.86
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 10 Å / Num. reflection obs: 3296 / σ(F): 3 / Rfactor obs: 0.216
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.86

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