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- PDB-2dgc: GCN4 BASIC DOMAIN, LEUCINE ZIPPER COMPLEXED WITH ATF/CREB SITE DNA -

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Basic information

Entry
Database: PDB / ID: 2dgc
TitleGCN4 BASIC DOMAIN, LEUCINE ZIPPER COMPLEXED WITH ATF/CREB SITE DNA
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 / BASIC DOMAIN / LEUCINE ZIPPER / DNA BINDING / EUKARYOTIC REGULATORY PROTEIN / 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 / SYNCHROTRON / Resolution: 2.2 Å
AuthorsKeller, W. / Koenig, P. / Richmond, T.J.
Citation
Journal: J.Mol.Biol. / Year: 1995
Title: Crystal structure of a bZIP/DNA complex at 2.2 A: determinants of DNA specific recognition.
Authors: Keller, W. / Konig, P. / Richmond, T.J.
#1: Journal: 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: Koenig, P. / Richmond, T.J.
#2: 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.
History
DepositionSep 28, 1995Deposition site: BNL / Processing site: BNL
Revision 1.0Mar 8, 1996Provider: 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 ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)13,1962
Polymers13,1962
Non-polymers00
Water82946
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)26,3934
Polymers26,3934
Non-polymers00
Water724
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, 86.880
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: SYMMETRY THE CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS PRESENTED BELOW GENERATE THE SUBUNITS OF THE POLYMERIC MOLECULE. APPLIED TO RESIDUES: A 229 .. 277 APPLIED TO RESIDUES: B -10 .. 9 SYMMETRY1 1 0.000000 -1.000000 0.000000 117.32000 SYMMETRY2 1 -1.000000 0.000000 0.000000 117.32000 SYMMETRY3 1 0.000000 0.000000 -1.000000 43.44000

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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: 7375.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P03069
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAMINO ACID NUMBERING (RESIDUE NUMBER) CORRESPONDS TO THE 281 AMINO ACIDS OF INTACT GCN4. RESIDUE ...AMINO ACID NUMBERING (RESIDUE NUMBER) CORRESPONDS TO THE 281 AMINO ACIDS OF INTACT GCN4. RESIDUE NUMBERING OF NUCLEOTIDES: 5' T G G A G A T G A C G T C A T C T -10 -9 -8 -7 -6 -5 -4 -3 -2 -1 1 2 3 4 5 6 7 C C 3' 8 9

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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: 2.78 Å3/Da / Density % sol: 55.82 %
Crystal growMethod: vapor diffusion / pH: 4.6 / Details: pH 4.60, VAPOR DIFFUSION
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2PEG 600011
3MGCL211
4NA CITRATE11
5NA AZIDE11
Crystal grow
*PLUS
Method: unknown / pH: 4.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDChemical formulaSol-IDDetails
10.2 mMprotein DNA complex1
25 mM1MgCl2
310 %PEG600012
430 mMsodium citrate12pH4.6
550 mMsodium acetate12
65 mM1MgCl22
71 mM1NaN32

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.92 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.2→15 Å / Num. obs: 6597 / % possible obs: 80.8 % / Observed criterion σ(F): 3 / Redundancy: 5 % / Rmerge(I) obs: 0.09
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 15 Å / % possible obs: 80.8 % / Observed criterion σ(F): 3

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Processing

Software
NameClassification
X-PLORrefinement
OSCREFdata reduction
OSCKRUNCHdata reduction
RefinementResolution: 2.2→6 Å / σ(F): 3
RfactorNum. reflection% reflection
Rfree0.316 --
Rwork0.214 --
obs0.214 5576 80.7 %
Displacement parametersBiso mean: 41.3 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: LAST / Resolution: 2.2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms427 386 0 46 859
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d
X-RAY DIFFRACTIONx_bond_d_na0.022
X-RAY DIFFRACTIONx_bond_d_prot0.006
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_angle_deg_na3.64
X-RAY DIFFRACTIONx_angle_deg_prot1.13
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
Xplor fileSerial no: 1 / Param file: PARAM11.DNA
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 6 Å / σ(F): 3
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 41.3 Å2

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