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- PDB-1t2k: Structure Of The DNA Binding Domains Of IRF3, ATF-2 and Jun Bound... -

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Basic information

Entry
Database: PDB / ID: 1t2k
TitleStructure Of The DNA Binding Domains Of IRF3, ATF-2 and Jun Bound To DNA
Components
  • (31-MER) x 2
  • Cyclic-AMP-dependent transcription factor ATF-2
  • Interferon regulatory factor 3IRF3
  • Transcription factor AP-1AP-1 transcription factor
KeywordsTranscription/DNA / PROTEIN DNA COMPLEX / transcription / Transcription-DNA COMPLEX
Function / homology
Function and homology information


abducens nucleus development / hypoglossal nucleus development / detection of cell density / H4 histone acetyltransferase complex / growth plate cartilage chondrocyte proliferation / facial nucleus development / growth plate cartilage chondrocyte differentiation / positive regulation of cardiac muscle myoblast proliferation / cellular response to anisomycin / positive regulation of transforming growth factor beta2 production ...abducens nucleus development / hypoglossal nucleus development / detection of cell density / H4 histone acetyltransferase complex / growth plate cartilage chondrocyte proliferation / facial nucleus development / growth plate cartilage chondrocyte differentiation / positive regulation of cardiac muscle myoblast proliferation / cellular response to anisomycin / positive regulation of transforming growth factor beta2 production / cAMP response element binding / transcription factor AP-1 complex / cellular lipid metabolic process / leucine zipper domain binding / integrated stress response signaling / positive regulation of DNA-templated transcription initiation / cAMP response element binding protein binding / IRF3 mediated activation of type 1 IFN / MDA-5 signaling pathway / release from viral latency / histone H2B acetyltransferase activity / macrophage apoptotic process / positive regulation of mitochondrial membrane permeability involved in apoptotic process / cellular response to leucine starvation / brainstem development / programmed necrotic cell death / histone H4 acetyltransferase activity / WNT5:FZD7-mediated leishmania damping / NK T cell differentiation / vacuole organization / neurofilament cytoskeleton organization / TRIF-dependent toll-like receptor signaling pathway / apoptotic process involved in development / NGF-stimulated transcription / SMAD protein signal transduction / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / IRF3-mediated induction of type I IFN / positive regulation of type I interferon-mediated signaling pathway / positive regulation by host of viral transcription / intrinsic apoptotic signaling pathway in response to hypoxia / mitotic intra-S DNA damage checkpoint signaling / mRNA transcription / motor neuron apoptotic process / toll-like receptor 4 signaling pathway / response to osmotic stress / TRAF6 mediated IRF7 activation / DNA-binding transcription activator activity / immune system process / nuclear chromosome / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / cellular response to exogenous dsRNA / cytoplasmic pattern recognition receptor signaling pathway / type I interferon-mediated signaling pathway / hepatocyte apoptotic process / negative regulation of DNA binding / outflow tract morphogenesis / Activation of the AP-1 family of transcription factors / ubiquitin-like protein ligase binding / p38MAPK cascade / positive regulation of interferon-alpha production / antiviral innate immune response / R-SMAD binding / Response of EIF2AK4 (GCN2) to amino acid deficiency / general transcription initiation factor binding / white fat cell differentiation / positive regulation of type I interferon production / negative regulation by host of viral transcription / BMP signaling pathway / adipose tissue development / cis-regulatory region sequence-specific DNA binding / hematopoietic progenitor cell differentiation / histone acetyltransferase activity / JNK cascade / lipopolysaccharide-mediated signaling pathway / transcription initiation-coupled chromatin remodeling / positive regulation of vascular associated smooth muscle cell proliferation / cellular response to cadmium ion / TICAM1-dependent activation of IRF3/IRF7 / Regulation of innate immune responses to cytosolic DNA / positive regulation of interferon-beta production / response to endoplasmic reticulum stress / GTPase activator activity / negative regulation of angiogenesis / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / transforming growth factor beta receptor signaling pathway / liver development / Regulation of PTEN gene transcription / Negative regulators of DDX58/IFIH1 signaling / promoter-specific chromatin binding / TP53 Regulates Transcription of DNA Repair Genes / FCERI mediated MAPK activation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / peptidyl-threonine phosphorylation / MAPK6/MAPK4 signaling / DDX58/IFIH1-mediated induction of interferon-alpha/beta / euchromatin / Heme signaling / mRNA transcription by RNA polymerase II / Transcriptional activation of mitochondrial biogenesis / response to organic cyclic compound
Similarity search - Function
Transcription factor cyclic AMP-dependent, CRE-BP1-type / Transcription factor Jun / Jun-like transcription factor / Jun-like transcription factor / Interferon regulatory factor-3 / Interferon-regulatory factor 3 / Interferon-regulatory factor 3 / Interferon regulatory factor, conserved site / IRF tryptophan pentad repeat DNA-binding domain signature. / bZIP transcription factor ...Transcription factor cyclic AMP-dependent, CRE-BP1-type / Transcription factor Jun / Jun-like transcription factor / Jun-like transcription factor / Interferon regulatory factor-3 / Interferon-regulatory factor 3 / Interferon-regulatory factor 3 / Interferon regulatory factor, conserved site / IRF tryptophan pentad repeat DNA-binding domain signature. / bZIP transcription factor / Interferon regulatory factor transcription factor / interferon regulatory factor / IRF tryptophan pentad repeat DNA-binding domain profile. / Interferon regulatory factor DNA-binding domain / Transcription factor, Skn-1-like, DNA-binding domain superfamily / SMAD-like domain superfamily / 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 superfamily / Basic-leucine zipper domain / SMAD/FHA domain superfamily / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Transcription factor Jun / Cyclic AMP-dependent transcription factor ATF-2 / Interferon regulatory factor 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsPanne, D. / Maniatis, T. / Harrison, S.C.
CitationJournal: Embo J. / Year: 2004
Title: Crystal structure of ATF-2/c-Jun and IRF-3 bound to the interferon-beta enhancer.
Authors: Panne, D. / Maniatis, T. / Harrison, S.C.
History
DepositionApr 21, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: 31-MER
F: 31-MER
A: Interferon regulatory factor 3
B: Interferon regulatory factor 3
C: Transcription factor AP-1
D: Cyclic-AMP-dependent transcription factor ATF-2


Theoretical massNumber of molelcules
Total (without water)59,6266
Polymers59,6266
Non-polymers00
Water1448
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)186.380, 65.210, 83.850
Angle α, β, γ (deg.)90.00, 93.44, 90.00
Int Tables number5
Space group name H-MC121

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Components

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DNA chain , 2 types, 2 molecules EF

#1: DNA chain 31-MER


Mass: 9724.338 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: interferon-b enhancer
#2: DNA chain 31-MER


Mass: 9336.002 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: interferon-b enhancer

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Protein , 3 types, 4 molecules ABCD

#3: Protein Interferon regulatory factor 3 / IRF3 / IRF-3


Mass: 13058.792 Da / Num. of mol.: 2 / Fragment: N-terminal DNA binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IRF3 / Plasmid: pTXB3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q14653
#4: Protein Transcription factor AP-1 / AP-1 transcription factor


Mass: 7314.744 Da / Num. of mol.: 1 / Fragment: bZip domain / Mutation: C269S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: JUN / Plasmid: pET21a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P05412
#5: Protein Cyclic-AMP-dependent transcription factor ATF-2 / Activating transcription factor 2 / cAMP response element binding protein CRE- BP1 / HB16


Mass: 7133.292 Da / Num. of mol.: 1 / Fragment: bZip domain / Mutation: C351S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATF2, CREB2, CREBP1 / Plasmid: pET21a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P15336

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Non-polymers , 1 types, 8 molecules

#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 4.5 Å3/Da / Density % sol: 73.4 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM NaCacodylate, pH 6.5, 12.5% (w/v) PEG 6000, 400 mM NH4OAc, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Components of the solutions
IDNameCrystal-IDSol-ID
1NaCacodylate11
2PEG 600011
3NH4OAc11
4H2O11
5PEG 600012
6NaCacodylate12
7H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 23, 2001
Details: Bent triangular asymmetric cut Si(111) monochromater; Rh-coated Si mirror for vertical focussing
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 20151 / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Biso Wilson estimate: 36.5 Å2 / Rsym value: 0.075 / Net I/σ(I): 19.4
Reflection shellResolution: 3→3.19 Å / Mean I/σ(I) obs: 5.7 / Rsym value: 0.413 / % possible all: 94

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IRF and 2DGC

2irf

2dgc


Resolution: 3→29.98 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 2048126.71 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.296 1178 5.8 %RANDOM
Rwork0.257 ---
obs0.257 20140 98.9 %-
all-20364 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 27.1663 Å2 / ksol: 0.280152 e/Å3
Displacement parametersBiso mean: 88 Å2
Baniso -1Baniso -2Baniso -3
1--36.81 Å20 Å26.64 Å2
2---17.53 Å20 Å2
3---54.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.56 Å0.49 Å
Luzzati d res low-30 Å
Luzzati sigma a0.5 Å0.57 Å
Refinement stepCycle: LAST / Resolution: 3→29.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2762 1265 0 8 4035
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.73
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.372 206 6.6 %
Rwork0.413 2934 -
obs--94 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP

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