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- PDB-5t01: Human c-Jun DNA binding domain homodimer in complex with methylat... -

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Basic information

Entry
Database: PDB / ID: 5t01
TitleHuman c-Jun DNA binding domain homodimer in complex with methylated DNA
Components
  • DNA (5'-D(*AP*AP*TP*GP*GP*AP*(5CM)P*GP*AP*GP*TP*CP*AP*TP*AP*GP*GP*AP*G)-3')
  • DNA (5'-D(P*CP*TP*CP*CP*TP*AP*TP*GP*AP*CP*TP*CP*GP*TP*CP*CP*AP*T)-3')
  • Transcription factor AP-1
KeywordsTRANSCRIPTION REGULATOR/DNA / Zta / Zebra / BZLF-1 / AP-1 / Epstein-Barr virus / EBV / 5-methylcytosine / 5mC / DNA methylation / transcription factor / basic leucine-zipper / bZIP / TRANSCRIPTION REGULATOR-DNA complex
Function / homology
Function and homology information


cAMP response element binding / transcription factor AP-1 complex / integrated stress response signaling / positive regulation of DNA-templated transcription initiation / release from viral latency / WNT5:FZD7-mediated leishmania damping / SMAD protein signal transduction / positive regulation by host of viral transcription / nuclear chromosome / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models ...cAMP response element binding / transcription factor AP-1 complex / integrated stress response signaling / positive regulation of DNA-templated transcription initiation / release from viral latency / WNT5:FZD7-mediated leishmania damping / SMAD protein signal transduction / positive regulation by host of viral transcription / nuclear chromosome / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / negative regulation of DNA binding / Activation of the AP-1 family of transcription factors / ubiquitin-like protein ligase binding / R-SMAD binding / general transcription initiation factor binding / negative regulation by host of viral transcription / positive regulation of vascular associated smooth muscle cell proliferation / cellular response to cadmium ion / response to endoplasmic reticulum stress / GTPase activator activity / transforming growth factor beta receptor signaling pathway / Regulation of PTEN gene transcription / TP53 Regulates Transcription of DNA Repair Genes / FCERI mediated MAPK activation / MAPK6/MAPK4 signaling / euchromatin / Pre-NOTCH Transcription and Translation / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of miRNA transcription / Activation of anterior HOX genes in hindbrain development during early embryogenesis / cellular response to reactive oxygen species / RNA polymerase II transcription regulator complex / sequence-specific double-stranded DNA binding / Signaling by ALK fusions and activated point mutants / regulation of cell population proliferation / Senescence-Associated Secretory Phenotype (SASP) / DNA-binding transcription activator activity, RNA polymerase II-specific / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of cell cycle / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / enzyme binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
Transcription factor Jun / Jun-like transcription factor / Jun-like transcription factor / bZIP transcription factor / Transcription factor, Skn-1-like, DNA-binding 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 ...Transcription factor Jun / Jun-like transcription factor / Jun-like transcription factor / bZIP transcription factor / Transcription factor, Skn-1-like, DNA-binding 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Transcription factor Jun
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsHong, S. / Horton, J.R. / Cheng, X.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Methyl-dependent and spatial-specific DNA recognition by the orthologous transcription factors human AP-1 and Epstein-Barr virus Zta.
Authors: Hong, S. / Wang, D. / Horton, J.R. / Zhang, X. / Speck, S.H. / Blumenthal, R.M. / Cheng, X.
History
DepositionAug 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1May 3, 2017Group: Database references
Revision 1.2Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
C: DNA (5'-D(P*CP*TP*CP*CP*TP*AP*TP*GP*AP*CP*TP*CP*GP*TP*CP*CP*AP*T)-3')
D: DNA (5'-D(*AP*AP*TP*GP*GP*AP*(5CM)P*GP*AP*GP*TP*CP*AP*TP*AP*GP*GP*AP*G)-3')
A: Transcription factor AP-1
B: Transcription factor AP-1


Theoretical massNumber of molelcules
Total (without water)26,8464
Polymers26,8464
Non-polymers00
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7000 Å2
ΔGint-42 kcal/mol
Surface area15190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.871, 42.490, 45.167
Angle α, β, γ (deg.)90.00, 98.01, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 5706.697 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*AP*AP*TP*GP*GP*AP*(5CM)P*GP*AP*GP*TP*CP*AP*TP*AP*GP*GP*AP*G)-3')


Mass: 5956.901 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein Transcription factor AP-1 / Activator protein 1 / AP1 / Proto-oncogene c-Jun / V-jun avian sarcoma virus 17 oncogene homolog / p39


Mass: 7591.038 Da / Num. of mol.: 2 / Fragment: DNA binding domain (UNP residues 254-315) / Mutation: C269S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: JUN / Production host: Escherichia coli (E. coli) / References: UniProt: P05412
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.81 Å3/Da / Density % sol: 56.25 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.05 M Citric acid 0.05 M Bis-Tris propane 16% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Feb 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.89→35 Å / Num. obs: 23735 / % possible obs: 98.5 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 20.3
Reflection shellResolution: 1.89→1.96 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.63 / % possible all: 90.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PHENIX1.9_1692model building
SERGUIdata collection
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FOS

1fos


Resolution: 1.89→27.75 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2271 1187 5.01 %
Rwork0.1931 --
obs0.1949 23712 97.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.89→27.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1012 758 0 120 1890
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141861
X-RAY DIFFRACTIONf_angle_d1.3742638
X-RAY DIFFRACTIONf_dihedral_angle_d23.914802
X-RAY DIFFRACTIONf_chiral_restr0.058296
X-RAY DIFFRACTIONf_plane_restr0.007205
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8896-1.97550.32261310.2982485X-RAY DIFFRACTION87
1.9755-2.07970.29081470.26952777X-RAY DIFFRACTION98
2.0797-2.20990.28351500.24032858X-RAY DIFFRACTION100
2.2099-2.38040.28511510.22482872X-RAY DIFFRACTION100
2.3804-2.61980.27341500.2382849X-RAY DIFFRACTION100
2.6198-2.99850.24971520.23362875X-RAY DIFFRACTION100
2.9985-3.77630.22921510.17982875X-RAY DIFFRACTION100
3.7763-27.75310.17671550.14962934X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -24.4193 Å / Origin y: 16.7252 Å / Origin z: 20.1421 Å
111213212223313233
T0.369 Å2-0.0006 Å2-0.067 Å2-0.3422 Å20.0003 Å2--0.3577 Å2
L0.4259 °20.3658 °2-0.0501 °2-0.3155 °20.6462 °2--0.3373 °2
S0.081 Å °-0.0335 Å °-0.0295 Å °0.2442 Å °-0.0105 Å °-0.2212 Å °0.0741 Å °0.1651 Å °0.0061 Å °
Refinement TLS groupSelection details: all

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