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- PDB-5fv8: Structure of cJun-FosW coiled coil complex. -

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Basic information

Entry
Database: PDB / ID: 5fv8
TitleStructure of cJun-FosW coiled coil complex.
Components
  • CJUN
  • FOSW
KeywordsSTRUCTURAL PROTEIN / COILED COIL DOMAIN / AP-1 / BZIP
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 / negative regulation of DNA binding / response to steroid hormone ...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 / negative regulation of DNA binding / response to steroid hormone / nuclear chromosome / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / Activation of the AP-1 family of transcription factors / R-SMAD binding / ubiquitin-like protein ligase binding / general transcription initiation factor binding / negative regulation by host of viral transcription / positive regulation of vascular associated smooth muscle cell proliferation / transforming growth factor beta receptor signaling pathway / GTPase activator activity / response to endoplasmic reticulum stress / Regulation of PTEN gene transcription / TP53 Regulates Transcription of DNA Repair Genes / FCERI mediated MAPK activation / euchromatin / MAPK6/MAPK4 signaling / Pre-NOTCH Transcription and Translation / positive regulation of miRNA transcription / DNA-binding transcription repressor activity, RNA polymerase II-specific / Activation of anterior HOX genes in hindbrain development during early embryogenesis / 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 / DNA-binding transcription activator activity, RNA polymerase II-specific / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / Estrogen-dependent gene expression / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / 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 / regulation of transcription by RNA polymerase II / chromatin / 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 / : / 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
Similarity search - Domain/homology
Chem-JEF / Transcription factor Jun
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsZaccai, N.R. / Mason, J.M. / Brady, R.L.
CitationJournal: To be Published
Title: Helix-Constrained Fos-Based Peptides Inhibit Oncogenic Activator Protein-1 and Cancer Cell Proliferation
Authors: Baxter, D. / Perry, S.R. / Hill, T.A. / Kok, W.M. / Zaccai, N.R. / Brady, R.L. / Fairlie, D.P. / Mason, J.M.
History
DepositionFeb 3, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FOSW
B: FOSW
D: CJUN
E: CJUN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3037
Polymers17,0154
Non-polymers1,2883
Water2,216123
1
A: FOSW
E: CJUN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,7034
Polymers8,5082
Non-polymers1,1962
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: FOSW
D: CJUN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,6003
Polymers8,5082
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.820, 63.820, 190.630
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11E-1038-

JEF

21A-2037-

HOH

31E-2029-

HOH

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Components

#1: Protein/peptide FOSW


Mass: 4387.873 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: SYNTHESIZED PEPTIDE / Source: (synth.) HOMO SAPIENS (human)
#2: Protein/peptide CJUN


Mass: 4119.718 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: SYNTHESIZED PEPTIDE / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P05412*PLUS
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-JEF / O-(O-(2-AMINOPROPYL)-O'-(2-METHOXYETHYL)POLYPROPYLENE GLYCOL 500) / JEFFAMINE


Mass: 597.822 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H63NO10
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsO-(O-(2-AMINOPROPYL)-O'-(2-METHOXYETHYL)POLYPROPYLENE GLYCOL 500) (JEF): PARTIALLY DISORDERED IN ...O-(O-(2-AMINOPROPYL)-O'-(2-METHOXYETHYL)POLYPROPYLENE GLYCOL 500) (JEF): PARTIALLY DISORDERED IN STRUCTURE. MOLECULE FROM CRYSTALLISATION BUFFER.
Sequence detailsFOSW SEQUENCE DERIVED FROM HUMAN CFOS SEQUENCE

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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: 2.85 Å3/Da / Density % sol: 56.87 % / Description: NONE
Crystal growpH: 7
Details: 1.1M SODIUM MALONATE DIBASIC MONOHYDRATE, 0.1M HEPES PH 7.00 AND 5% V/V JEFFAMINE ED-2003.

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949
DetectorType: DECTRIS PIXEL / Detector: PIXEL / Date: Aug 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.99→47.66 Å / Num. obs: 13418 / % possible obs: 96.2 % / Observed criterion σ(I): 2 / Redundancy: 17.4 % / Biso Wilson estimate: 29.11 Å2 / Rmerge(I) obs: 0.02 / Net I/σ(I): 19.7
Reflection shellResolution: 1.99→2.04 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.5 / % possible all: 78.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A02

1a02


Resolution: 1.99→47.657 Å / SU ML: 0.3 / σ(F): 0.03 / Phase error: 31.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2464 1180 4.8 %
Rwork0.2086 --
obs0.2105 13377 95.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.9 Å2
Refinement stepCycle: LAST / Resolution: 1.99→47.657 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1124 0 35 123 1282
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071171
X-RAY DIFFRACTIONf_angle_d0.9771558
X-RAY DIFFRACTIONf_dihedral_angle_d20.114736
X-RAY DIFFRACTIONf_chiral_restr0.039180
X-RAY DIFFRACTIONf_plane_restr0.003203
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9903-2.08080.48341290.44892408X-RAY DIFFRACTION80
2.0808-2.19050.41931140.38612828X-RAY DIFFRACTION91
2.1905-2.32780.36111480.31963008X-RAY DIFFRACTION98
2.3278-2.50750.30741180.24613121X-RAY DIFFRACTION100
2.5075-2.75980.24051490.2173049X-RAY DIFFRACTION99
2.7598-3.15910.24752030.19623005X-RAY DIFFRACTION100
3.1591-3.97980.21341660.15363062X-RAY DIFFRACTION100
3.9798-47.67110.17611530.15713077X-RAY DIFFRACTION100

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