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- PDB-5vpa: Transcription factor FosB/JunD bZIP domain -

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Basic information

Entry
Database: PDB / ID: 5vpa
TitleTranscription factor FosB/JunD bZIP domain
Components
  • Protein fosB
  • Transcription factor jun-D
KeywordsTRANSCRIPTION / activator protein-1 / basic leucine zipper / bZIP / fos / jun / transcription factor / DNA-binding protein / redox switch / coiled-coil
Function / homology
Function and homology information


transcription factor AP-1 complex / positive regulation of peroxisome proliferator activated receptor signaling pathway / NGF-stimulated transcription / positive regulation of macrophage activation / cellular response to fatty acid / response to steroid hormone / osteoblast development / response to morphine / response to corticosterone / response to light stimulus ...transcription factor AP-1 complex / positive regulation of peroxisome proliferator activated receptor signaling pathway / NGF-stimulated transcription / positive regulation of macrophage activation / cellular response to fatty acid / response to steroid hormone / osteoblast development / response to morphine / response to corticosterone / response to light stimulus / response to cAMP / response to mechanical stimulus / positive regulation of osteoblast differentiation / cellular response to hormone stimulus / behavioral response to cocaine / transcription repressor complex / cellular response to calcium ion / response to progesterone / response to amphetamine / nuclear receptor binding / transcription coregulator binding / response to nicotine / female pregnancy / protein-DNA complex / circadian rhythm / response to peptide hormone / RNA polymerase II transcription regulator complex / sequence-specific double-stranded DNA binding / regulation of cell population proliferation / DNA-binding transcription activator activity, RNA polymerase II-specific / response to ethanol / response to lipopolysaccharide / cellular response to hypoxia / transcription regulator complex / Estrogen-dependent gene expression / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription coactivator activity / transcription cis-regulatory region binding / regulation of cell cycle / RNA polymerase II cis-regulatory region sequence-specific DNA binding / response to xenobiotic stimulus / intracellular membrane-bounded organelle / regulation of transcription by RNA polymerase II / chromatin / enzyme binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
AP-1 transcription factor / 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. ...AP-1 transcription factor / 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 / Basic-leucine zipper domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcription factor JunD / Protein FosB
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.83 Å
AuthorsYin, Z. / Machius, M. / Rudenko, G.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)R01 DA040621 United States
Brain and Behavior Research Foundation United States
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Activator Protein-1: redox switch controlling structure and DNA-binding.
Authors: Yin, Z. / Machius, M. / Nestler, E.J. / Rudenko, G.
History
DepositionMay 4, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Database references / Category: citation
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 15, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 11, 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
Revision 1.5Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein fosB
B: Transcription factor jun-D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3154
Polymers16,2572
Non-polymers582
Water905
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-35 kcal/mol
Surface area8890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.605, 95.352, 98.200
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Protein fosB / G0/G1 switch regulatory protein 3


Mass: 8267.290 Da / Num. of mol.: 1 / Fragment: unp residues 153-219
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FOSB, G0S3 / Plasmid: pET21-NESG / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) / References: UniProt: P53539
#2: Protein Transcription factor jun-D


Mass: 7989.425 Da / Num. of mol.: 1 / Fragment: unp residues 266-332
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: JUND / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) / References: UniProt: P17535
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.79 Å3/Da / Density % sol: 67.52 % / Description: thin plates
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 3 M 1,6-Hexanediol, 50 mM Tris pH 8.5 and 5 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.999 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 13, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 2.83→34.204 Å / Num. obs: 6010 / % possible obs: 100 % / Redundancy: 9.5 % / Biso Wilson estimate: 32.12 Å2 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.033 / Rrim(I) all: 0.102 / Χ2: 0.976 / Net I/σ(I): 25
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.83-2.859.51.1672.20.8260.391.2321.049100
2.85-2.99.41.0620.8550.3581.1221.006100
2.9-2.969.80.8630.9210.2840.911.003100
2.96-3.0210.20.8860.9350.2840.9311.056100
3.02-3.0810.10.7260.9510.2360.7641.024100
3.08-3.159.90.8530.9230.2810.8991.001100
3.15-3.239.80.5410.9750.1770.570.976100
3.23-3.329.30.4490.9730.1510.4740.933100
3.32-3.428.90.3560.980.1230.3771.012100
3.42-3.539.30.2730.9930.0920.2890.989100
3.53-3.659.50.190.9920.0640.2011.049100
3.65-3.810.10.1450.9920.0480.1530.976100
3.8-3.979.80.0980.9980.0320.1030.934100
3.97-4.189.80.0850.9980.0270.0890.957100
4.18-4.4490.0730.9980.0250.0770.996100
4.44-4.799.10.060.9990.020.0630.921100
4.79-5.2710.20.0570.9990.0190.060.907100
5.27-6.039.60.0750.9980.0250.0790.825100
6.03-7.598.60.0530.9990.0180.0570.894100
7.59-34.2048.70.0610.9920.0220.0651.00999.7

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FOS

1fos


Resolution: 2.83→34.204 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.57
RfactorNum. reflection% reflection
Rfree0.2828 433 9.8 %
Rwork0.2446 --
obs0.2484 4417 71.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 185.72 Å2 / Biso mean: 66.4615 Å2 / Biso min: 4.48 Å2
Refinement stepCycle: final / Resolution: 2.83→34.204 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms879 0 2 5 886
Biso mean--46.79 14.68 -
Num. residues----112
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006903
X-RAY DIFFRACTIONf_angle_d0.6851209
X-RAY DIFFRACTIONf_chiral_restr0.029144
X-RAY DIFFRACTIONf_plane_restr0.003158
X-RAY DIFFRACTIONf_dihedral_angle_d13.159599
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8297-3.23890.3372760.271569977539
3.2389-4.07960.27841450.24931374151974
4.0796-34.20690.27462120.235919112123100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.80591.2732-0.64824.44980.85791.80380.52910.0036-0.83530.43380.16410.07690.8482-0.369-0.52230.3855-0.1781-0.09610.377-0.07370.78893.95419.4427285.432
22.7939-1.8837-2.63944.74934.46826.6989-0.09060.1695-0.11820.2003-0.07470.3608-0.0351-0.29750.21930.09250.0763-0.07690.4611-0.10440.123-2.121827.1751317.0291
31.1253-0.3911-1.45631.02851.122.6817-0.08070.1284-0.0127-0.10530.0882-0.0019-0.11310.1051-0.24180.0746-0.05660.09410.4294-0.0305-0.05686.769124.593308.7369
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 164 through 177 )A164 - 177
2X-RAY DIFFRACTION2chain 'A' and (resid 178 through 217 )A178 - 217
3X-RAY DIFFRACTION3chain 'B' and (resid 275 through 332 )B275 - 332

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