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- PDB-7ucd: Transcription factor FosB/JunD bZIP domain covalently modified wi... -

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Basic information

Entry
Database: PDB / ID: 7ucd
TitleTranscription factor FosB/JunD bZIP domain covalently modified with the cysteine-targeting alpha-haloketone compound Z2159931480
Components
  • Protein fosB
  • Transcription factor jun-D
KeywordsDNA BINDING PROTEIN / FosB / JunD / redox switch / redox sensor / transcription factor
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 / transcription regulator complex / cellular response to hypoxia / 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 / : / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper ...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 / : / 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
7-acetyl-4-methoxy-1-benzofuran-3(2H)-one / Transcription factor JunD / Protein FosB
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.21 Å
AuthorsKumar, A. / Machius, M.C. / Rudenko, G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)R01DA040621 United States
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: Chemically targeting the redox switch in AP1 transcription factor Delta FOSB.
Authors: Kumar, A. / Aglyamova, G. / Yim, Y.Y. / Bailey, A.O. / Lynch, H.M. / Powell, R.T. / Nguyen, N.D. / Rosenthal, Z. / Zhao, W.N. / Li, Y. / Chen, J. / Fan, S. / Lee, H. / Russell, W.K. / ...Authors: Kumar, A. / Aglyamova, G. / Yim, Y.Y. / Bailey, A.O. / Lynch, H.M. / Powell, R.T. / Nguyen, N.D. / Rosenthal, Z. / Zhao, W.N. / Li, Y. / Chen, J. / Fan, S. / Lee, H. / Russell, W.K. / Stephan, C. / Robison, A.J. / Haggarty, S.J. / Nestler, E.J. / Zhou, J. / Machius, M. / Rudenko, G.
History
DepositionMar 16, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
F: Protein fosB
J: Transcription factor jun-D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6057
Polymers16,2572
Non-polymers3485
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-34 kcal/mol
Surface area10330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.260, 67.670, 122.943
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11F-302-

CL

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Components

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


Mass: 8267.290 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FOSB, G0S3 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / Variant (production host): D3 / 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 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / Variant (production host): D3 / References: UniProt: P17535
#3: Chemical ChemComp-MV0 / 7-acetyl-4-methoxy-1-benzofuran-3(2H)-one


Mass: 206.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H10O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
Has ligand of interestY
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: 3.28 Å3/Da / Density % sol: 62.53 % / Description: Diamond shaped, size 200-300 micrometer
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 100 mM Tris HCl pH 7.0, 40% (v/v) Ethanol / Temp details: Room Temperature

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Apr 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.446→44.923 Å / Num. obs: 3060 / % possible obs: 84.9 % / Redundancy: 7.2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.216 / Rpim(I) all: 0.085 / Rrim(I) all: 0.233 / Net I/σ(I): 6.7
Reflection shellResolution: 2.446→2.779 Å / Redundancy: 7 % / Rmerge(I) obs: 2.605 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 191 / CC1/2: 0.664 / Rpim(I) all: 1.019 / Rrim(I) all: 2.804 / % possible all: 72.7

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
XDSdata reduction
STARANISOdata scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VPF, poly-alanine

5vpf


Resolution: 3.21→35.05 Å / SU ML: 0.4022 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.932
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3297 191 7.6 %
Rwork0.2804 2323 -
obs0.2845 2514 71.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.65 Å2
Refinement stepCycle: LAST / Resolution: 3.21→35.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1017 0 19 0 1036
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00871037
X-RAY DIFFRACTIONf_angle_d1.09041387
X-RAY DIFFRACTIONf_chiral_restr0.0417164
X-RAY DIFFRACTIONf_plane_restr0.0077192
X-RAY DIFFRACTIONf_dihedral_angle_d5.2757158
LS refinement shellResolution: 3.21→35.05 Å
RfactorNum. reflection% reflection
Rfree0.3297 191 -
Rwork0.2804 2323 -
obs--71.24 %
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)
10.966422683901-0.08925083352990.3119163566942.08905536935-0.6644020282781.53770314862-0.191083509236-0.1089316360310.0536819154592-0.0762546897373-0.0978079845936-0.0557166407393-0.127048261566-0.0580653342312-0.8195315574120.2752896820810.0824787899237-0.04383338139440.008346481128460.03894784436680.435905894909-0.91195843608718.140711486714.5482757905
20.2751430536130.11121210304-0.05953695437490.635098793826-0.4144017835891.1881620486-0.278024220651-0.0206657690076-0.244366793421-0.117312918878-0.13773753020.2222785544260.3452911887180.00782181155017-1.53510549760.4544256346150.0553837839847-0.01062527519250.1832746506240.2550581654310.663395173911-7.3308558163512.475013478814.334045343
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'F' and (resid 154 through 217 )FA154 - 2171 - 64
22chain 'J' and (resid 265 through 332 )JC265 - 3321 - 68

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