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- PDB-7ucc: Transcription factor FosB/JunD bZIP domain in the reduced form -

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Basic information

Entry
Database: PDB / ID: 7ucc
TitleTranscription factor FosB/JunD bZIP domain in the reduced form
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 / NGF-stimulated transcription / response to morphine / osteoblast development / response to corticosterone / behavioral response to cocaine / positive regulation of osteoblast differentiation / response to mechanical stimulus / cellular response to hormone stimulus / response to cAMP ...transcription factor AP-1 complex / NGF-stimulated transcription / response to morphine / osteoblast development / response to corticosterone / behavioral response to cocaine / positive regulation of osteoblast differentiation / response to mechanical stimulus / cellular response to hormone stimulus / response to cAMP / response to amphetamine / cellular response to calcium ion / transcription repressor complex / transcription coregulator binding / response to progesterone / female pregnancy / RNA polymerase II transcription regulator complex / sequence-specific double-stranded DNA binding / regulation of cell population proliferation / gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / response to ethanol / Estrogen-dependent gene expression / transcription regulator complex / transcription by RNA polymerase II / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of cell cycle / response to xenobiotic stimulus / RNA polymerase II cis-regulatory region sequence-specific DNA binding / intracellular membrane-bounded organelle / chromatin / regulation of transcription by RNA polymerase II / 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 / Basic-leucine zipper domain superfamily / Basic-leucine zipper domain
Similarity search - Domain/homology
ETHANOL / Transcription factor JunD / Protein FosB
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 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

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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)16,4327
Polymers16,2572
Non-polymers1755
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-48 kcal/mol
Surface area10860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.939, 70.244, 122.170
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
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

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Protein , 2 types, 2 molecules FJ

#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

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Non-polymers , 4 types, 146 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.16 Å3/Da / Density % sol: 61.12 % / Description: diamond-shaped, size 200-300 micrometers
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 100 mM Tris, 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: Sep 10, 2020
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.94→50 Å / Num. obs: 13357 / % possible obs: 84.1 % / Redundancy: 10.8 % / Biso Wilson estimate: 19.41 Å2 / CC1/2: 0.976 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.02 / Rrim(I) all: 0.07 / Χ2: 0.94 / Net I/σ(I): 9.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.94-1.975.80.3281940.9590.120.3520.78325.1
1.97-2.016.60.333270.9720.1110.350.88841.7
2.01-2.057.10.253790.9910.080.2640.87849
2.05-2.096.90.3134930.9760.1010.330.82261.9
2.09-2.147.50.2865520.9770.0920.3020.88770.6
2.14-2.187.80.2925900.9770.0930.3080.94176.6
2.18-2.248.60.2356180.9890.0730.2470.94779.9
2.24-2.39.20.2366640.9890.0730.2480.95884.1
2.3-2.379.60.2127220.9910.0650.2220.98991.9
2.37-2.4410.40.2057810.9920.0630.2150.97498.5
2.44-2.5311.90.197800.9960.0560.1990.95999.6
2.53-2.6312.10.1677830.9970.050.1740.949100
2.63-2.7511.40.1517820.9950.0470.1580.945100
2.75-2.9120.1118010.9970.0330.1160.969100
2.9-3.0812.70.0887880.9970.0260.0920.994100
3.08-3.3213.60.0788020.9980.0220.0810.992100
3.32-3.6513.30.068060.9980.0170.0620.971100
3.65-4.18130.0498040.9990.0140.0510.88599.5
4.18-5.2611.20.0488150.9960.0150.0510.86299.6
5.26-33.2312.30.0428760.9990.0130.0440.89499.4

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-20002.3.15data reduction
HKL-20002.3.15data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VPF, poly-alanine

5vpf


Resolution: 1.94→33.23 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 31.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2673 565 4.98 %0.05
Rwork0.2045 10770 --
obs0.2077 11335 72.51 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.53 Å2 / Biso mean: 32.4423 Å2 / Biso min: 5.84 Å2
Refinement stepCycle: final / Resolution: 1.94→33.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1073 0 13 152 1238
Biso mean--42.39 31.4 -
Num. residues----132
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.94-2.140.2788570.20421101115830
2.14-2.450.2471230.2012335245864
2.45-3.080.29141840.21573510369495
3.08-33.230.26042010.19973824402599
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)
10.29050.12570.95180.16030.24733.48870.0913-0.0648-0.07620.1886-0.0738-0.01530.10210.0205-0.05460.1177-0.018-0.15040.1401-0.0317-0.0017-16.1493-22.086-13.8265
20.30620.20180.4880.4990.63281.76290.0435-0.01370.04390.01280.00960.03070.0328-0.03520.05190.0454-0.1152-0.05410.1269-0.16240.0865-22.9723-16.5521-14.2495
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'J' and (resid 265 through 332 )J265 - 332
2X-RAY DIFFRACTION2chain 'F' and (resid 155 through 217 )F155 - 217

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