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- PDB-5vpe: Transcription factor FosB/JunD bZIP domain in complex with cognat... -

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Basic information

Entry
Database: PDB / ID: 5vpe
TitleTranscription factor FosB/JunD bZIP domain in complex with cognate DNA, type-I crystal
Components
  • DNA (5'-D(*CP*GP*TP*CP*GP*GP*TP*GP*AP*CP*TP*CP*AP*CP*CP*GP*AP*CP*G)-3')
  • DNA (5'-D(*CP*GP*TP*CP*GP*GP*TP*GP*AP*GP*TP*CP*AP*CP*CP*GP*AP*CP*G)-3')
  • Protein fosB
  • Transcription factor jun-D
Keywordstranscription/dna / activator protein-1 / basic leucine zipper / bZIP / fos / jun / transcription factor / DNA-binding protein / redox switch / coiled-coil / transcription-dna complex
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 / 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 ...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 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
PHOSPHATE ION / DNA / DNA (> 10) / Transcription factor JunD / Protein FosB
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.053 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Protein fosB
D: Transcription factor jun-D
G: DNA (5'-D(*CP*GP*TP*CP*GP*GP*TP*GP*AP*CP*TP*CP*AP*CP*CP*GP*AP*CP*G)-3')
H: DNA (5'-D(*CP*GP*TP*CP*GP*GP*TP*GP*AP*GP*TP*CP*AP*CP*CP*GP*AP*CP*G)-3')
A: Protein fosB
B: Transcription factor jun-D
E: DNA (5'-D(*CP*GP*TP*CP*GP*GP*TP*GP*AP*CP*TP*CP*AP*CP*CP*GP*AP*CP*G)-3')
F: DNA (5'-D(*CP*GP*TP*CP*GP*GP*TP*GP*AP*GP*TP*CP*AP*CP*CP*GP*AP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,89326
Polymers55,8208
Non-polymers1,07218
Water4,107228
1
C: Protein fosB
D: Transcription factor jun-D
G: DNA (5'-D(*CP*GP*TP*CP*GP*GP*TP*GP*AP*CP*TP*CP*AP*CP*CP*GP*AP*CP*G)-3')
H: DNA (5'-D(*CP*GP*TP*CP*GP*GP*TP*GP*AP*GP*TP*CP*AP*CP*CP*GP*AP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,43013
Polymers27,9104
Non-polymers5209
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8550 Å2
ΔGint-83 kcal/mol
Surface area14770 Å2
MethodPISA
2
A: Protein fosB
B: Transcription factor jun-D
E: DNA (5'-D(*CP*GP*TP*CP*GP*GP*TP*GP*AP*CP*TP*CP*AP*CP*CP*GP*AP*CP*G)-3')
F: DNA (5'-D(*CP*GP*TP*CP*GP*GP*TP*GP*AP*GP*TP*CP*AP*CP*CP*GP*AP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,46313
Polymers27,9104
Non-polymers5529
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8230 Å2
ΔGint-59 kcal/mol
Surface area15120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.479, 90.755, 105.618
Angle α, β, γ (deg.)90.000, 117.930, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 4 molecules CADB

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


Mass: 8267.290 Da / Num. of mol.: 2 / 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.: 2 / 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

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DNA chain , 2 types, 4 molecules GEHF

#3: DNA chain DNA (5'-D(*CP*GP*TP*CP*GP*GP*TP*GP*AP*CP*TP*CP*AP*CP*CP*GP*AP*CP*G)-3')


Mass: 5806.749 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: DNA chain DNA (5'-D(*CP*GP*TP*CP*GP*GP*TP*GP*AP*GP*TP*CP*AP*CP*CP*GP*AP*CP*G)-3')


Mass: 5846.772 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 5 types, 246 molecules

#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 228 / 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: 4.42 Å3/Da / Density % sol: 72.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.9 M Na2HPO4 and 24% (v/v) ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 16, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.06→50 Å / Num. obs: 58932 / % possible obs: 98.3 % / Redundancy: 6.1 % / Biso Wilson estimate: 24.63 Å2 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.024 / Rrim(I) all: 0.06 / Χ2: 0.927 / Net I/σ(I): 15.9 / Num. measured all: 357830
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.06-2.15.90.93129330.6110.4141.0220.89498.2
2.1-2.135.90.80129250.6920.3550.8780.88597.8
2.13-2.175.80.70429440.7720.3180.7750.87198.4
2.17-2.225.40.55228710.8620.2570.6110.87597
2.22-2.275.40.43628850.8810.2040.4830.9496.6
2.27-2.326.20.38929590.9340.1680.4250.85698.7
2.32-2.386.20.30529460.9610.1320.3330.94898.7
2.38-2.446.30.23829380.9750.1020.260.89598.6
2.44-2.516.10.17629270.9790.0770.1920.87698.8
2.51-2.660.13929580.9860.0610.1520.86399
2.6-2.695.60.11529400.9880.0530.1270.91898
2.69-2.85.90.09529100.9880.0430.1050.91597.3
2.8-2.926.50.07829760.9930.0330.0850.91199.2
2.92-3.086.40.06329890.9960.0270.0680.9899.5
3.08-3.276.40.05929500.9960.0280.0661.00398.9
3.27-3.525.90.05129310.9960.0240.0560.98797.2
3.52-3.886.50.04829680.9940.0210.0530.99498.7
3.88-4.446.60.04129790.9970.0170.0450.99599.6
4.44-5.596.10.03629750.9980.0150.0390.96797.8
5.59-506.40.04330280.9950.0190.0470.94198.2

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Processing

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

1fos


Resolution: 2.053→47.307 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2537 2000 3.77 %
Rwork0.2177 51064 -
obs0.2191 53064 87.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 159.95 Å2 / Biso mean: 41.4457 Å2 / Biso min: 7.9 Å2
Refinement stepCycle: final / Resolution: 2.053→47.307 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2182 1470 129 230 4011
Biso mean--77.16 33.82 -
Num. residues----339
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053990
X-RAY DIFFRACTIONf_angle_d0.7475638
X-RAY DIFFRACTIONf_chiral_restr0.036631
X-RAY DIFFRACTIONf_plane_restr0.003479
X-RAY DIFFRACTIONf_dihedral_angle_d20.7712289
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0534-2.10480.3857660.29981695176141
2.1048-2.16170.29271010.28642557265862
2.1617-2.22530.26691100.26552834294469
2.2253-2.29710.25951300.24753306343679
2.2971-2.37920.30431460.24583743388990
2.3792-2.47450.29781580.24254046420497
2.4745-2.58710.2651610.23654093425499
2.5871-2.72350.26741590.23784050420997
2.7235-2.89410.27161600.24364118427899
2.8941-3.11750.26111630.23554142430599
3.1175-3.43120.26681600.20874072423298
3.4312-3.92740.20521600.18434091425197
3.9274-4.94730.22071640.17324179434399
4.9473-47.31940.25241620.21454138430097
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)
10.2029-0.1862-0.4450.3370.50595.2113-0.011-0.04020.14820.0443-0.2117-0.0562-0.23050.21770.00790.3168-0.22530.09210.2768-0.18440.245-32.0801-7.5777108.0989
22.48730.7289-3.35420.5752-1.36775.8853-0.0330.12380.1009-0.03830.0488-0.09950.01840.294-0.00250.2881-0.12910.10870.1672-0.06660.1999-35.7705-15.8024107.2282
32.7642-1.51821.87952.340.14842.8762-0.2058-0.95710.13870.7872-0.0938-1.075-0.50020.6880.32530.3576-0.1276-0.23390.8998-0.1340.8181-26.1541-10.2071138.9993
42.28421.67910.24962.5184-0.2042.5993-0.0238-0.06050.3703-0.09050.2280.0097-0.27630.0245-0.13990.2623-0.0190.0010.1197-0.07910.3091-49.1441-12.4087129.4877
52.77152.172-3.93662.1733-3.26866.3532-0.92271.1372-0.3351-1.05650.2965-0.8724-0.28460.18590.57470.2983-0.14120.03670.3840.01640.3817-66.2743-14.1117116.5837
64.21931.26142.14591.54130.40912.85970.0303-0.2597-0.16610.01480.1912-0.20560.07070.0366-0.20560.247-0.0482-0.00780.0968-0.04780.2968-50.5709-13.364129.7484
72-2.8768-0.65011.2678-1.35685.3534-0.02920.43490.0486-0.02770.1895-0.6126-0.15380.7049-0.18450.3391-0.0778-0.24581.1868-0.01041.1278-21.3751-14.5701133.759
84.18171.3138-4.2020.5811-1.4214.2043-0.0516-0.243-0.4667-0.0381-0.19820.06070.19680.10980.34260.3288-0.15230.09460.2792-0.03470.2621-71.8272-38.374588.126
91.2824-0.4764-2.63560.31931.17246.56410.16170.0726-0.0563-0.06830.0972-0.02850.0294-0.2619-0.19930.3397-0.15550.10290.3337-0.00650.2021-68.7005-29.529590.0838
101.525-0.39811.02722.213-0.43721.1399-0.0510.3177-0.3131-0.40970.04740.86440.0699-0.7569-0.08350.4383-0.1064-0.35880.8737-0.09480.6444-100.2146-37.4599100.5874
117.39780.97571.63113.15151.44741.61060.1302-0.0338-0.3902-0.03570.26120.06120.269-0.0209-0.30830.2472-0.1077-0.00390.26510.03130.2417-79.4712-33.3521113.2224
122.39921.12750.95782.39462.09911.8411-0.15650.8209-0.6007-0.9810.2438-0.0445-0.57690.2847-0.07290.4228-0.0232-0.08940.2832-0.06430.2407-59.1488-30.7201119.9631
134.4002-1.48035.9583.71930.16759.5321-0.3759-0.2658-0.09260.2721-0.11720.3243-0.4751-0.66790.48550.2125-0.1114-0.02920.4041-0.03330.2937-66.3794-30.3006124.5962
146.221.5244-0.03933.17242.04021.9069-0.12510.37660.144-0.21260.05480.2388-0.1432-0.21020.2180.2731-0.1765-0.03670.33960.05780.2453-84.8997-33.5654109.8931
153.66520.52013.05580.55420.85433.9154-0.18620.48540.1234-0.35070.2517-0.0978-0.09430.4112-0.04040.5732-0.065-0.40561.097-0.02470.7281-99.4154-32.976393.5124
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'C' and (resid 153 through 218 )C153 - 218
2X-RAY DIFFRACTION2chain 'D' and (resid 265 through 331 )D265 - 331
3X-RAY DIFFRACTION3chain 'G' and (resid 2 through 6 )G2 - 6
4X-RAY DIFFRACTION4chain 'G' and (resid 7 through 16 )G7 - 16
5X-RAY DIFFRACTION5chain 'G' and (resid 17 through 19 )G17 - 19
6X-RAY DIFFRACTION6chain 'H' and (resid 1 through 15 )H1 - 15
7X-RAY DIFFRACTION7chain 'H' and (resid 16 through 18 )H16 - 18
8X-RAY DIFFRACTION8chain 'A' and (resid 152 through 218 )A152 - 218
9X-RAY DIFFRACTION9chain 'B' and (resid 265 through 331 )B265 - 331
10X-RAY DIFFRACTION10chain 'E' and (resid 2 through 6 )E2 - 6
11X-RAY DIFFRACTION11chain 'E' and (resid 7 through 16 )E7 - 16
12X-RAY DIFFRACTION12chain 'E' and (resid 17 through 19 )E17 - 19
13X-RAY DIFFRACTION13chain 'F' and (resid 1 through 5 )F1 - 5
14X-RAY DIFFRACTION14chain 'F' and (resid 6 through 15 )F6 - 15
15X-RAY DIFFRACTION15chain 'F' and (resid 16 through 18 )F16 - 18

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