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- PDB-5vpc: Transcription factor FosB/JunD bZIP domain in its oxidized form, ... -

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Basic information

Entry
Database: PDB / ID: 5vpc
TitleTranscription factor FosB/JunD bZIP domain in its oxidized form, type-II crystal
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 / response to peptide hormone / circadian rhythm / 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 / : / 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: 2.498 Å
AuthorsYin, Z. / Machius, M.C. / 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.5Oct 30, 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
C: Protein fosB
D: Transcription factor jun-D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,68910
Polymers32,5134
Non-polymers1756
Water52229
1
A: Protein fosB
B: Transcription factor jun-D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4328
Polymers16,2572
Non-polymers1756
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-74 kcal/mol
Surface area9760 Å2
MethodPISA
2
C: Protein fosB
D: Transcription factor jun-D


Theoretical massNumber of molelcules
Total (without water)16,2572
Polymers16,2572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-28 kcal/mol
Surface area9070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.177, 49.949, 97.746
Angle α, β, γ (deg.)90.000, 122.940, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 163 through 174 or (resid 175...
21(chain C and resid 163 through 217)
12(chain B and (resid 270 or (resid 271 and (name...
22chain D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLUGLUASNASN(chain A and (resid 163 through 174 or (resid 175...AA163 - 17412 - 23
121ARGARGARGARG(chain A and (resid 163 through 174 or (resid 175...AA17524
131GLUGLUALAALA(chain A and (resid 163 through 174 or (resid 175...AA163 - 21712 - 66
141GLUGLUALAALA(chain A and (resid 163 through 174 or (resid 175...AA163 - 21712 - 66
151GLUGLUALAALA(chain A and (resid 163 through 174 or (resid 175...AA163 - 21712 - 66
161GLUGLUALAALA(chain A and (resid 163 through 174 or (resid 175...AA163 - 21712 - 66
211GLUGLUALAALA(chain C and resid 163 through 217)CC163 - 21712 - 66
112LYSLYSLYSLYS(chain B and (resid 270 or (resid 271 and (name...BB2706
122ALAALAALAALA(chain B and (resid 270 or (resid 271 and (name...BB2717
132SERSERVALVAL(chain B and (resid 270 or (resid 271 and (name...BB265 - 3321 - 68
142SERSERVALVAL(chain B and (resid 270 or (resid 271 and (name...BB265 - 3321 - 68
152SERSERVALVAL(chain B and (resid 270 or (resid 271 and (name...BB265 - 3321 - 68
212LYSLYSVALVALchain DDD270 - 3326 - 68

NCS ensembles :
ID
1
2

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Components

#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
#3: Chemical ChemComp-NA / SODIUM ION


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


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 3.5 Å3/Da / Density % sol: 64.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 12% (v/v) ethanol, 0.3 M NaCl and 2% (v/v) Jeffamine M-600

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 22, 2016
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.498→44.04 Å / Num. obs: 15500 / % possible obs: 99.7 % / Redundancy: 3.8 % / Biso Wilson estimate: 34.75 Å2 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.043 / Rrim(I) all: 0.083 / Χ2: 0.919 / Net I/σ(I): 17
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.498-2.543.80.5822.20.860.3490.680.848100
2.54-2.593.80.4750.9040.2830.5540.856100
2.59-2.643.80.4210.9180.2550.4930.8999.9
2.64-2.693.80.3480.9670.2080.4060.875100
2.69-2.753.80.290.9570.1740.3390.876100
2.75-2.823.80.2230.9770.1330.260.92899.9
2.82-2.893.80.2030.9780.1210.2370.97100
2.89-2.963.80.1540.9850.0920.180.941100
2.96-3.053.80.1330.9890.0790.1550.945100
3.05-3.153.80.120.9850.0720.140.955100
3.15-3.263.80.1030.9870.0610.121.014100
3.26-3.393.80.0880.9910.0520.1021.012100
3.39-3.553.80.0750.9910.0450.0870.98100
3.55-3.733.80.0690.9870.0420.080.958100
3.73-3.973.80.0680.9910.040.0790.931100
3.97-4.273.80.0580.9920.0350.0680.90699.9
4.27-4.73.80.0590.990.0350.0690.903100
4.7-5.383.70.0530.9890.0330.0620.874100
5.38-6.783.70.0420.9950.0260.0490.86100
6.78-44.043.50.0330.9950.0210.0390.83895.3

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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: 5VPA

5vpa


Resolution: 2.498→44.036 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.22
RfactorNum. reflection% reflection
Rfree0.2885 1401 9.94 %
Rwork0.2512 --
obs0.2549 14089 88.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 170.85 Å2 / Biso mean: 63.4841 Å2 / Biso min: 11.76 Å2
Refinement stepCycle: final / Resolution: 2.498→44.036 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1907 0 6 30 1943
Biso mean--58.37 37.65 -
Num. residues----243
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031910
X-RAY DIFFRACTIONf_angle_d0.5082548
X-RAY DIFFRACTIONf_chiral_restr0.026305
X-RAY DIFFRACTIONf_plane_restr0.002330
X-RAY DIFFRACTIONf_dihedral_angle_d10.8641256
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A597X-RAY DIFFRACTION8.554TORSIONAL
12C597X-RAY DIFFRACTION8.554TORSIONAL
21B724X-RAY DIFFRACTION8.554TORSIONAL
22D724X-RAY DIFFRACTION8.554TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4975-2.58680.3466630.302354360639
2.5868-2.69030.34031020.301187998163
2.6903-2.81280.39941340.30761239137387
2.8128-2.9610.38161550.326714251580100
2.961-3.14650.36581530.298814181571100
3.1465-3.38940.34921560.295614381594100
3.3894-3.73030.32361640.256414301594100
3.7303-4.26970.24231570.200314261583100
4.2697-5.37780.21741560.198614321588100
5.3778-44.04280.221610.22991458161997
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)
12.23822.333-0.25753.51340.75027.1108-0.683-0.4393-0.00390.1675-0.04290.1211-0.4287-0.09521.49860.6991-0.0147-0.0620.5937-0.03220.757177.173630.721187.5312
21.44421.02932.99431.55423.47848.8529-0.17970.05190.0725-0.18530.06060.0182-1.1178-0.0888-0.66420.3751-0.12880.05970.1610.00210.1154175.446436.6173123.9571
30.2112-0.1086-0.5280.18630.66512.85030.0254-0.03080.0263-0.15820.1951-0.0143-0.32050.37-0.34970.2776-0.1047-0.01960.2104-0.07450.047178.446127.2104107.9613
44.59270.9426-0.51495.9515-4.10564.7657-0.3361.7441-0.8432-0.99980.57470.44830.59370.0613-0.07050.3967-0.16330.02680.7073-0.26670.6402167.464537.6272103.1068
52.62950.1798-0.10740.2108-0.42910.8765-0.5259-0.1129-1.33320.18920.00380.35090.4181-0.05030.1130.2978-0.02810.21880.19920.00020.4326201.098931.250485.341
60.4999-0.4962-0.45340.47930.46690.5314-0.19730.1505-0.38240.06120.00230.22670.0518-0.2470.21750.1126-0.06110.09640.1564-0.06590.2576190.71340.601192.3832
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 163 through 177 )A163 - 177
2X-RAY DIFFRACTION2chain 'A' and (resid 178 through 217 )A178 - 217
3X-RAY DIFFRACTION3chain 'B' and (resid 266 through 332 )B266 - 332
4X-RAY DIFFRACTION4chain 'C' and (resid 163 through 178 )C163 - 178
5X-RAY DIFFRACTION5chain 'C' and (resid 179 through 218 )C179 - 218
6X-RAY DIFFRACTION6chain 'D' and (resid 270 through 332 )D270 - 332

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