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

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Basic information

Entry
Database: PDB / ID: 5vpb
TitleTranscription factor FosB/JunD bZIP domain in its oxidized form, type-I 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 / 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
Transcription factor JunD / Protein FosB
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.691 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 / 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

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


Theoretical massNumber of molelcules
Total (without water)32,97417
Polymers32,5134
Non-polymers46113
Water19811
1
C: Protein fosB
D: Transcription factor jun-D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3996
Polymers16,2572
Non-polymers1424
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-68 kcal/mol
Surface area8990 Å2
MethodPISA
2
A: Protein fosB
B: Transcription factor jun-D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,57611
Polymers16,2572
Non-polymers3199
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-90 kcal/mol
Surface area9380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.825, 99.261, 49.860
Angle α, β, γ (deg.)90.000, 109.400, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain B and (resid 267 through 276 or (resid 277...
21(chain D and ((resid 267 through 274 and (name N...
12(chain A and (resid 163 through 166 or (resid 167...
22(chain C and (resid 163 through 165 or (resid 166...

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
111GLUGLULEULEU(chain B and (resid 267 through 276 or (resid 277...BD267 - 2763 - 12
121ARGARGARGARG(chain B and (resid 267 through 276 or (resid 277...BD27713
131GLNGLNVALVAL(chain B and (resid 267 through 276 or (resid 277...BD266 - 3322 - 68
141GLNGLNVALVAL(chain B and (resid 267 through 276 or (resid 277...BD266 - 3322 - 68
151GLNGLNVALVAL(chain B and (resid 267 through 276 or (resid 277...BD266 - 3322 - 68
161GLNGLNVALVAL(chain B and (resid 267 through 276 or (resid 277...BD266 - 3322 - 68
211GLUGLULYSLYS(chain D and ((resid 267 through 274 and (name N...DB267 - 2743 - 10
221GLUGLUVALVAL(chain D and ((resid 267 through 274 and (name N...DB267 - 3323 - 68
231GLUGLUVALVAL(chain D and ((resid 267 through 274 and (name N...DB267 - 3323 - 68
241GLUGLUVALVAL(chain D and ((resid 267 through 274 and (name N...DB267 - 3323 - 68
251GLUGLUVALVAL(chain D and ((resid 267 through 274 and (name N...DB267 - 3323 - 68
112GLUGLULYSLYS(chain A and (resid 163 through 166 or (resid 167...AC163 - 16612 - 15
122LEULEULYSLYS(chain A and (resid 163 through 166 or (resid 167...AC167 - 17116 - 20
132ARGARGLYSLYS(chain A and (resid 163 through 166 or (resid 167...AC161 - 21910 - 68
142ARGARGLYSLYS(chain A and (resid 163 through 166 or (resid 167...AC161 - 21910 - 68
152ARGARGLYSLYS(chain A and (resid 163 through 166 or (resid 167...AC161 - 21910 - 68
162ARGARGLYSLYS(chain A and (resid 163 through 166 or (resid 167...AC161 - 21910 - 68
212GLUGLUASNASN(chain C and (resid 163 through 165 or (resid 166...CA163 - 16512 - 14
222LYSLYSLYSLYS(chain C and (resid 163 through 165 or (resid 166...CA166 - 17115 - 20
232GLUGLUVALVAL(chain C and (resid 163 through 165 or (resid 166...CA163 - 21612 - 65
242GLUGLUVALVAL(chain C and (resid 163 through 165 or (resid 166...CA163 - 21612 - 65
252GLUGLUVALVAL(chain C and (resid 163 through 165 or (resid 166...CA163 - 21612 - 65
262GLUGLUVALVAL(chain C and (resid 163 through 165 or (resid 166...CA163 - 21612 - 65

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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 3.33 Å3/Da / Density % sol: 63.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 45% (v/v) 2-methyl-2,4-pentanediol (MPD), 0.3 M NaCl and 0.1 M HEPES pH 7.5

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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: 2.691→43.74 Å / Num. obs: 11872 / % possible obs: 99.9 % / Redundancy: 3.8 % / Biso Wilson estimate: 35.88 Å2 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.038 / Rrim(I) all: 0.074 / Χ2: 0.931 / Net I/σ(I): 20
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.691-2.753.80.64120.9020.3840.7480.863100
2.75-2.83.80.580.8930.3470.6770.902100
2.8-2.853.80.3760.9620.2230.4370.896100
2.85-2.913.80.3620.9480.2160.4220.908100
2.91-2.973.80.2760.9730.1650.3220.814100
2.97-3.043.80.2720.9740.1630.3180.933100
3.04-3.123.80.2120.9750.1270.2480.977100
3.12-3.23.80.1920.9650.1150.2241.008100
3.2-3.33.80.1580.9750.0950.1851.035100
3.3-3.43.80.1260.9840.0750.1470.987100
3.4-3.523.80.1030.9870.0610.121.036100
3.52-3.663.80.0830.990.0490.0961.004100
3.66-3.833.80.0670.9950.040.0780.981100
3.83-4.033.80.0590.9950.0350.0690.954100
4.03-4.293.80.0530.9960.0310.0610.923100
4.29-4.623.80.0510.9960.030.0590.881100
4.62-5.083.70.0480.9950.0280.0560.896100
5.08-5.813.80.0460.9970.0270.0530.891100
5.81-7.323.70.0330.9980.020.0390.832100
7.32-43.743.60.0370.9970.0230.0440.88997.7

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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: 5VPA

5vpa


Resolution: 2.691→43.738 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 31.14
RfactorNum. reflection% reflection
Rfree0.2746 1021 10.01 %
Rwork0.2377 --
obs0.2415 10200 85.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 166.57 Å2 / Biso mean: 53.7652 Å2 / Biso min: 4.94 Å2
Refinement stepCycle: final / Resolution: 2.691→43.738 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1904 0 13 11 1928
Biso mean--60.15 24.86 -
Num. residues----246
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021920
X-RAY DIFFRACTIONf_angle_d0.4192569
X-RAY DIFFRACTIONf_chiral_restr0.024309
X-RAY DIFFRACTIONf_plane_restr0.002336
X-RAY DIFFRACTIONf_dihedral_angle_d8.9181268
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11B741X-RAY DIFFRACTION7.544TORSIONAL
12D741X-RAY DIFFRACTION7.544TORSIONAL
21A544X-RAY DIFFRACTION7.544TORSIONAL
22C544X-RAY DIFFRACTION7.544TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6913-2.83320.4435720.319364771942
2.8332-3.01070.33331150.2891036115168
3.0107-3.24310.29731540.27651386154091
3.2431-3.56930.35071710.267515381709100
3.5693-4.08540.26011660.197414991665100
4.0854-5.14590.21561710.20315361707100
5.1459-43.74370.25041720.24051537170999
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)
19.5545-5.1007-2.9153.58954.0848.2698-0.60.6072-0.43930.3478-0.1085-0.11280.3979-0.59550.70020.5333-0.23250.05330.78750.06090.5486267.3949-21.305857.7488
26.74426.3495-0.13667.19470.24960.1978-0.3270.30130.2368-0.56620.4407-0.0899-0.09040.1127-0.06480.3380.03650.11620.1427-0.0410.1221284.86789.682458.5119
31.05161.596-0.17073.725-0.73720.3201-0.03990.2154-0.08070.0790.145-0.10.02330.0120.02860.1257-0.0465-0.04460.0554-0.01810.0429277.838-1.951965.2436
44.9142-2.62870.18186.4011.09133.4917-0.3043-0.34360.5019-0.08640.04190.7805-0.4135-0.34230.30020.27520.1983-0.06630.57420.09910.459270.1317-0.078152.0439
50.5128-0.53620.15890.8608-0.44820.46010.04380.00470.10140.06340.09970.0692-0.2784-0.11470.13830.31240.09250.17620.120.02020.1455283.8877-34.801862.4024
60.3031-0.55030.38062.1986-0.99450.6209-0.02520.00150.10870.03690.0008-0.0003-0.0643-0.0469-0.01750.12640.08340.10530.11390.17990.1602282.6181-21.718152.0359
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'C' and (resid 163 through 176 )C163 - 176
2X-RAY DIFFRACTION2chain 'C' and (resid 177 through 216 )C177 - 216
3X-RAY DIFFRACTION3chain 'D' and (resid 267 through 332 )D267 - 332
4X-RAY DIFFRACTION4chain 'A' and (resid 161 through 176 )A161 - 176
5X-RAY DIFFRACTION5chain 'A' and (resid 177 through 219 )A177 - 219
6X-RAY DIFFRACTION6chain 'B' and (resid 266 through 332 )B266 - 332

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