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

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Basic information

Entry
Database: PDB / ID: 5vpd
TitleTranscription factor FosB/JunD bZIP domain in its oxidized form, type-III 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: 2.79 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
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)32,6669
Polymers32,5134
Non-polymers1525
Water724
1
A: Protein fosB
B: Transcription factor jun-D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2803
Polymers16,2572
Non-polymers231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-40 kcal/mol
Surface area9960 Å2
MethodPISA
2
C: Protein fosB
D: Transcription factor jun-D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3866
Polymers16,2572
Non-polymers1294
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-47 kcal/mol
Surface area9700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.008, 98.051, 50.251
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 164 through 175 or (resid 177...
21(chain C and ((resid 164 and (name N or name...
12(chain B and ((resid 270 through 272 and (name N...
22(chain D and (resid 270 through 291 or resid 293 through 307 or resid 309 through 332))

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
111ARGARGARGARG(chain A and (resid 164 through 175 or (resid 177...AA164 - 17513 - 24
121ARGARGGLUGLU(chain A and (resid 164 through 175 or (resid 177...AA177 - 17826 - 27
131ARGARGHISHIS(chain A and (resid 164 through 175 or (resid 177...AA164 - 21813 - 67
141ARGARGHISHIS(chain A and (resid 164 through 175 or (resid 177...AA164 - 21813 - 67
151ARGARGHISHIS(chain A and (resid 164 through 175 or (resid 177...AA164 - 21813 - 67
161ARGARGHISHIS(chain A and (resid 164 through 175 or (resid 177...AA164 - 21813 - 67
211ARGARGARGARG(chain C and ((resid 164 and (name N or name...CC16413
221ARGARGALAALA(chain C and ((resid 164 and (name N or name...CC161 - 21710 - 66
231ARGARGALAALA(chain C and ((resid 164 and (name N or name...CC161 - 21710 - 66
241ARGARGALAALA(chain C and ((resid 164 and (name N or name...CC161 - 21710 - 66
251ARGARGALAALA(chain C and ((resid 164 and (name N or name...CC161 - 21710 - 66
112LYSLYSGLUGLU(chain B and ((resid 270 through 272 and (name N...BB270 - 2726 - 8
122GLNGLNVALVAL(chain B and ((resid 270 through 272 and (name N...BB266 - 3322 - 68
132GLNGLNVALVAL(chain B and ((resid 270 through 272 and (name N...BB266 - 3322 - 68
142GLNGLNVALVAL(chain B and ((resid 270 through 272 and (name N...BB266 - 3322 - 68
152GLNGLNVALVAL(chain B and ((resid 270 through 272 and (name N...BB266 - 3322 - 68
212LYSLYSGLUGLU(chain D and (resid 270 through 291 or resid 293 through 307 or resid 309 through 332))DD270 - 2916 - 27
222ILEILEASNASN(chain D and (resid 270 through 291 or resid 293 through 307 or resid 309 through 332))DD293 - 30729 - 43
232GLUGLUVALVAL(chain D and (resid 270 through 291 or resid 293 through 307 or resid 309 through 332))DD309 - 33245 - 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.: 2 / 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.: 4 / 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: 3.49 Å3/Da / Density % sol: 64.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20% (v/v) 2-methyl-2,4-pentanediol (MPD), 0.1 M NaCl, 50 mM sodium cacodylate pH 6 and 10 mM spermine

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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: 2.79→44.72 Å / Num. obs: 11778 / % possible obs: 99.9 % / Redundancy: 7.1 % / Biso Wilson estimate: 43.31 Å2 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.043 / Rrim(I) all: 0.116 / Χ2: 0.91 / Net I/σ(I): 7.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.79-2.827.10.90620.9020.3630.9770.858100
2.82-2.877.20.8430.9170.3370.9090.86299.8
2.87-2.927.20.680.9320.2730.7340.855100
2.92-2.987.20.4860.9750.1930.5230.855100
2.98-3.057.20.4410.9710.1770.4760.845100
3.05-3.127.30.4790.9450.190.5160.896100
3.12-3.27.30.360.9740.1430.3880.93100
3.2-3.287.30.3250.980.1290.350.963100
3.28-3.387.20.2580.9810.1020.2780.973100
3.38-3.497.30.2230.9810.0890.241.023100
3.49-3.617.30.1630.990.0650.1760.956100
3.61-3.767.30.1260.9940.050.1360.997100
3.76-3.937.20.1020.9970.0410.110.994100
3.93-4.147.20.0940.9970.0370.1010.982100
4.14-4.47.20.0840.9970.0330.090.96100
4.4-4.747.20.0750.9980.030.0810.921100
4.74-5.217.10.0620.9990.0250.0670.866100
5.21-5.967.10.0690.9970.0280.0740.82100
5.96-7.516.90.0490.9980.020.0530.809100
7.51-44.726.20.0330.9990.0150.0370.82598.4

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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: 2.79→44.72 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.75
RfactorNum. reflection% reflection
Rfree0.3002 1068 9.9 %
Rwork0.2493 --
obs0.2547 10789 91.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 206.5 Å2 / Biso mean: 55.163 Å2 / Biso min: 12.72 Å2
Refinement stepCycle: final / Resolution: 2.79→44.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1958 0 5 4 1967
Biso mean--61.58 26.56 -
Num. residues----242
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031994
X-RAY DIFFRACTIONf_angle_d0.5852655
X-RAY DIFFRACTIONf_chiral_restr0.029310
X-RAY DIFFRACTIONf_plane_restr0.004344
X-RAY DIFFRACTIONf_dihedral_angle_d12.8251333
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A573X-RAY DIFFRACTION11.341TORSIONAL
12C573X-RAY DIFFRACTION11.341TORSIONAL
21B696X-RAY DIFFRACTION11.341TORSIONAL
22D696X-RAY DIFFRACTION11.341TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7898-2.91680.3559700.326370277254
2.9168-3.07050.36111120.31271028114078
3.0705-3.26290.3871360.30981277141397
3.2629-3.51470.37151410.288513151456100
3.5147-3.86820.28731480.233213181466100
3.8682-4.42750.26141540.202313171471100
4.4275-5.57650.2831490.22461353150299
5.5765-44.72580.2561580.23931411156999
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)
10.48290.3646-0.3510.7508-2.07517.1382-0.1384-0.62560.311-0.35730.39630.2470.7913-0.0033-0.28960.39650.1313-0.20560.8789-0.07650.6283-9.5510.0926-16.85
23.3058-2.1313-1.46884.0741.58991.3071-0.3865-0.31380.12240.40640.4738-0.20620.01130.3688-0.12780.52660.25140.00310.3744-0.03710.1926-26.711932.2956-9.8081
31.5528-2.5757-0.62595.11431.20960.2775-0.1295-0.2123-0.1984-0.01310.02910.3520.0810.13040.07070.25870.12960.00190.22390.00960.2133-21.273316.7447-19.7572
42.55621.49640.18221.56690.60893.9137-0.02180.40530.37540.12660.51010.4051-0.5375-0.5253-0.44620.36340.0492-0.09080.70490.04430.408-10.280622.1889-10.1293
53.77032.89561.62862.72491.54071.3777-0.27760.4643-0.202-0.33690.501-0.27560.05110.2824-0.11550.5344-0.1349-0.16060.2322-0.01420.2695-27.5901-13.1765-15.3474
63.14445.40432.06919.47983.79021.6102-0.1710.20060.18860.07840.29440.3712-0.05240.20340.21010.2351-0.03240.01230.2681-0.00020.1787-22.9366-1.3353-5.936
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 164 through 176 )A164 - 176
2X-RAY DIFFRACTION2chain 'A' and (resid 177 through 218 )A177 - 218
3X-RAY DIFFRACTION3chain 'B' and (resid 266 through 332 )B266 - 332
4X-RAY DIFFRACTION4chain 'C' and (resid 161 through 177 )C161 - 177
5X-RAY DIFFRACTION5chain 'C' and (resid 178 through 217 )C178 - 217
6X-RAY DIFFRACTION6chain 'D' and (resid 270 through 332 )D270 - 332

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