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- PDB-6uci: Transcription factor DeltaFosB bZIP domain self-assembly, oxidize... -

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Basic information

Entry
Database: PDB / ID: 6uci
TitleTranscription factor DeltaFosB bZIP domain self-assembly, oxidized form
ComponentsProtein fosB
KeywordsTRANSCRIPTION / activator protein-1 / basic leucine zipper / bZIP / deltaFosB / fos / jun / transcription factor / DNA-binding protein / coiled-coil
Function / homology
Function and homology information


NGF-stimulated transcription / response to morphine / response to corticosterone / behavioral response to cocaine / response to mechanical stimulus / cellular response to hormone stimulus / response to cAMP / response to amphetamine / cellular response to calcium ion / response to progesterone ...NGF-stimulated transcription / response to morphine / response to corticosterone / behavioral response to cocaine / response to mechanical stimulus / cellular response to hormone stimulus / response to cAMP / response to amphetamine / cellular response to calcium ion / response to progesterone / female pregnancy / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / response to ethanol / Estrogen-dependent gene expression / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / 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 / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
AP-1 transcription factor / bZIP transcription factor / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.09 Å
AuthorsYin, Z. / Machius, M. / Rudenko, G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01 DA040621 United States
CitationJournal: Curr Res Struct Biol / Year: 2020
Title: Self-assembly of the bZIP transcription factor Delta FosB.
Authors: Yin, Z. / Venkannagari, H. / Lynch, H. / Aglyamova, G. / Bhandari, M. / Machius, M. / Nestler, E.J. / Robison, A.J. / Rudenko, G.
History
DepositionSep 16, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_id_ISSN ..._citation.country / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein fosB
B: Protein fosB
C: Protein fosB
D: Protein fosB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,36210
Polymers33,0694
Non-polymers2936
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, see details in publication
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9470 Å2
ΔGint-83 kcal/mol
Surface area14560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.278, 97.497, 45.197
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 8267.290 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: alternative splice form; identical to the mouse sequence in the region cloned
Source: (gene. exp.) Homo sapiens (human) / Gene: FOSB, G0S3 / Plasmid: pET21 NESG / Production host: Escherichia coli (E. coli) / References: UniProt: P53539
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O
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: 2.41 Å3/Da / Density % sol: 48.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 2.5 M sodium chloride, 0.1 M sodium acetate, pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9787 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. obs: 19503 / % possible obs: 99.5 % / Redundancy: 4 % / Biso Wilson estimate: 27.06 Å2 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.027 / Rrim(I) all: 0.055 / Χ2: 0.89 / Net I/σ(I): 14.3 / Num. measured all: 78088
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.09-2.133.90.7469580.670.4310.8650.88999.9
2.13-2.1640.6299690.7490.3570.7250.902100
2.16-2.213.90.559330.7370.3190.6380.92899.8
2.21-2.2540.4569760.8040.2620.5280.94999.7
2.25-2.33.90.4129590.8580.2380.4780.958100
2.3-2.3540.3039660.9060.1740.3510.91399.8
2.35-2.4140.2379510.9460.1360.2740.88199.8
2.41-2.4840.1799690.9690.1030.2070.96399.9
2.48-2.5540.1479610.9760.0840.170.902100
2.55-2.634.10.1229730.9820.070.1410.925100
2.63-2.734.10.1089600.9840.0610.1250.891100
2.73-2.844.20.0759910.9920.0420.0860.845100
2.84-2.974.10.0589660.9960.0330.0670.81899.9
2.97-3.124.20.0469670.9950.0260.0540.82599.9
3.12-3.324.10.0389940.9970.0210.0440.866100
3.32-3.574.10.0339870.9980.0180.0380.93699.9
3.57-3.9340.0289870.9980.0150.0320.92699.9
3.93-4.53.90.02310160.9980.0130.0260.882100
4.5-5.673.90.0210180.9990.0110.0230.83599.9
5.67-503.80.01710020.9990.010.020.77991.7

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
SCALEPACKdata scaling
PDB_EXTRACT3.22data extraction
DENZOdata reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.09→35.665 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.53
RfactorNum. reflection% reflection
Rfree0.2407 1890 10 %
Rwork0.2066 --
obs0.2101 18902 96.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 201.05 Å2 / Biso mean: 53.0408 Å2 / Biso min: 11.29 Å2
Refinement stepCycle: final / Resolution: 2.09→35.665 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1863 0 33 68 1964
Biso mean--79.99 41.84 -
Num. residues----230
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051938
X-RAY DIFFRACTIONf_angle_d0.582593
X-RAY DIFFRACTIONf_chiral_restr0.027292
X-RAY DIFFRACTIONf_plane_restr0.003354
X-RAY DIFFRACTIONf_dihedral_angle_d11.9811279
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.09-2.14220.26491070.231596577
2.1422-2.20020.26631190.2221106887
2.2002-2.26490.25871330.2199119395
2.2649-2.3380.25251340.2147120699
2.338-2.42150.26181360.2065123599
2.4215-2.51850.24131380.20781236100
2.5185-2.6330.26311370.2041239100
2.633-2.77180.2721390.22521242100
2.7718-2.94540.24771390.21791255100
2.9454-3.17270.25321400.20541254100
3.1727-3.49170.24151400.20211270100
3.4917-3.99640.24071400.17561261100
3.9964-5.03280.17131450.17211302100
5.0328-35.6650.28321430.2661128694
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)
10.5539-0.2628-0.25151.68812.12844.5973-0.1087-0.17140.06490.11360.2184-0.02060.01740.42890.00360.25530.1007-0.05170.2711-0.09670.1755102.261321.716113.3669
20.03310.77350.26511.53560.83841.1852-0.1197-0.12170.0717-0.2616-0.30060.6955-0.2892-0.2835-0.03390.09020.056-0.05460.194-0.07470.262995.6287-1.381383.6128
30.5011-0.6513-0.79842.91483.3225.7816-0.2925-0.0698-0.03390.1310.28130.30150.01870.601-0.08110.0955-0.00350.00930.12330.01350.1375102.959-7.582284.3024
41.50330.0796-0.26375.07663.4963.6663-0.272-0.1458-0.21050.0421-0.00990.52740.0247-0.1352-0.03830.16520.03270.03230.1857-0.03030.295693.91616.1563108.9438
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'D' and (resid 153 through 219 )D153 - 219
2X-RAY DIFFRACTION2chain 'A' and (resid 162 through 218 )A162 - 218
3X-RAY DIFFRACTION3chain 'B' and (resid 156 through 216 )B156 - 216
4X-RAY DIFFRACTION4chain 'C' and (resid 172 through 216 )C172 - 216

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