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- PDB-6ucl: Transcription factor deltaFosB bZIP domain self-assembly, type-I ... -

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Basic information

Entry
Database: PDB / ID: 6ucl
TitleTranscription factor deltaFosB bZIP domain self-assembly, type-I crystal
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 / response to cAMP / response to mechanical stimulus / cellular response to hormone stimulus / behavioral response to cocaine / cellular response to calcium ion / response to progesterone / response to amphetamine ...NGF-stimulated transcription / response to morphine / response to corticosterone / response to cAMP / response to mechanical stimulus / cellular response to hormone stimulus / behavioral response to cocaine / cellular response to calcium ion / response to progesterone / response to amphetamine / response to nicotine / 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 / 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 / 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 / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.207 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
Revision 1.2Oct 11, 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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein fosB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,3744
Polymers8,2671
Non-polymers1063
Water19811
1
A: Protein fosB
hetero molecules

A: Protein fosB
hetero molecules

A: Protein fosB
hetero molecules

A: Protein fosB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,49516
Polymers33,0694
Non-polymers42512
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area8400 Å2
ΔGint-111 kcal/mol
Surface area15440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.506, 51.956, 150.454
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number22
Space group name H-MF222

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Components

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


Mass: 8267.290 Da / Num. of mol.: 1
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 / Cell (production host): Rosetta 2 (DE3) / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.33 Å3/Da / Density % sol: 47.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7 / Details: 17% (w/v) PEG 4000, 0.2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.9787 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.19→50 Å / Num. obs: 4096 / % possible obs: 99.6 % / Redundancy: 5.3 % / Biso Wilson estimate: 33.44 Å2 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.03 / Rrim(I) all: 0.066 / Χ2: 0.953 / Net I/σ(I): 7.3 / Num. measured all: 21906
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.19-2.235.20.8451940.8860.3890.9341.277100
2.23-2.275.50.6651980.9390.3120.7371.07199.5
2.27-2.315.70.472080.990.2140.5181.104100
2.31-2.365.50.5091920.9780.2390.5640.998100
2.36-2.415.50.2832050.9950.1330.3140.968100
2.41-2.475.30.2812080.9950.1340.3120.97599.5
2.47-2.535.10.2661890.9860.1350.2990.902100
2.53-2.65.30.2422060.9970.1150.2690.994100
2.6-2.675.60.2262080.9930.1060.2510.934100
2.67-2.765.60.1762000.9970.0810.1950.837100
2.76-2.865.40.1152060.9980.0550.1280.924100
2.86-2.975.40.0972030.9980.0470.1080.881100
2.97-3.115.30.0781930.9990.0390.0880.898100
3.11-3.275.10.0882200.9960.0460.10.907100
3.27-3.485.80.071950.9980.0320.0770.995100
3.48-3.745.40.0632090.9980.0310.071.008100
3.74-4.125.30.052120.9990.0240.0561.003100
4.12-4.725.40.0412120.9980.0210.0470.907100
4.72-5.945.10.032100.9990.0160.0340.74999.5
5.94-504.70.0382280.9930.0230.0450.72495

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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: 5VPE

5vpe


Resolution: 2.207→30.782 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 30.82
RfactorNum. reflection% reflection
Rfree0.287 294 10.04 %
Rwork0.2705 --
obs0.2723 2929 71.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 92.76 Å2 / Biso mean: 44.4932 Å2 / Biso min: 11.88 Å2
Refinement stepCycle: final / Resolution: 2.207→30.782 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms449 0 3 11 463
Biso mean--59.2 35.03 -
Num. residues----60
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003460
X-RAY DIFFRACTIONf_angle_d0.476621
X-RAY DIFFRACTIONf_chiral_restr0.02275
X-RAY DIFFRACTIONf_plane_restr0.00284
X-RAY DIFFRACTIONf_dihedral_angle_d13.857176
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2074-2.78080.3402860.299577743
2.7808-30.7820.27812080.2657185899

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