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- PDB-6ucm: Transcription factor DeltaFosB bZIP domain self-assembly, type-II... -

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Basic information

Entry
Database: PDB / ID: 6ucm
TitleTranscription factor DeltaFosB bZIP domain self-assembly, type-II 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 corticosterone / response to mechanical stimulus / cellular response to hormone stimulus / response to cAMP / 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 ...NGF-stimulated transcription / response to corticosterone / response to mechanical stimulus / cellular response to hormone stimulus / response to cAMP / 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 / 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
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 / MOLECULAR REPLACEMENT / Resolution: 2.424 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,21410
Polymers24,8023
Non-polymers4127
Water28816
1
A: Protein fosB
B: Protein fosB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7215
Polymers16,5352
Non-polymers1863
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-16 kcal/mol
Surface area7030 Å2
MethodPISA
2
C: Protein fosB
hetero molecules

C: Protein fosB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,98710
Polymers16,5352
Non-polymers4538
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-2/31
Buried area2560 Å2
ΔGint-21 kcal/mol
Surface area11030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.925, 101.925, 51.347
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 8267.290 Da / Num. of mol.: 3
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 3.1 Å3/Da / Density % sol: 60.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 2 M ammonium sulfate, 5% (v/v) isopropanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.424→50 Å / Num. obs: 11940 / % possible obs: 100 % / Redundancy: 10.5 % / Biso Wilson estimate: 32.58 Å2 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.028 / Rrim(I) all: 0.091 / Χ2: 0.952 / Net I/σ(I): 9
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
2.43-2.479.81.4485800.6380.4951.5310.851
2.47-2.5210.81.3775730.7240.4411.4460.895
2.52-2.5710.71.0995950.7730.3551.1560.876
2.57-2.6210.70.8965910.8370.290.9430.947
2.62-2.6710.80.6915940.9070.2220.7260.964
2.67-2.7410.70.5655960.9190.1830.5950.911
2.74-2.8110.70.4785810.9530.1540.5030.962
2.81-2.8810.60.425860.9540.1370.4420.989
2.88-2.9710.80.3345900.9680.1070.3510.999
2.97-3.0610.60.2285920.9830.0740.240.972
3.06-3.1710.70.1775960.9880.0570.1860.997
3.17-3.310.70.1426090.9920.0460.1490.997
3.3-3.4510.60.1125860.9940.0360.1171.006
3.45-3.6310.70.0885870.9950.0290.0930.995
3.63-3.8610.60.075950.9960.0230.0740.947
3.86-4.1510.50.0615970.9980.020.0640.908
4.15-4.5710.50.0576130.9980.0180.060.951
4.57-5.2310.20.0636100.9970.020.0660.917
5.23-6.59100.0496200.9980.0160.0521.02
6.59-509.50.0326490.9980.0110.0340.922

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
SCALEPACKdata scaling
PDB_EXTRACT3.22data extraction
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VPE

5vpe


Resolution: 2.424→44.384 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.14
RfactorNum. reflection% reflection
Rfree0.2449 1172 10.06 %
Rwork0.2082 --
obs0.212 11649 97.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 142.22 Å2 / Biso mean: 57.5489 Å2 / Biso min: 14.86 Å2
Refinement stepCycle: final / Resolution: 2.424→44.384 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1248 0 61 16 1325
Biso mean--60.04 42.42 -
Num. residues----154
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051294
X-RAY DIFFRACTIONf_angle_d0.5771721
X-RAY DIFFRACTIONf_chiral_restr0.025193
X-RAY DIFFRACTIONf_plane_restr0.002235
X-RAY DIFFRACTIONf_dihedral_angle_d12.614851
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4241-2.53440.27931190.2417109783
2.5344-2.6680.27111390.2271130899
2.668-2.83520.28391490.21751327100
2.8352-3.0540.29821480.22031321100
3.054-3.36130.24591540.20631332100
3.3613-3.84740.22711530.19561329100
3.8474-4.84640.20991540.17231354100
4.8464-44.3840.24531560.23521409100
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)
12.17130.04210.74873.8568-0.97581.9057-0.2371-0.13910.02920.9128-0.0064-0.5184-0.2095-0.01020.18010.29480.05250.00020.16580.0060.202-43.442329.9855-3.373
22.76380.87611.06631.8011-1.05213.2319-0.37040.1867-0.186-0.65860.0884-1.06170.57550.5574-0.29880.35840.08760.04360.2672-0.01280.4085-36.147822.4724-7.7074
32.18911.67011.14932.18792.41943.2137-0.37710.41620.2013-0.24120.4066-0.0720.099-0.0078-0.00410.7363-0.4149-0.69940.2617-0.21181.0455-31.526357.3933-0.9331
40.37430.25360.18042.0770.4876-0.8174-0.07230.06270.058-0.8308-0.06480.58170.0344-0.07720.04960.5778-0.0042-0.02370.21320.02710.2295-51.387714.5716-17.3896
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 177 through 215 )A177 - 215
2X-RAY DIFFRACTION2chain 'B' and (resid 166 through 209 )B166 - 209
3X-RAY DIFFRACTION3chain 'B' and (resid 210 through 215 )B210 - 215
4X-RAY DIFFRACTION4chain 'C' and (resid 153 through 217 )C153 - 217

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