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- PDB-6usb: Barrier-to-autointegration factor soaked in urea: 1 of 14 in MSCS set -

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Basic information

Entry
Database: PDB / ID: 6usb
TitleBarrier-to-autointegration factor soaked in urea: 1 of 14 in MSCS set
ComponentsBarrier-to-autointegration factor
KeywordsDNA BINDING PROTEIN / alpha helical / MSCS / minor groove binder
Function / homology
Function and homology information


negative regulation of protein ADP-ribosylation / Nuclear Envelope Breakdown / mitotic nuclear membrane reassembly / Initiation of Nuclear Envelope (NE) Reformation / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / negative regulation of type I interferon production / negative regulation of cGAS/STING signaling pathway / negative regulation of viral genome replication / 2-LTR circle formation ...negative regulation of protein ADP-ribosylation / Nuclear Envelope Breakdown / mitotic nuclear membrane reassembly / Initiation of Nuclear Envelope (NE) Reformation / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / negative regulation of type I interferon production / negative regulation of cGAS/STING signaling pathway / negative regulation of viral genome replication / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / condensed chromosome / negative regulation of innate immune response / response to virus / DNA integration / nuclear envelope / chromatin organization / double-stranded DNA binding / response to oxidative stress / chromatin / protein homodimerization activity / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Barrier- to-autointegration factor, BAF / Barrier-to-autointegration factor, BAF superfamily / Barrier to autointegration factor / Barrier to autointegration factor
Similarity search - Domain/homology
ETHANOL / Barrier-to-autointegration factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsAgarwal, S. / Smith, M. / De La Rosa, I. / Kliment, A.V. / Swartz, P. / Segura-Totten, M. / Mattos, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2020
Title: Development of a structure-analysis pipeline using multiple-solvent crystal structures of barrier-to-autointegration factor.
Authors: Agarwal, S. / Smith, M. / De La Rosa, I. / Verba, K.A. / Swartz, P. / Segura-Totten, M. / Mattos, C.
History
DepositionOct 25, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
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

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Assembly

Deposited unit
A: Barrier-to-autointegration factor
B: Barrier-to-autointegration factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2394
Polymers20,1472
Non-polymers922
Water2,810156
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.850, 41.850, 214.410
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Barrier-to-autointegration factor / / Breakpoint cluster region protein 1


Mass: 10073.588 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BANF1, BAF, BCRG1 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O75531
#2: Chemical ChemComp-EOH / ETHANOL / Ethanol


Mass: 46.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 47.21 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 80 mM Tris pH 8.5, 16% Ethanol, 10% PEG-1450

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 12, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.68→41.075 Å / Num. obs: 22915 / % possible obs: 99.91 % / Redundancy: 13.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.63
Reflection shellResolution: 1.68→1.74 Å / Rmerge(I) obs: 0.86 / Num. unique obs: 2226

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6URE

6ure


Resolution: 1.68→41.075 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.92
RfactorNum. reflection% reflection
Rfree0.2101 1998 8.72 %
Rwork0.1637 --
obs0.1678 22900 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 141.07 Å2 / Biso mean: 35.9373 Å2 / Biso min: 14.56 Å2
Refinement stepCycle: final / Resolution: 1.68→41.075 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1402 0 18 156 1576
Biso mean--55.36 40.97 -
Num. residues----177
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6801-1.72210.31311370.26461432100
1.7221-1.76860.27421390.23221457100
1.7686-1.82070.26441410.21391462100
1.8207-1.87950.23631380.20421444100
1.8795-1.94660.27221370.18331450100
1.9466-2.02460.27471410.18781471100
2.0246-2.11670.20871430.17871484100
2.1167-2.22830.19521410.17261478100
2.2283-2.36790.22031410.15871477100
2.3679-2.55070.19581410.15721477100
2.5507-2.80730.20951450.17131516100
2.8073-3.21340.22731460.16011527100
3.2134-4.0480.21480.14511545100
4.048-41.0750.17581600.1472168299
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)
10.0718-0.0119-0.06270.02780.00530.0462-0.15540.0712-0.0054-0.26530.04690.22340.0080.0945-0.05630.2651-0.1278-0.00980.223-0.00540.240316.31370.1477-1.6044
20.12830.19080.01490.3070.10970.2324-0.0443-0.1193-0.02150.079-0.12680.31050.0253-0.0922-0.24890.2565-0.27670.09980.3326-0.10530.24126.3068-7.83939.9948
30.04880.05330.02330.07650.0960.1045-0.06680.0619-0.0560.149-0.01380.14970.3311-0.156-0.00030.1936-0.0550.03480.2137-0.03720.220320.6971-3.756511.8183
40.0440.00170.03430.01450.00970.05630.0640.1004-0.17490.0831-0.0127-0.00550.5587-0.20840.00160.3705-0.10510.00210.2108-0.01490.216317.8987-14.288.6662
50.0189-0.01570.05120.0425-0.07750.16260.0264-0.1560.0026-0.1272-0.06750.03330.10610.15070.00270.2262-0.16580.03290.206-0.03510.167522.6896-4.78031.4108
60.11080.07710.14040.56010.12110.3028-0.1474-0.09190.0468-0.11510.1396-0.3498-0.09380.31560.00940.1317-0.0364-0.00780.3094-0.03190.235134.86965.181719.8053
70.00810.00260.00560.05190.06360.0556-0.0808-0.1235-0.01040.12320.01740.15190.1609-0.1722-0.00010.1546-0.05070.03230.2483-0.04330.197422.40591.773817.5805
80.01170.01140.01320.0133-0.01240.0642-0.0126-0.38-0.15550.0796-0.07350.0471-0.1678-0.08970.00010.1831-0.02940.02370.3407-0.01860.193424.38363.209328.6941
90.14110.01760.0080.0869-0.02730.02270.0013-0.11070.0682-0.01350.1497-0.0234-0.23850.07770.00330.1971-0.09260.01330.2789-0.04420.204426.105211.112918.7868
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 27 )A1 - 27
2X-RAY DIFFRACTION2chain 'A' and (resid 28 through 37 )A28 - 37
3X-RAY DIFFRACTION3chain 'A' and (resid 38 through 55 )A38 - 55
4X-RAY DIFFRACTION4chain 'A' and (resid 56 through 70 )A56 - 70
5X-RAY DIFFRACTION5chain 'A' and (resid 71 through 89 )A71 - 89
6X-RAY DIFFRACTION6chain 'B' and (resid 2 through 41 )B2 - 41
7X-RAY DIFFRACTION7chain 'B' and (resid 42 through 55 )B42 - 55
8X-RAY DIFFRACTION8chain 'B' and (resid 56 through 70 )B56 - 70
9X-RAY DIFFRACTION9chain 'B' and (resid 71 through 89 )B71 - 89

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