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- PDB-7abm: X-ray structure of phosphorylated Barrier-to-autointegration fact... -

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Basic information

Entry
Database: PDB / ID: 7abm
TitleX-ray structure of phosphorylated Barrier-to-autointegration factor (BAF)
ComponentsBarrier-to-autointegration factor
KeywordsDNA BINDING PROTEIN / Barrier-to-Autointegration Factor chromosome compaction Phosphorylation
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 viral genome replication / negative regulation of cGAS/STING signaling pathway / 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 viral genome replication / negative regulation of cGAS/STING signaling pathway / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / chromosome organization / condensed chromosome / negative regulation of innate immune response / response to virus / DNA integration / chromatin organization / nuclear envelope / double-stranded DNA binding / response to oxidative stress / chromatin / protein homodimerization activity / DNA binding / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
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
: / Barrier-to-autointegration factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.004 Å
AuthorsZinn-Justin, S. / Marcelot, A. / Le Du, M.H. / Ropars, V.
Funding supportEuropean Union, France, 2items
OrganizationGrant numberCountry
European Communitys Seventh Framework Programme653706European Union
French Infrastructure for Integrated Structural Biology (FRISBI) France
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Di-phosphorylated BAF shows altered structural dynamics and binding to DNA, but interacts with its nuclear envelope partners.
Authors: Marcelot, A. / Petitalot, A. / Ropars, V. / Le Du, M.H. / Samson, C. / Dubois, S. / Hoffmann, G. / Miron, S. / Cuniasse, P. / Marquez, J.A. / Thai, R. / Theillet, F.X. / Zinn-Justin, S.
History
DepositionSep 8, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9463
Polymers9,6801
Non-polymers2662
Water1448
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area290 Å2
ΔGint-35 kcal/mol
Surface area5330 Å2
Unit cell
Length a, b, c (Å)70.320, 70.320, 40.625
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 Barrier-to-autointegration factor / Breakpoint cluster region protein 1


Mass: 9679.849 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Phosphorylation of Serine at position 4 / Source: (gene. exp.) Homo sapiens (human) / Gene: BANF1, BAF, BCRG1 / Production host: Escherichia coli (E. coli) / References: UniProt: O75531
#2: Chemical ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cs
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.95 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: pBAF was crystallized by the hanging drop method against 0.2 M sodium fluoride, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3→36 Å / Num. obs: 2463 / % possible obs: 100 % / Redundancy: 19.4 % / CC1/2: 0.998 / Net I/σ(I): 7.8
Reflection shellResolution: 3→3.18 Å / Num. unique obs: 390 / CC1/2: 0.963 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (19-MAR-2020)refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
STARANISOdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ci4

1ci4


Resolution: 3.004→35.16 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.821 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.668
RfactorNum. reflection% reflectionSelection details
Rfree0.3261 171 9.51 %RANDOM
Rwork0.196 ---
obs0.2076 1799 73.2 %-
Displacement parametersBiso max: 216.4 Å2 / Biso mean: 68.68 Å2 / Biso min: 22.86 Å2
Baniso -1Baniso -2Baniso -3
1--4.2693 Å20 Å20 Å2
2---4.2693 Å20 Å2
3---8.5385 Å2
Refine analyzeLuzzati coordinate error obs: 0.49 Å
Refinement stepCycle: final / Resolution: 3.004→35.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms675 0 2 8 685
Biso mean--178.38 38.74 -
Num. residues----86
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d243SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes118HARMONIC5
X-RAY DIFFRACTIONt_it688HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion80SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact539SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d688HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg924HARMONIC20.97
X-RAY DIFFRACTIONt_omega_torsion2.72
X-RAY DIFFRACTIONt_other_torsion24.39
LS refinement shellResolution: 3.16→3.3 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.3951 32 14.22 %
Rwork0.2273 193 -
obs--38.23 %
Refinement TLS params.Method: refined / Origin x: 26.9615 Å / Origin y: -7.0185 Å / Origin z: -1.6666 Å
111213212223313233
T-0.0008 Å20.0351 Å2-0.0743 Å2--0.2468 Å2-0.0956 Å2---0.2305 Å2
L5.9751 °2-1.8316 °2-2.3581 °2-12.687 °21.4938 °2--14.8564 °2
S-0.1588 Å °0.76 Å °-0.413 Å °-1.1314 Å °-0.3168 Å °0.5965 Å °-0.3331 Å °-0.5327 Å °0.4756 Å °
Refinement TLS groupSelection details: { A|* }

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