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- PDB-2bzf: Structural basis for DNA bridging by barrier-to-autointegration f... -

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Basic information

Entry
Database: PDB / ID: 2bzf
TitleStructural basis for DNA bridging by barrier-to-autointegration factor (BAF)
Components
  • 5'-D(*CP*CP*TP*CP*CP*AP*CP)-3'
  • 5'-D(*GP*TP*GP*GP*AP*GP*GP)-3'
  • BARRIER-TO-AUTOINTEGRATION FACTOR
KeywordsDNA BINDING PROTEIN / DNA-BINDING PROTEIN / RETROVIRAL INTEGRATION / NON-SPECIFIC DNA-BINDING / DNA COMPACTION / NUCLEAR ORGANIZATION / LEM FAMILY
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 / 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 / Barrier-to-autointegration factor, BAF superfamily / Barrier to autointegration factor / Barrier to autointegration factor / DNA polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / Barrier-to-autointegration factor
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.87 Å
AuthorsBradley, C.M. / Ronning, D.R. / Ghirlando, R. / Craigie, R. / Dyda, F.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2005
Title: Structural Basis for DNA Bridging by Barrier-to-Autointegration Factor.
Authors: Bradley, C.M. / Ronning, D.R. / Ghirlando, R. / Craigie, R. / Dyda, F.
History
DepositionAug 16, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 15, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 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: BARRIER-TO-AUTOINTEGRATION FACTOR
B: 5'-D(*GP*TP*GP*GP*AP*GP*GP)-3'
C: 5'-D(*CP*CP*TP*CP*CP*AP*CP)-3'


Theoretical massNumber of molelcules
Total (without water)14,3103
Polymers14,3103
Non-polymers00
Water905
1
A: BARRIER-TO-AUTOINTEGRATION FACTOR
B: 5'-D(*GP*TP*GP*GP*AP*GP*GP)-3'
C: 5'-D(*CP*CP*TP*CP*CP*AP*CP)-3'

A: BARRIER-TO-AUTOINTEGRATION FACTOR
B: 5'-D(*GP*TP*GP*GP*AP*GP*GP)-3'
C: 5'-D(*CP*CP*TP*CP*CP*AP*CP)-3'


Theoretical massNumber of molelcules
Total (without water)28,6216
Polymers28,6216
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_554y,x,-z-11
MethodPQS
Unit cell
Length a, b, c (Å)45.830, 45.830, 241.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein BARRIER-TO-AUTOINTEGRATION FACTOR /


Mass: 10073.588 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O75531
#2: DNA chain 5'-D(*GP*TP*GP*GP*AP*GP*GP)-3'


Mass: 2218.471 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain 5'-D(*CP*CP*TP*CP*CP*AP*CP)-3'


Mass: 2018.351 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Compound detailsRESPONSIBLE FOR INHIBITING SELF-DESTRUCTING AUTOINTEGRATION OF RETROVIRAL DNA, THEREBY PROMOTING ...RESPONSIBLE FOR INHIBITING SELF-DESTRUCTING AUTOINTEGRATION OF RETROVIRAL DNA, THEREBY PROMOTING INTEGRATION OF RETROVIRAL DNA INTO THE HOST CHROMOSOME.
Sequence detailsMET 1 IS NOT SEEN IN THE STRUCTURE.

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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: 4.44 Å3/Da / Density % sol: 72.29 %
Crystal growpH: 7.4 / Details: pH 7.40

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU/MSC RAXIS IV / Detector: IMAGE PLATE / Date: Aug 12, 2005 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.87→50 Å / Num. obs: 6542 / % possible obs: 97.9 % / Observed criterion σ(I): 2 / Redundancy: 4.89 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 19.2
Reflection shellResolution: 2.87→2.97 Å / Redundancy: 3.85 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 5.05 / % possible all: 97.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CI4

1ci4


Resolution: 2.87→50 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.268 -5.6 %RANDOM
Rwork0.244 ---
obs0.244 6060 97.9 %-
Refinement stepCycle: LAST / Resolution: 2.87→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms697 281 0 5 983
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.11
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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