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- PDB-1ci4: THE CRYSTAL STRUCTURE OF HUMAN BARRIER-TO-AUTOINTEGRATION FACTOR (BAF) -

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Basic information

Entry
Database: PDB / ID: 1ci4
TitleTHE CRYSTAL STRUCTURE OF HUMAN BARRIER-TO-AUTOINTEGRATION FACTOR (BAF)
ComponentsPROTEIN (BARRIER-TO-AUTOINTEGRATION FACTOR (BAF))
KeywordsDNA BINDING PROTEIN / RETROVIRAL INTEGRATION / PREINTEGRATION COMPLEX
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 / 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
Barrier-to-autointegration factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsUmland, T.C. / Wei, S.-Q. / Craigie, R. / Davies, D.R.
Citation
Journal: Biochemistry / Year: 2000
Title: Structural basis of DNA bridging by barrier-to-autointegration factor.
Authors: Umland, T.C. / Wei, S.Q. / Craigie, R. / Davies, D.R.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: A previously unidentified host protein protects retroviral DNA from autointegration.
Authors: Lee, M.S. / Craigie, R.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994
Title: Protection of retroviral DNA from autointegration: involvement of a cellular factor.
Authors: Lee, M.S. / Craigie, R.
History
DepositionApr 7, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Aug 16, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Nov 27, 2019Group: Atomic model / Database references / Derived calculations
Category: atom_site / citation ...atom_site / citation / struct_conn / struct_ref_seq_dif
Item: _atom_site.occupancy / _citation.pdbx_database_id_DOI ..._atom_site.occupancy / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 2.1Dec 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry / pdbx_validate_symm_contact
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 (BARRIER-TO-AUTOINTEGRATION FACTOR (BAF))
B: PROTEIN (BARRIER-TO-AUTOINTEGRATION FACTOR (BAF))


Theoretical massNumber of molelcules
Total (without water)20,3352
Polymers20,3352
Non-polymers00
Water4,107228
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-9 kcal/mol
Surface area8520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.800, 41.800, 214.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-199-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
/ NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(-0.86468, 0.3456, -0.36454), (0.36982, -0.05314, -0.92758), (-0.33995, -0.93688, -0.08186)46.96663, 3.67135, 21.67661
2given(-0.86468, 0.36982, -0.33995), (0.3456, -0.05314, -0.93688), (-0.36454, -0.92758, -0.08186)46.62228, 4.27167, 22.301

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Components

#1: Protein PROTEIN (BARRIER-TO-AUTOINTEGRATION FACTOR (BAF))


Mass: 10167.377 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: SELENOMETHIONINE (RESIDUE NAME MSE) HAS BEEN SUBSTITUTED FOR METHIONINE
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)LYSS / References: UniProt: O75531
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / Source method: isolated from a natural source / Formula: H2O

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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: 2.3 Å3/Da / Density % sol: 44 %
Crystal growpH: 6.5
Details: DIALYSIS OF PROTEIN AT 8.3 MG/ML IN 20MM TRIS HCL AT PH7.0, 10%(W/V) GLYCEROL, 150MM NACL, 10MM DTT, AND 0.1MM EDTA AGAINST 20MM IMIDAZOLE AT PH 6.5, 80MM NACL, AND 10MM DTT. DIALYSIS DONE ...Details: DIALYSIS OF PROTEIN AT 8.3 MG/ML IN 20MM TRIS HCL AT PH7.0, 10%(W/V) GLYCEROL, 150MM NACL, 10MM DTT, AND 0.1MM EDTA AGAINST 20MM IMIDAZOLE AT PH 6.5, 80MM NACL, AND 10MM DTT. DIALYSIS DONE AT ROOM TEMPERATURE.(ALL CONCENTRATIONS ARE IN MILLI-MOLAR)
Crystal grow
*PLUS
Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mMimidazole11
280 mM11NaCl
310 mMdithiothreitol11

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.9793,0.9789,0.9686
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 27, 1998 / Details: BENT MIRRORS
RadiationMonochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.97891
30.96861
ReflectionResolution: 1.9→40 Å / Num. obs: 16011 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 13.7 % / Biso Wilson estimate: 17.3 Å2 / Rsym value: 6.1 / Net I/σ(I): 16
Reflection shellResolution: 1.9→1.94 Å / Rsym value: 18.4 / % possible all: 100
Reflection
*PLUS
Num. measured all: 219206 / Rmerge(I) obs: 0.061
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.184

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Processing

Software
NameVersionClassification
SOLVEphasing
PHASES-95model building
CNS0.4refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASESV. 95phasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→40 Å / Rfactor Rfree error: 0.007 / Data cutoff high rms absF: 281646.63 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLI
Details: REFINEMENT TARGET: MAXIMUM LIKELIHOOD TARGET USING INTENSITIES
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1588 10.1 %RANDOM
Rwork0.21 ---
obs-15702 98.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.72 Å2 / ksol: 0.351 e/Å3
Displacement parametersBiso mean: 24.1 Å2
Baniso -1Baniso -2Baniso -3
1-4.27 Å20 Å20 Å2
2--4.27 Å20 Å2
3----8.54 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1389 0 0 228 1617
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.21.5
X-RAY DIFFRACTIONc_mcangle_it3.232
X-RAY DIFFRACTIONc_scbond_it3.582
X-RAY DIFFRACTIONc_scangle_it4.792.5
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDNCS model detailsRms dev Biso (Å2)Rms dev position (Å)Weight Biso Weight position
11RESTRAINTS2.160.198320
222.450.364310
334.361.0855
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.318 248 10 %
Rwork0.26 2234 -
obs--97.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 14112 / Rfactor Rfree: 0.265 / Rfactor Rwork: 0.214
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0099
X-RAY DIFFRACTIONc_angle_deg1.37
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.91

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