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- PDB-1qck: SOLUTION STRUCTURE OF HUMAN BARRIER-TO-AUTOINTEGRATION FACTOR BAF... -

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Basic information

Entry
Database: PDB / ID: 1qck
TitleSOLUTION STRUCTURE OF HUMAN BARRIER-TO-AUTOINTEGRATION FACTOR BAF, NMR, REGULARIZED MEAN STRUCTURE PLUS 20 INDIVIDUAL SIMULATED ANNEALING STRUCTURES
ComponentsPROTEIN (BARRIER-TO-AUTOINTEGRATION FACTOR)
KeywordsDNA BINDING PROTEIN / DNA-BINDING PROTEIN / INTEGRATION / AIDS / RETROVIRUSES
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)
MethodSOLUTION NMR / SEE REMARK 7
AuthorsClore, G.M.
Citation
Journal: J.Am.Chem.Soc. / Year: 1999
Title: IMPROVING THE PACKING AND ACCURACY OF NMR STRUCTURES WITH A PSEUDOPOTENTIAL FOR THE RADIUS OF GYRATION
Authors: Juszewski, J. / Gronenborn, A.M. / Clore, G.M.
#1: Journal: Nat.Struct.Biol. / Year: 1998
Title: Solution Structure of the Cellular Factor Baf Responsible for Protecting Retroviral DNA from Autointegration
Authors: Cai, M. / Huang, Y. / Zheng, R. / Wei, S.Q. / Ghirlando, R. / Lee, M.S. / Craigie, R. / Gronenborn, A.M. / Clore, G.M.
History
DepositionMay 6, 1999Deposition site: RCSB / Processing site: NDB
Revision 1.0Jun 23, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (BARRIER-TO-AUTOINTEGRATION FACTOR)
B: PROTEIN (BARRIER-TO-AUTOINTEGRATION FACTOR)


Theoretical massNumber of molelcules
Total (without water)20,1472
Polymers20,1472
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)21 / 20INDIVIDUAL SIMULATED ANNEALING STRUCTURES
RepresentativeModel #1restrained minimized mean

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Components

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


Mass: 10073.588 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: O75531

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: THE FIRST STRUCTURE IN THIS ENTRY IS THE RESTRAINED REGULARIZED MEAN STRUCTURE. THE REMAINING STRUCTURES ARE THE 20 SIMULATED ANNEALING STRUCTURES

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Sample preparation

Sample conditionspH: 6.5 / Temperature: 313 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMX600BrukerDMX6005001
Bruker DMX500BrukerDMX5006002

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Processing

NMR software
NameVersionDeveloperClassification
CNS/XPLORMODIFIEDBRUNGER,ADAMS,CLORE,DELANO,GROS, GROSSE-KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READrefinement
CNS/XPLORMODIFIEDBRUNGER,ADAMS,CLORE,DELANO,GROS, GROSSE-KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READstructure solution
RefinementMethod: SEE REMARK 7 / Software ordinal: 1
Details: SEE REMARK 7 THE STRUCTURES WERE CALCULATED USING THE SIMULATED ANNEALING PROTOCOL OF NILGES ET AL. (1988) FEBS LETT. 229, 129 - 136 USING THE PROGRAM (BRUNGER) MODIFIED TO INCORPORATE ...Details: SEE REMARK 7 THE STRUCTURES WERE CALCULATED USING THE SIMULATED ANNEALING PROTOCOL OF NILGES ET AL. (1988) FEBS LETT. 229, 129 - 136 USING THE PROGRAM (BRUNGER) MODIFIED TO INCORPORATE COUPLING CONSTANT (GARRETT ET AL. (1984) J.MAGN.RESON. SERIES B 104, 99 - 103), CARBON CHEMICAL SHIFT (KUSZEWSKI ET AL. (1995) J.MAGN.RESON. SERIES B 106, 92 - 96) RESTRAINTS, 1H CHEMICAL SHIFT RESTRAINTS (KUSZEWSKI ET AL. (1995) J.MAGN.RESON. SERIES B 107, 293-297; (1996) J.MAGN.RESON. SERIES B 112, 79-81), A CONFORMATIONAL DATABASE POTENTIAL (KUSZWESKI ET AL. (1996) PROTEIN SCI. 5, 1067-108 AND (1997) J.MAGN.RESON. 125, 171-177), AND A TERM FOR THE RADIUS OF GYRATION (KUSZEWSKI ET AL. (1999) J. AM. CHEM. SOC. 121, 2337-2338). THE 3D STRUCTURE OF THE 21 KDA BAF DIMER WAS SOLVED BY MULTI-DIMENSIONAL HETERONUCLEAR-EDITED AND -FILTERED NMR BASED ON 1655 EXPERIMENTAL RESTRAINTS (PER MONOMER): (A) INTRASUBUNIT: 288 SEQUENTIAL (|I-J|=1), 267 MEDIUM RANGE (1 < |I-J| >=5) AND 190 LONG RANGE (|I-J| >5) INTERRESIDUE, AND 7 INTRARESIDUE APPROXIMATE INTERPROTON DISTANCE RESTRAINTS; 64 DISTANCE RESTRAINTS FOR 32 HYDROGEN BONDS; 257 TORSION ANGLE (84 PHI, 78 PSI, 60 CHI1 29 CHI2 AND 6 CHI3) RESTRAINTS; 66 THREE-BOND HN-HA COUPLING CONSTANT RESTRAINTS; 165 (87 CALPHA AND 78 CBETA) 13C SHIFT RESTRAINTS; 44 1H METHYL PROTON CHEMICAL SHIFTS; 259 DIPOLAR COUPLINGS (76 N-H, 76 CALPHA-C', 55 N-C' AND 52 HN-C'). (B) 48 INTERSUBUNIT INTERPROTON DISTANCE RESTRAINTS. RMS DEVIATIONS FOR RESTRAINED MINIMIZED MEAN STRUCTURE BOND LENGTHS : 0.0065 BOND ANGLES : 0.645 IMPROPER ANGLES : 0.809 TORSION ANGLES : 0.44 NOE : 0.024 3JHNA COUP : 0.95 13C SHIFTS RMS CA, CB (PPM): 1.06, 1.22 DIPOLAR COUPLINGS NH CACO NCO HNCO RMS DIPOLAR (HZ): 0.48 1.35 0.49 1.27 1H METHYL SHIFTS: 0.213 RESIDUE 500 WITH ATOMS OO, X, Y AND Z REPRESENTS THE MOLECULAR ALIGNMENT TENSOR FOR THE DIPOLAR COUPLINGS MEASURED IN A DILUTE LIQUID CRYSTAL. ATOM 2811 X ANI 500 206.152-144.189 1.390 1.00 94.16 ATOM 2812 Y ANI 500 205.428-140.345 3.032 1.00 94.09 ATOM 2813 Z ANI 500 202.691-142.020 0.244 1.00 93.80 ATOM 2814 OO ANI 500 205.638-141.460 0.255 1.00 93.81 THE STRUCTURE IN THIS ENTRY IS THE RESTRAINED REGULARIZED MEAN STRUCTURE AND THE LAST NUMERIC COLUMN REPRESENTS THE RMS OF THE 40 INDIVIDUAL SIMULATED ANNEALING STRUCTURES FOUND IN PDB ENTRY 2EZY ABOUT THE MEAN COORDINATE POSITIONS. THE LAST NUMERIC COLUMN IN THE INDIVIDUAL SA STRUCTURES HAS NO MEANING.
NMR representativeSelection criteria: restrained minimized mean
NMR ensembleConformer selection criteria: INDIVIDUAL SIMULATED ANNEALING STRUCTURES
Conformers calculated total number: 20 / Conformers submitted total number: 21

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