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Yorodumi- PDB-2ezx: SOLUTION STRUCTURE OF HUMAN BARRIER-TO-AUTOINTEGRATION FACTOR BAF... -
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-Basic information
Entry | Database: PDB / ID: 2ezx | ||||||
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Title | SOLUTION STRUCTURE OF HUMAN BARRIER-TO-AUTOINTEGRATION FACTOR BAF, NMR, REGULARIZED MEAN STRUCTURE | ||||||
Components | BARRIER-TO-AUTOINTEGRATION FACTOR | ||||||
Keywords | DNA 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 | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / SEE REMARK 3 | ||||||
Authors | Clore, G.M. / Cai, M. / Gronenborn, A.M. | ||||||
Citation | 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ezx.cif.gz | 70 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ezx.ent.gz | 54.3 KB | Display | PDB format |
PDBx/mmJSON format | 2ezx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ezx_validation.pdf.gz | 247 KB | Display | wwPDB validaton report |
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Full document | 2ezx_full_validation.pdf.gz | 246.7 KB | Display | |
Data in XML | 2ezx_validation.xml.gz | 4.2 KB | Display | |
Data in CIF | 2ezx_validation.cif.gz | 5.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ez/2ezx ftp://data.pdbj.org/pub/pdb/validation_reports/ez/2ezx | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | 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
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR details | Text: THE STRUCTURE IN THIS ENTRY IS THE RESTRAINED REGULARIZED MEAN STRUCTURE. |
-Sample preparation
Sample conditions | pH: 6.5 / Temperature: 313 K |
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Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer |
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-Processing
Software |
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NMR software |
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Refinement | Method: SEE REMARK 3 / Software ordinal: 1 Details: THE STRUCTURES WERE CALCULATED USING THE SIMULATED ANNEALING PROTOCOL OF NILGES ET AL. (1988) FEBS LETT. 229, 129 - 136 USING THE PROGRAM X-PLOR 3.1 (BRUNGER) MODIFIED TO INCORPORATE ...Details: THE STRUCTURES WERE CALCULATED USING THE SIMULATED ANNEALING PROTOCOL OF NILGES ET AL. (1988) FEBS LETT. 229, 129 - 136 USING THE PROGRAM X-PLOR 3.1 (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), AND A CONFORMATIONAL DATABASE POTENTIAL (KUSZWESKI ET AL. (1996) PROTEIN SCI. 5, 1067-108 AND (1997) J.MAGN.RESON. 125, 171-177). 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. BOND LENGTHS : 0.004931 BOND ANGLES : 0.543143 IMPROPER ANGLES : 0.551732 CDIH : 0.128297 NOE : 0.022087 COUP : 0.943946 13C SHIFTS RMS CA, CB (PPM): 1.04812, 1.20411 JHNHA RMS (HZ): 0.943946 0 DIPOLAR COUPLINGS NH CACO NCO HNCO RMS DIPOLAR (HZ): 0.421677 1.31903 0.483471 1.20095 1H METHYL SHIFTS: 0.118116 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 ensemble | Conformer selection criteria: REGULARIZED MEAN STRUCTURE / Conformers calculated total number: 40 / Conformers submitted total number: 1 |