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Yorodumi- PDB-1ci4: THE CRYSTAL STRUCTURE OF HUMAN BARRIER-TO-AUTOINTEGRATION FACTOR (BAF) -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ci4 | |||||||||
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Title | THE CRYSTAL STRUCTURE OF HUMAN BARRIER-TO-AUTOINTEGRATION FACTOR (BAF) | |||||||||
Components | PROTEIN (BARRIER-TO-AUTOINTEGRATION FACTOR (BAF)) | |||||||||
Keywords | DNA 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 / condensed chromosome / negative regulation of viral genome replication / negative regulation of cGAS/STING signaling pathway ...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 / condensed chromosome / 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 / 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 / DNA binding / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å | |||||||||
Authors | Umland, 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ci4.cif.gz | 51.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ci4.ent.gz | 37.3 KB | Display | PDB format |
PDBx/mmJSON format | 1ci4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ci4_validation.pdf.gz | 427.4 KB | Display | wwPDB validaton report |
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Full document | 1ci4_full_validation.pdf.gz | 428.9 KB | Display | |
Data in XML | 1ci4_validation.xml.gz | 11.3 KB | Display | |
Data in CIF | 1ci4_validation.cif.gz | 16.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ci/1ci4 ftp://data.pdbj.org/pub/pdb/validation_reports/ci/1ci4 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS oper:
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-Components
#1: Protein | 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 / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 44 % | ||||||||||||||||||||||||
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Crystal grow | pH: 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
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-Data collection
Diffraction | Mean temperature: 95 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.9793,0.9789,0.9686 | ||||||||||||
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 27, 1998 / Details: BENT MIRRORS | ||||||||||||
Radiation | Monochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method 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
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 36.72 Å2 / ksol: 0.351 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→40 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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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
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