+Open data
-Basic information
Entry | Database: PDB / ID: 6hip | ||||||
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Title | Structure of SPF45 UHM bound to HIV-1 Rev ULM | ||||||
Components |
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Keywords | SPLICING / Splicing factor / viral protein | ||||||
Function / homology | Function and homology information alternative mRNA splicing, via spliceosome / host cell nucleolus / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / mRNA cis splicing, via spliceosome / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / precatalytic spliceosome / Minus-strand DNA synthesis / Plus-strand DNA synthesis ...alternative mRNA splicing, via spliceosome / host cell nucleolus / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / mRNA cis splicing, via spliceosome / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / precatalytic spliceosome / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / mRNA transport / Binding and entry of HIV virion / viral process / mRNA Splicing - Major Pathway / Assembly Of The HIV Virion / Budding and maturation of HIV virion / host cell cytoplasm / DNA-binding transcription factor activity / RNA binding / nucleoplasm / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | Pabis, M. / Corsini, L. / Sattler, M. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2019 Title: Modulation of HIV-1 gene expression by binding of a ULM motif in the Rev protein to UHM-containing splicing factors. Authors: Pabis, M. / Corsini, L. / Vincendeau, M. / Tripsianes, K. / Gibson, T.J. / Brack-Werner, R. / Sattler, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hip.cif.gz | 118.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hip.ent.gz | 91.4 KB | Display | PDB format |
PDBx/mmJSON format | 6hip.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6hip_validation.pdf.gz | 455.5 KB | Display | wwPDB validaton report |
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Full document | 6hip_full_validation.pdf.gz | 457.2 KB | Display | |
Data in XML | 6hip_validation.xml.gz | 14.6 KB | Display | |
Data in CIF | 6hip_validation.cif.gz | 21.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hi/6hip ftp://data.pdbj.org/pub/pdb/validation_reports/hi/6hip | HTTPS FTP |
-Related structure data
Related structure data | 2pe8S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 11633.431 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RBM17, SPF45 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96I25 #2: Protein/peptide | | Mass: 1404.630 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: synthetic construct (others) / References: UniProt: P04618*PLUS #3: Chemical | ChemComp-TRP / | #4: Chemical | ChemComp-NA / | #5: 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: 2.1 Å3/Da / Density % sol: 41.54 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 22.5 % (w/v) PEG 3350, 0.1 M HEPES pH 6.0, 0.2 M sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99984 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 6, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99984 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→18.49 Å / Num. obs: 64821 / % possible obs: 98.5 % / Redundancy: 7.82 % / Rrim(I) all: 0.17 / Net I/σ(I): 8.18 |
Reflection shell | Resolution: 1.2→1.27 Å / Redundancy: 4 % / Num. unique obs: 9278 / Rrim(I) all: 0.647 / % possible all: 91.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2PE8 Resolution: 1.2→18.49 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.15 / SU ML: 0.024 / Cross valid method: THROUGHOUT / ESU R: 0.042 / ESU R Free: 0.041 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.526 Å2
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Refinement step | Cycle: 1 / Resolution: 1.2→18.49 Å
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