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Yorodumi- PDB-4b4n: CPSF6 defines a conserved capsid interface that modulates HIV-1 r... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4b4n | ||||||
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Title | CPSF6 defines a conserved capsid interface that modulates HIV-1 replication | ||||||
Components |
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Keywords | VIRAL PROTEIN/RNA BINDING PROTEIN / VIRAL PROTEIN-RNA BINDING PROTEIN COMPLEX / HIV-1 / CYCLOPHILIN | ||||||
Function / homology | Function and homology information exon-exon junction complex binding / : / positive regulation of RNA export from nucleus / mRNA cleavage factor complex / interchromatin granule / Processing of Intronless Pre-mRNAs / perichromatin fibrils / mRNA cleavage and polyadenylation specificity factor complex / mRNA alternative polyadenylation / paraspeckles ...exon-exon junction complex binding / : / positive regulation of RNA export from nucleus / mRNA cleavage factor complex / interchromatin granule / Processing of Intronless Pre-mRNAs / perichromatin fibrils / mRNA cleavage and polyadenylation specificity factor complex / mRNA alternative polyadenylation / paraspeckles / mRNA 3'-end processing / mRNA 3'-end processing / Signaling by cytosolic FGFR1 fusion mutants / RNA Polymerase II Transcription Termination / protein heterotetramerization / ribosomal large subunit binding / Processing of Capped Intron-Containing Pre-mRNA / localization / Signaling by FGFR1 in disease / viral process / protein tetramerization / mRNA processing / viral capsid / nuclear speck / ribonucleoprotein complex / mRNA binding / RNA binding / nucleoplasm / membrane / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | HUMAN IMMUNODEFICIENCY VIRUS 1 HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.813 Å | ||||||
Authors | Price, A.J. / James, L.C. | ||||||
Citation | Journal: Plos Pathog. / Year: 2012 Title: Cpsf6 Defines a Conserved Capsid Interface that Modulates HIV-1 Replication. Authors: Price, A.J. / Fletcher, A.J. / Schaller, T. / Elliott, T. / Lee, K. / Kewalramani, V.N. / Chin, J.W. / Towers, G.J. / James, L.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4b4n.cif.gz | 77.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4b4n.ent.gz | 57.7 KB | Display | PDB format |
PDBx/mmJSON format | 4b4n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b4/4b4n ftp://data.pdbj.org/pub/pdb/validation_reports/b4/4b4n | HTTPS FTP |
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-Related structure data
Related structure data | 2gonS 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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Unit cell |
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-Components
#1: Protein | Mass: 16204.573 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN, RESIDUES 33-178 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HUMAN IMMUNODEFICIENCY VIRUS 1 / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: A9PKC6 |
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#2: Protein/peptide | Mass: 1550.796 Da / Num. of mol.: 1 / Fragment: RESIDUES 313-327 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: Q16630 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.52 % / Description: NONE |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop Details: 17 DEGREES (SITTING DROPS).PROTEIN/ PEPTIDE SOLUTION (0.37 MM HIV-1 CAN AND 4 MM CPSF6313-327 IN 20 MM HEPES PH 7, 50 MM NACL, 1 MM DTT) WAS MIXED WITH RESERVOIR SOLUTION (20% W/V PEG 3350, ...Details: 17 DEGREES (SITTING DROPS).PROTEIN/ PEPTIDE SOLUTION (0.37 MM HIV-1 CAN AND 4 MM CPSF6313-327 IN 20 MM HEPES PH 7, 50 MM NACL, 1 MM DTT) WAS MIXED WITH RESERVOIR SOLUTION (20% W/V PEG 3350, 0.2 M POTASSIUM PHOSPHATE DIBASIC) IN A 1:1 MIX. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5418 |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. obs: 13664 / % possible obs: 95.8 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rsym value: 0.044 / Net I/σ(I): 14.5 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2GON Resolution: 1.813→36.251 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.918 / SU B: 8.731 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.334 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.696 Å2
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Refinement step | Cycle: LAST / Resolution: 1.813→36.251 Å
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