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- PDB-4u0a: Hexameric HIV-1 CA in complex with CPSF6 peptide, P6 crystal form -
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Open data
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Basic information
Entry | Database: PDB / ID: 4u0a | ||||||
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Title | Hexameric HIV-1 CA in complex with CPSF6 peptide, P6 crystal form | ||||||
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![]() | VIRAL PROTEIN / Capsid | ||||||
Function / homology | ![]() 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 / viral budding via host ESCRT complex / ribosomal large subunit binding / Processing of Capped Intron-Containing Pre-mRNA / localization / Signaling by FGFR1 in disease / protein tetramerization / mRNA processing / ISG15 antiviral mechanism / host multivesicular body / viral nucleocapsid / nuclear speck / ribonucleoprotein complex / mRNA binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / RNA binding / zinc ion binding / nucleoplasm / membrane / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Price, A.J. / Jacques, D.A. / James, L.C. | ||||||
![]() | ![]() Title: Host Cofactors and Pharmacologic Ligands Share an Essential Interface in HIV-1 Capsid That Is Lost upon Disassembly. Authors: Price, A.J. / Jacques, D.A. / McEwan, W.A. / Fletcher, A.J. / Essig, S. / Chin, J.W. / Halambage, U.D. / Aiken, C. / James, L.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 102.2 KB | Display | ![]() |
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PDB format | ![]() | 76.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 431.1 KB | Display | ![]() |
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Full document | ![]() | 431.4 KB | Display | |
Data in XML | ![]() | 11.3 KB | Display | |
Data in CIF | ![]() | 15.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4u0bC ![]() 4u0cC ![]() 4u0dC ![]() 4u0eC ![]() 4u0fC ![]() 3h47S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Details | biological unit is the same as asym. |
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Components
#1: Protein | Mass: 25461.271 Da / Num. of mol.: 1 / Mutation: A14C,E45C,W184A,M185A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: isolate NY5 / Gene: gag / Plasmid: pET11a / Production host: ![]() ![]() |
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#2: Protein/peptide | Mass: 1550.796 Da / Num. of mol.: 1 / Fragment: UNP residues 313-327 / Source method: obtained synthetically / Source: (synth.) ![]() |
#3: Chemical | ChemComp-CL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.82 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.6M sodium potassium tartrate tetrahydrate, 0.1M TRIS |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 6, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.05→79.284 Å / Num. all: 17251 / Num. obs: 17251 / % possible obs: 100 % / Redundancy: 7.3 % / Rsym value: 0.266 / Net I/σ(I): 4.6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3H47 Resolution: 2.05→79.28 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.899 / WRfactor Rfree: 0.2656 / WRfactor Rwork: 0.2259 / FOM work R set: 0.8054 / SU B: 10.218 / SU ML: 0.141 / SU R Cruickshank DPI: 0.2041 / SU Rfree: 0.1785 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.204 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 79.22 Å2 / Biso mean: 27.74 Å2 / Biso min: 12.44 Å2
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Refinement step | Cycle: final / Resolution: 2.05→79.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.103 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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