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- PDB-4u0d: Hexameric HIV-1 CA in complex with Nup153 peptide, P212121 crysta... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4u0d | ||||||
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Title | Hexameric HIV-1 CA in complex with Nup153 peptide, P212121 crystal form | ||||||
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![]() | VIRAL PROTEIN / Capsid | ||||||
Function / homology | ![]() negative regulation of RNA export from nucleus / nuclear pore complex assembly / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / nuclear pore nuclear basket / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA ...negative regulation of RNA export from nucleus / nuclear pore complex assembly / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / nuclear pore nuclear basket / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / SUMOylation of SUMOylation proteins / Transport of Mature mRNA Derived from an Intronless Transcript / Rev-mediated nuclear export of HIV RNA / structural constituent of nuclear pore / SUMOylation of RNA binding proteins / Nuclear import of Rev protein / Transport of Mature mRNA derived from an Intron-Containing Transcript / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / RNA export from nucleus / nucleocytoplasmic transport / Viral Messenger RNA Synthesis / nuclear localization sequence binding / SUMOylation of ubiquitinylation proteins / viral budding via host ESCRT complex / Vpr-mediated nuclear import of PICs / SUMOylation of DNA replication proteins / Regulation of HSF1-mediated heat shock response / mRNA transport / SUMOylation of DNA damage response and repair proteins / nuclear pore / protein-membrane adaptor activity / SUMOylation of chromatin organization proteins / nuclear periphery / HCMV Late Events / molecular condensate scaffold activity / Transcriptional regulation by small RNAs / ISG15 antiviral mechanism / host multivesicular body / HCMV Early Events / viral penetration into host nucleus / protein import into nucleus / host cell / nuclear envelope / snRNP Assembly / viral nucleocapsid / nuclear membrane / amyloid fibril formation / symbiont entry into host cell / host cell nucleus / nucleolus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / structural molecule activity / virion membrane / DNA binding / RNA binding / zinc ion binding / nucleoplasm / identical protein binding / membrane / metal ion binding / cytosol 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 | ![]() | 955.8 KB | Display | ![]() |
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PDB format | ![]() | 802.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 505.1 KB | Display | ![]() |
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Full document | ![]() | 511.2 KB | Display | |
Data in XML | ![]() | 76.4 KB | Display | |
Data in CIF | ![]() | 102.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4u0aC ![]() 4u0bC ![]() 4u0cC ![]() 4u0eC ![]() 4u0fC ![]() 3h47S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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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.: 12 / Mutation: yes Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: isolate NY5 / Gene: gag / Plasmid: pET11a / Production host: ![]() ![]() #2: Protein/peptide | Mass: 1687.721 Da / Num. of mol.: 6 / Fragment: UNP residues 1407-1423 / Source method: obtained synthetically / Source: (synth.) ![]() #3: Chemical | ChemComp-CL / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.14 Å3/Da / Density % sol: 60.78 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 10% w/v PEG 8K, 0.1M imidazole |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 20, 2014 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 3→46.07 Å / Num. obs: 77432 / Redundancy: 3.2 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 8.6 | |||||||||||||||||||||||||||
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: 3H47 Resolution: 3→115.67 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.901 / WRfactor Rfree: 0.2402 / WRfactor Rwork: 0.2209 / FOM work R set: 0.7754 / SU B: 46.735 / SU ML: 0.376 / SU R Cruickshank DPI: 0.3986 / SU Rfree: 0.4221 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.422 / 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: 209.14 Å2 / Biso mean: 77.183 Å2 / Biso min: 33.36 Å2
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Refinement step | Cycle: final / Resolution: 3→115.67 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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