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- PDB-4u0c: Hexameric HIV-1 CA in complex with Nup153 peptide, P6 crystal form -
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Open data
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Basic information
Entry | Database: PDB / ID: 4u0c | ||||||
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Title | Hexameric HIV-1 CA in complex with Nup153 peptide, P6 crystal form | ||||||
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![]() | VIRAL PROTEIN / Capsid / Nuclear Pore / FG repeat | ||||||
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 | ![]() | 63.8 KB | Display | ![]() |
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PDB format | ![]() | 44.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 426 KB | Display | ![]() |
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Full document | ![]() | 427 KB | Display | |
Data in XML | ![]() | 11.8 KB | Display | |
Data in CIF | ![]() | 17.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4u0aC ![]() 4u0bC ![]() 4u0dC ![]() 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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1 | ![]()
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Unit cell |
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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: yes 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: 1687.721 Da / Num. of mol.: 1 / Fragment: UNP residues 1407-1423 / Source method: obtained synthetically / Source: (synth.) ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.49 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: 30% v/v PEG 400, 0.1 M CHES |
-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: 1.77→35.67 Å / Num. obs: 24947 / % possible obs: 95.1 % / Redundancy: 3.2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.066 / Net I/σ(I): 7.3 / Num. measured all: 79253 / Scaling rejects: 3 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3H47 Resolution: 1.77→35.67 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.2042 / WRfactor Rwork: 0.1857 / FOM work R set: 0.8272 / SU B: 2.793 / SU ML: 0.085 / SU R Cruickshank DPI: 0.1212 / SU Rfree: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: 76.61 Å2 / Biso mean: 24.339 Å2 / Biso min: 10.52 Å2
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Refinement step | Cycle: final / Resolution: 1.77→35.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.774→1.82 Å / Total num. of bins used: 20
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