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Yorodumi- 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 | ||||||
Components |
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Keywords | VIRAL PROTEIN / Capsid | ||||||
| Function / homology | Function and homology informationnegative regulation of RNA export from nucleus / nuclear pore complex assembly / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / nuclear pore nuclear basket / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Transport of Ribonucleoproteins into the Host Nucleus / 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 / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Transport of Ribonucleoproteins into the Host Nucleus / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / SUMOylation of SUMOylation proteins / nuclear localization sequence binding / structural constituent of nuclear pore / Transport of Mature mRNA Derived from an Intronless Transcript / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / SUMOylation of RNA binding proteins / NEP/NS2 Interacts with the Cellular Export Machinery / RNA export from nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / tRNA processing in the nucleus / nucleocytoplasmic transport / Viral Messenger RNA Synthesis / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / viral budding via host ESCRT complex / SUMOylation of DNA replication proteins / Regulation of HSF1-mediated heat shock response / mRNA transport / nuclear pore / SUMOylation of DNA damage response and repair proteins / protein-membrane adaptor activity / nuclear periphery / SUMOylation of chromatin organization proteins / HCMV Late Events / molecular condensate scaffold activity / Transcriptional regulation by small RNAs / host multivesicular body / ISG15 antiviral mechanism / viral penetration into host nucleus / protein import into nucleus / HCMV Early Events / nuclear envelope / host cell / viral nucleocapsid / snRNP Assembly / nuclear membrane / amyloid fibril formation / viral translational frameshifting / symbiont entry into host cell / nucleolus / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / structural molecule activity / DNA binding / RNA binding / zinc ion binding / nucleoplasm / identical protein binding / membrane / cytosol Similarity search - Function | ||||||
| Biological species | Human immunodeficiency virus type 1 group M subtype B Homo sapiens (human) | ||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å | ||||||
Authors | Price, A.J. / Jacques, D.A. / James, L.C. | ||||||
Citation | Journal: Plos Pathog. / Year: 2014Title: 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: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 4u0d.cif.gz | 955.6 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb4u0d.ent.gz | 802.9 KB | Display | PDB format |
| PDBx/mmJSON format | 4u0d.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 4u0d_validation.pdf.gz | 505.1 KB | Display | wwPDB validaton report |
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| Full document | 4u0d_full_validation.pdf.gz | 511.2 KB | Display | |
| Data in XML | 4u0d_validation.xml.gz | 76.4 KB | Display | |
| Data in CIF | 4u0d_validation.cif.gz | 102.5 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u0/4u0d ftp://data.pdbj.org/pub/pdb/validation_reports/u0/4u0d | 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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| 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.) Human immunodeficiency virus type 1 group M subtype BStrain: 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.) Homo sapiens (human) / References: UniProt: P49790#3: Chemical | ChemComp-CL / | Has protein modification | Y | |
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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: 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: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å | |||||||||||||||||||||||||||
| 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: molecular replacement | |||||||||
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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: MOLECULAR REPLACEMENTStarting 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 NCS | Refine-ID: X-RAY DIFFRACTION
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About Yorodumi



Human immunodeficiency virus type 1 group M subtype B
Homo sapiens (human)
X-RAY DIFFRACTION
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