+Open data
-Basic information
Entry | Database: PDB / ID: 1nd2 | ||||||
---|---|---|---|---|---|---|---|
Title | The structure of Rhinovirus 16 | ||||||
Components | (coat protein ...) x 4 | ||||||
Keywords | VIRUS / HRV 16 / rhinovirus / piconaviridae / pocket factor / Icosahedral virus | ||||||
Function / homology | Function and homology information symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / ribonucleoside triphosphate phosphatase activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / ribonucleoside triphosphate phosphatase activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / DNA replication / RNA helicase activity / induction by virus of host autophagy / cysteine-type endopeptidase activity / RNA-directed RNA polymerase / viral RNA genome replication / virus-mediated perturbation of host defense response / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Human rhinovirus 16 | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Zhang, Y. / Simpson, A.A. / Bator, C.M. / Chakravarty, S. / Pevear, D.C. / Skochko, G.A. / Tull, T.M. / Diana, G. / Rossmann, M.G. | ||||||
Citation | Journal: J.Virol. / Year: 2004 Title: Structural and virological studies of the stages of virus replication that are affected by antirhinovirus compounds Authors: Zhang, Y. / Simpson, A.A. / Ledford, R.M. / Bator, C.M. / Chakravarty, S. / Skochko, G.A. / Demenczuk, T.M. / Watanyar, A. / Pevear, D.C. / Rossmann, M.G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1nd2.cif.gz | 180.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1nd2.ent.gz | 141.8 KB | Display | PDB format |
PDBx/mmJSON format | 1nd2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nd2_validation.pdf.gz | 395.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1nd2_full_validation.pdf.gz | 403.9 KB | Display | |
Data in XML | 1nd2_validation.xml.gz | 17.8 KB | Display | |
Data in CIF | 1nd2_validation.cif.gz | 29.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nd/1nd2 ftp://data.pdbj.org/pub/pdb/validation_reports/nd/1nd2 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| x 60||||||||
2 |
| ||||||||
3 |
| x 5||||||||
4 |
| x 6||||||||
5 |
| ||||||||
Unit cell |
| ||||||||
Symmetry | Point symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral)) |
-Components
-Coat protein ... , 4 types, 4 molecules ABCD
#1: Protein | Mass: 32501.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human rhinovirus 16 / Genus: Rhinovirus / Cell line: Hela cells / Species: Human rhinovirus A / References: UniProt: Q82122 |
---|---|
#2: Protein | Mass: 28990.615 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human rhinovirus 16 / Genus: Rhinovirus / Cell line: Hela cells / Species: Human rhinovirus A / References: UniProt: Q82122 |
#3: Protein | Mass: 26314.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human rhinovirus 16 / Genus: Rhinovirus / Cell line: Hela cells / Species: Human rhinovirus A / References: UniProt: Q82122 |
#4: Protein | Mass: 7374.025 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human rhinovirus 16 / Genus: Rhinovirus / Cell line: Hela cells / Species: Human rhinovirus A / References: UniProt: Q82122 |
-Non-polymers , 3 types, 496 molecules
#5: Chemical | ChemComp-ZN / | ||
---|---|---|---|
#6: Chemical | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Components of the solutions | *PLUS
|
-Data collection
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
---|---|
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. obs: 710094 / Observed criterion σ(I): 0 |
Reflection | *PLUS % possible obs: 52.3 % / Num. measured all: 1294215 / Rmerge(I) obs: 0.038 |
Reflection shell | *PLUS % possible obs: 20.9 % / Rmerge(I) obs: 0.081 |
-Processing
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
| ||||||||||||||||
Refine LS restraints | *PLUS
|