+Open data
-Basic information
Entry | Database: PDB / ID: 1na1 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | The structure of HRV14 when complexed with Pleconaril | |||||||||
Components | (Coat protein ...) x 4 | |||||||||
Keywords | VIRUS / HRV14 / human rhinovirus 14 / Pleconaril / Icosahedral virus | |||||||||
Function / homology | Function and homology information lysis of host organelle involved in viral entry into host cell / 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 / 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 ...lysis of host organelle involved in viral entry into host cell / 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 / 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 / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Human rhinovirus 14 | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 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 |
| |||||||||
Remark 999 | AUTHORS STATE THAT RESIDUE 170 (CHAIN B) CAN BE ILE OR LEU, AS SEEN IN OTHER DATABASE REFERENCE SEQUENCES. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1na1.cif.gz | 176.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1na1.ent.gz | 138.3 KB | Display | PDB format |
PDBx/mmJSON format | 1na1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1na1_validation.pdf.gz | 475.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1na1_full_validation.pdf.gz | 499 KB | Display | |
Data in XML | 1na1_validation.xml.gz | 20 KB | Display | |
Data in CIF | 1na1_validation.cif.gz | 31.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/na/1na1 ftp://data.pdbj.org/pub/pdb/validation_reports/na/1na1 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| x 60||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
2 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3 |
| x 5||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
4 |
| x 6||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
5 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
6 |
| x 20||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral)) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
|
-Components
-Coat protein ... , 4 types, 4 molecules ABCD
#1: Protein | Mass: 32560.549 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human rhinovirus 14 / Genus: Rhinovirus / Cell line: HELA CELLS / Species: Human rhinovirus B / References: UniProt: P03303 |
---|---|
#2: Protein | Mass: 28501.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human rhinovirus 14 / Genus: Rhinovirus / Cell line: HELA CELLS / Species: Human rhinovirus B / References: UniProt: P03303 |
#3: Protein | Mass: 26236.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human rhinovirus 14 / Genus: Rhinovirus / Cell line: HELA CELLS / Species: Human rhinovirus B / References: UniProt: P03303 |
#4: Protein | Mass: 7183.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human rhinovirus 14 / Genus: Rhinovirus / Cell line: HELA CELLS / Species: Human rhinovirus B / References: UniProt: P03303 |
-Non-polymers , 2 types, 243 molecules
#5: Chemical | ChemComp-W11 / |
---|---|
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: HEPES, NaCl, CaCl2, PEG8K, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Sep 14, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→20 Å / Num. all: 320952 / Num. obs: 320952 / % possible obs: 77.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.164 |
Reflection shell | Highest resolution: 3.3 Å / % possible all: 77.8 |
Reflection | *PLUS Num. measured all: 545390 / Rmerge(I) obs: 0.164 |
Reflection shell | *PLUS % possible obs: 68.2 % / Rmerge(I) obs: 0.477 |
-Processing
Software |
| |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.3→20 Å
| |||||||||||||||||||||
Refine LS restraints | *PLUS
|