[English] 日本語
![](img/lk-miru.gif)
- PDB-1ncq: The structure of HRV14 when complexed with pleconaril, an antivir... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1ncq | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | The structure of HRV14 when complexed with pleconaril, an antiviral compound | |||||||||
![]() | (COAT PROTEIN ...) x 4 | |||||||||
![]() | VIRUS / rhinovirus 14 / HRV / pleconaril / Icosahedral virus | |||||||||
Function / homology | ![]() 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 / symbiont-mediated suppression of host gene expression / DNA replication / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / 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 | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Zhang, Y. / Simpson, A.A. / Bator, C.M. / Chakravarty, S. / Pevear, D.C. / Skochko, G.A. / Tull, T.M. / Diana, G. / Rossmann, M.G. | |||||||||
![]() | ![]() 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: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 173.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 136.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 474.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 495.4 KB | Display | |
Data in XML | ![]() | 19.5 KB | Display | |
Data in CIF | ![]() | 30.6 KB | Display | |
Arichive directory | ![]() ![]() | 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) ![]() |
---|---|
#2: Protein | Mass: 28501.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#3: Protein | Mass: 26236.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#4: Protein | Mass: 7183.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Non-polymers , 2 types, 243 molecules ![](data/chem/img/W11.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-W11 / |
---|---|
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal grow | Details: The crystal was soaked in stabilization buffer containing 2ug/ml pleconaril before data collection | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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: 671838 / Observed criterion σ(I): 0 |
Reflection | *PLUS Num. measured all: 1675367 / Rmerge(I) obs: 70.3 / Rmerge F obs: 0.077 |
Reflection shell | *PLUS % possible obs: 26.3 % / Rmerge(I) obs: 0.456 |
-
Processing
Refinement | Method to determine structure: ![]()
| ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
| ||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.216 / Rfactor Rwork: 0.217 | ||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||
Refine LS restraints | *PLUS
|