[English] 日本語
Yorodumi
- PDB-1ncr: The structure of Rhinovirus 16 when complexed with pleconaril, an... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 1ncr
TitleThe structure of Rhinovirus 16 when complexed with pleconaril, an antiviral compound
Components(coat protein ...) x 4
KeywordsVIRUS / HRV16 / rhinovirus / pleconaril / piconavirus / Icosahedral virus / Virus
Function / homology
Function and homology information


suppression by virus of host translation initiation factor activity / positive stranded viral RNA replication / picornain 2A / pore-mediated entry of viral genome into host cell / suppression by virus of host mRNA export from nucleus / suppression by virus of host RIG-I activity / picornain 3C / endocytosis involved in viral entry into host cell / RNA-protein covalent cross-linking / T=pseudo3 icosahedral viral capsid ...suppression by virus of host translation initiation factor activity / positive stranded viral RNA replication / picornain 2A / pore-mediated entry of viral genome into host cell / suppression by virus of host mRNA export from nucleus / suppression by virus of host RIG-I activity / picornain 3C / endocytosis involved in viral entry into host cell / RNA-protein covalent cross-linking / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / pore formation by virus in membrane of host cell / integral to membrane of host cell / RNA helicase activity / nucleoside-triphosphate phosphatase / RNA-directed RNA polymerase / induction by virus of host autophagy / suppression by virus of host gene expression / ion channel activity / protein complex oligomerization / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-directed 5'-3' RNA polymerase activity / DNA replication / transcription, DNA-templated / virion attachment to host cell / structural molecule activity / RNA binding / membrane / ATP binding
P-loop containing nucleoside triphosphate hydrolase / Viral coat protein subunit / Poliovirus 3A protein-like / Helicase, superfamily 3, single-stranded RNA virus / Peptidase S1, PA clan / RNA-directed RNA polymerase, catalytic domain / Picornavirus coat protein VP4 / Picornavirus 2B protein / Picornavirus capsid / RNA-directed RNA polymerase, C-terminal domain ...P-loop containing nucleoside triphosphate hydrolase / Viral coat protein subunit / Poliovirus 3A protein-like / Helicase, superfamily 3, single-stranded RNA virus / Peptidase S1, PA clan / RNA-directed RNA polymerase, catalytic domain / Picornavirus coat protein VP4 / Picornavirus 2B protein / Picornavirus capsid / RNA-directed RNA polymerase, C-terminal domain / Helicase, superfamily 3, single-stranded DNA/RNA virus / Peptidase C3A/C3B, picornaviral / Peptidase C3, picornavirus core protein 2A / Picornavirus/Calicivirus coat protein / Poliovirus core protein 3a, soluble domain / Picornavirus coat protein VP4 superfamily / picornavirus capsid protein / Picornavirus coat protein (VP4) / Picornavirus core protein 2A / RNA helicase / RNA dependent RNA polymerase / Poliovirus 3A protein like / RdRp of positive ssRNA viruses catalytic domain profile. / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Picornavirales 3C/3C-like protease domain profile. / 3C cysteine protease (picornain 3C) / Picornavirus 2B protein
Genome polyprotein
Biological speciesHuman rhinovirus 16
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsZhang, Y. / Simpson, A.A. / Bator, C.M. / Chakravarty, S. / Pevear, D.C. / Skochko, G.A. / Tull, T.M. / Diana, G. / Rossmann, M.G.
CitationJournal: 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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Dec 5, 2002 / Release: Dec 16, 2003
RevisionDateData content typeGroupProviderType
1.0Dec 16, 2003Structure modelrepositoryInitial release
1.1Apr 28, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: coat protein VP1
B: coat protein VP2
C: coat protein VP3
D: coat protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,8557
Polymers95,1804
Non-polymers6753
Water6,089338
1
A: coat protein VP1
B: coat protein VP2
C: coat protein VP3
D: coat protein VP4
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,751,319420
Polymers5,710,811240
Non-polymers40,508180
Water4,324240
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
A: coat protein VP1
B: coat protein VP2
C: coat protein VP3
D: coat protein VP4
hetero molecules
x 5


  • icosahedral pentamer
  • 479 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)479,27735
Polymers475,90120
Non-polymers3,37615
Water36020
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: coat protein VP1
B: coat protein VP2
C: coat protein VP3
D: coat protein VP4
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 575 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)575,13242
Polymers571,08124
Non-polymers4,05118
Water43224
TypeNameSymmetry operationNumber
point symmetry operation6
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
Unit cell
γ
α
β
Length a, b, c (Å)359.494, 343.657, 332.184
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))

-
Components

-
Coat protein ... , 4 types, 4 molecules ABCD

#1: Protein/peptide coat protein VP1


Mass: 32501.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human rhinovirus 16 / Genus: Rhinovirus / Species: Human rhinovirus A / References: UniProt: Q82122
#2: Protein/peptide coat protein VP2


Mass: 28990.615 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human rhinovirus 16 / Genus: Rhinovirus / Species: Human rhinovirus A / References: UniProt: Q82122
#3: Protein/peptide coat protein VP3


Mass: 26314.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human rhinovirus 16 / Genus: Rhinovirus / Species: Human rhinovirus A / References: UniProt: Q82122
#4: Protein/peptide coat protein VP4


Mass: 7374.025 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human rhinovirus 16 / Genus: Rhinovirus / Species: Human rhinovirus A / References: UniProt: Q82122

-
Non-polymers , 4 types, 341 molecules

#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Zinc
#6: Chemical ChemComp-W11 / 3-{3,5-DIMETHYL-4-[3-(3-METHYL-ISOXAZOL-5-YL)-PROPOXY]-PHENYL}-5-TRIFLUOROMETHYL-[1,2,4]OXADIAZOLE / WIN63843


Mass: 381.349 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H18F3N3O3
#7: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2 / Myristic acid
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / Source method: isolated from a natural source / Formula: H2O / Water

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS

Crystal-ID: 1

IDConc.Common nameSol-IDChemical formula
10.25 MHEPESreservoir
20.25 MreservoirNaCl
30.1 MreservoirCaCl2
40.3 %PEG8000reservoir
520000 mg/mlproteindrop

-
Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 452981 / Observed criterion σ(I): 0
Reflection
*PLUS
% possible obs: 40.9 % / Num. measured all: 1107533 / Rmerge(I) obs: 0.133
Reflection shell
*PLUS
% possible obs: 34.9 % / Rmerge(I) obs: 0.395

-
Processing

SoftwareName: CNS / Version: 1 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflectionSelection details
Rfree0.247 -random
Rwork0.243 --
All0.247 --
Obs0.247 452981 -
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6336 0 43 338 6717
Refinement
*PLUS
Rfactor Rfree: 0.248 / Rfactor Rwork: 0.249
Refine LS restraints
*PLUS
Refinement-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.0061
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.37

+
About Yorodumi

-
News

-
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.: Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator

External links: EMDB at PDBe / Contact to PDBj

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more