[English] 日本語
Yorodumi
- PDB-5zvt: Structure of RNA polymerase complex and genome within a dsRNA vir... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 5zvt
TitleStructure of RNA polymerase complex and genome within a dsRNA virus provides insights into the mechanisms of transcription and assembly
Components
  • C-terminus of outer capsid protein VP5
  • Core protein VP6
  • N-terminus of outer capsid protein VP5
  • Outer capsid VP7
  • VP1
  • VP3
KeywordsVIRUS / icosahedral capsid / symmetry-mismatch / genome / RNA-dependent RNA polymerase
Function / homologyMu1 membrane penetration protein, subdomain 3 / Reovirus core-spike protein lambda-2 (L2) / Reoviral Sigma1/Sigma2 family / Mu1/VP4 superfamily / Outer capsid protein VP7 / Mu1 membrane penetration protein, subdomain 2 / Immunoglobulin-like fold / Zinc finger C2H2-type / Reovirus core-spike lambda-2 / Outer capsid protein Mu1/VP4 ...Mu1 membrane penetration protein, subdomain 3 / Reovirus core-spike protein lambda-2 (L2) / Reoviral Sigma1/Sigma2 family / Mu1/VP4 superfamily / Outer capsid protein VP7 / Mu1 membrane penetration protein, subdomain 2 / Immunoglobulin-like fold / Zinc finger C2H2-type / Reovirus core-spike lambda-2 / Outer capsid protein Mu1/VP4 / Sigma1/sigma2, reoviral / Outer capsid protein VP7 / Zinc finger C2H2 type domain signature. / Zinc finger C2H2 type domain profile. / Reovirus major virion structural protein Mu-1/Mu-1C (M2) / mRNA guanylyltransferase activity / host cell surface binding / viral outer capsid / mRNA (guanine-N7-)-methyltransferase activity / viral capsid / nucleic acid binding / viral entry into host cell / pathogenesis / ATP binding / Outer capsid VP7 / Core protein VP6 / Putative outer capsid VP4 / VP3 / VP1
Function and homology information
Specimen sourceGrass carp reovirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.3 Å resolution
AuthorsLiu, H. / Fang, Q. / Cheng, L.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Structure of RNA polymerase complex and genome within a dsRNA virus provides insights into the mechanisms of transcription and assembly.
Authors: Xurong Wang / Fuxian Zhang / Rui Su / Xiaowu Li / Wenyuan Chen / Qingxiu Chen / Tao Yang / Jiawei Wang / Hongrong Liu / Qin Fang / Lingpeng Cheng
Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 12, 2018 / Release: Jul 4, 2018

-
Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
  • Imaged by Jmol
  • Download
  • Biological unit as icosahedral pentamer
  • Imaged by Jmol
  • Download
  • Biological unit as icosahedral 23 hexamer
  • Imaged by Jmol
  • Download
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-6969
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-6969
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
l: Outer capsid VP7
b: Outer capsid VP7
f: Outer capsid VP7
d: Outer capsid VP7
h: Outer capsid VP7
j: Outer capsid VP7
n: Outer capsid VP7
p: Outer capsid VP7
r: Outer capsid VP7
t: Outer capsid VP7
A: N-terminus of outer capsid protein VP5
B: C-terminus of outer capsid protein VP5
C: N-terminus of outer capsid protein VP5
D: C-terminus of outer capsid protein VP5
E: N-terminus of outer capsid protein VP5
F: C-terminus of outer capsid protein VP5
G: N-terminus of outer capsid protein VP5
H: C-terminus of outer capsid protein VP5
I: N-terminus of outer capsid protein VP5
J: C-terminus of outer capsid protein VP5
K: N-terminus of outer capsid protein VP5
L: C-terminus of outer capsid protein VP5
M: N-terminus of outer capsid protein VP5
N: C-terminus of outer capsid protein VP5
O: N-terminus of outer capsid protein VP5
P: C-terminus of outer capsid protein VP5
Q: N-terminus of outer capsid protein VP5
R: C-terminus of outer capsid protein VP5
S: N-terminus of outer capsid protein VP5
T: C-terminus of outer capsid protein VP5
U: Core protein VP6
V: Core protein VP6
W: VP1
X: VP3
Y: VP3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,482,51045
Polyers1,480,22635
Non-polymers2,28410
Water0
1
l: Outer capsid VP7
b: Outer capsid VP7
f: Outer capsid VP7
d: Outer capsid VP7
h: Outer capsid VP7
j: Outer capsid VP7
n: Outer capsid VP7
p: Outer capsid VP7
r: Outer capsid VP7
t: Outer capsid VP7
A: N-terminus of outer capsid protein VP5
B: C-terminus of outer capsid protein VP5
C: N-terminus of outer capsid protein VP5
D: C-terminus of outer capsid protein VP5
E: N-terminus of outer capsid protein VP5
F: C-terminus of outer capsid protein VP5
G: N-terminus of outer capsid protein VP5
H: C-terminus of outer capsid protein VP5
I: N-terminus of outer capsid protein VP5
J: C-terminus of outer capsid protein VP5
K: N-terminus of outer capsid protein VP5
L: C-terminus of outer capsid protein VP5
M: N-terminus of outer capsid protein VP5
N: C-terminus of outer capsid protein VP5
O: N-terminus of outer capsid protein VP5
P: C-terminus of outer capsid protein VP5
Q: N-terminus of outer capsid protein VP5
R: C-terminus of outer capsid protein VP5
S: N-terminus of outer capsid protein VP5
T: C-terminus of outer capsid protein VP5
U: Core protein VP6
V: Core protein VP6
W: VP1
X: VP3
Y: VP3
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)88,950,5862700
Polyers88,813,5632100
Non-polymers137,023600
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
l: Outer capsid VP7
b: Outer capsid VP7
f: Outer capsid VP7
d: Outer capsid VP7
h: Outer capsid VP7
j: Outer capsid VP7
n: Outer capsid VP7
p: Outer capsid VP7
r: Outer capsid VP7
t: Outer capsid VP7
A: N-terminus of outer capsid protein VP5
B: C-terminus of outer capsid protein VP5
C: N-terminus of outer capsid protein VP5
D: C-terminus of outer capsid protein VP5
E: N-terminus of outer capsid protein VP5
F: C-terminus of outer capsid protein VP5
G: N-terminus of outer capsid protein VP5
H: C-terminus of outer capsid protein VP5
I: N-terminus of outer capsid protein VP5
J: C-terminus of outer capsid protein VP5
K: N-terminus of outer capsid protein VP5
L: C-terminus of outer capsid protein VP5
M: N-terminus of outer capsid protein VP5
N: C-terminus of outer capsid protein VP5
O: N-terminus of outer capsid protein VP5
P: C-terminus of outer capsid protein VP5
Q: N-terminus of outer capsid protein VP5
R: C-terminus of outer capsid protein VP5
S: N-terminus of outer capsid protein VP5
T: C-terminus of outer capsid protein VP5
U: Core protein VP6
V: Core protein VP6
W: VP1
X: VP3
Y: VP3
hetero molecules
x 5


  • icosahedral pentamer
  • 7.41 MDa, 175 polymers
Theoretical massNumber of molelcules
Total (without water)7,412,549225
Polyers7,401,130175
Non-polymers11,41950
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
l: Outer capsid VP7
b: Outer capsid VP7
f: Outer capsid VP7
d: Outer capsid VP7
h: Outer capsid VP7
j: Outer capsid VP7
n: Outer capsid VP7
p: Outer capsid VP7
r: Outer capsid VP7
t: Outer capsid VP7
A: N-terminus of outer capsid protein VP5
B: C-terminus of outer capsid protein VP5
C: N-terminus of outer capsid protein VP5
D: C-terminus of outer capsid protein VP5
E: N-terminus of outer capsid protein VP5
F: C-terminus of outer capsid protein VP5
G: N-terminus of outer capsid protein VP5
H: C-terminus of outer capsid protein VP5
I: N-terminus of outer capsid protein VP5
J: C-terminus of outer capsid protein VP5
K: N-terminus of outer capsid protein VP5
L: C-terminus of outer capsid protein VP5
M: N-terminus of outer capsid protein VP5
N: C-terminus of outer capsid protein VP5
O: N-terminus of outer capsid protein VP5
P: C-terminus of outer capsid protein VP5
Q: N-terminus of outer capsid protein VP5
R: C-terminus of outer capsid protein VP5
S: N-terminus of outer capsid protein VP5
T: C-terminus of outer capsid protein VP5
U: Core protein VP6
V: Core protein VP6
W: VP1
X: VP3
Y: VP3
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 8.9 MDa, 210 polymers
Theoretical massNumber of molelcules
Total (without water)8,895,059270
Polyers8,881,356210
Non-polymers13,70260
Water0
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

-
Components

-
Protein/peptide , 6 types, 35 molecules lbfdhjnprtACEGIKMOQSBDFHJLNPRT...

#1: Protein/peptide
Outer capsid VP7


Mass: 29844.648 Da / Num. of mol.: 10 / Source: (gene. exp.) Grass carp reovirus / Production host: Ctenopharyngodon idella (grass carp) / References: UniProt: Q8JU63
#2: Protein/peptide
N-terminus of outer capsid protein VP5 / N-terminus of outer capsid VP4


Mass: 4302.686 Da / Num. of mol.: 10 / Source: (gene. exp.) Grass carp reovirus / Production host: Ctenopharyngodon idella (grass carp) / References: UniProt: Q8JU67
#3: Protein/peptide
C-terminus of outer capsid protein VP5 / C-terminus of outer capsid protein VP4


Mass: 64362.086 Da / Num. of mol.: 10 / Source: (gene. exp.) Grass carp reovirus / Production host: Ctenopharyngodon idella (grass carp) / References: UniProt: Q8JU67
#4: Protein/peptide Core protein VP6 / inner capsid protein VP6


Mass: 44606.535 Da / Num. of mol.: 2 / Source: (gene. exp.) Grass carp reovirus / Production host: Ctenopharyngodon idella (grass carp) / References: UniProt: Q8JU64
#5: Protein/peptide VP1


Mass: 141512.156 Da / Num. of mol.: 1 / Source: (gene. exp.) Grass carp reovirus / Production host: Ctenopharyngodon idella (grass carp) / References: UniProt: Q9E3W0
#6: Protein/peptide VP3


Mass: 132203.312 Da / Num. of mol.: 2 / Source: (gene. exp.) Grass carp reovirus / Production host: Ctenopharyngodon idella (grass carp) / References: UniProt: Q9E3V8

-
Non-polymers , 1 types, 10 molecules

#7: Chemical
ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 10 / Formula: C14H28O2 / Myristic acid

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Grass carp reovirus / Type: VIRUS / Entity ID: 1,2,3,4,5,6 / Source: RECOMBINANT
Source (natural)Organism: Grass carp reovirus
Source (recombinant)Organism: Ctenopharyngodon idella (grass carp)
Details of virusEmpty: NO / Enveloped: NO / Virus isolate: STRAIN / Virus type: VIRION
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 25 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

-
Processing

SoftwareName: PHENIX / Version: 1.13_2998: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 41000 / Symmetry type: POINT

+
About Yorodumi

-
News

-
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

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

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