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- PDB-5zvt: Structure of RNA polymerase complex and genome within a dsRNA vir... -

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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 / homology
Function and homology information


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
C2H2-type zinc finger / Reovirus core-spike lambda-2 / Outer capsid protein VP7 / 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 ...C2H2-type zinc finger / Reovirus core-spike lambda-2 / Outer capsid protein VP7 / 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 / Mu1 membrane penetration protein, subdomain 3 / Outer capsid protein Mu1/VP4 / Sigma1/sigma2, reoviral / Protein mu-1, chain B, domain 3 / Reovirus components fold / Reovirus components / Reovirus components / Reovirus core / Protein mu-1, chain B, domain 3 / Reovirus components fold / Helix Hairpins - #1520 / Membrane penetration protein mu1, Chain B, domain 4 / 3-Layer(bab) Sandwich / Vaccinia Virus protein VP39 / Helix Hairpins / Jelly Rolls / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Outer capsid VP7 / VP3 / Core protein VP6 / Putative outer capsid VP4 / VP1
Biological speciesGrass carp reovirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsLiu, H. / Fang, Q. / Cheng, L.
Funding support China, 5items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2016YFA0501100 China
Ministry of Science and Technology (China)2015CB910104 China
National Natural Science Foundation of China91530321 China
National Natural Science Foundation of China31672693 China
National Natural Science Foundation of China31570727 China
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 /
Abstract: Most double-stranded RNA (dsRNA) viruses transcribe RNA plus strands within a common innermost capsid shell. This process requires coordinated efforts by RNA-dependent RNA polymerase (RdRp) together ...Most double-stranded RNA (dsRNA) viruses transcribe RNA plus strands within a common innermost capsid shell. This process requires coordinated efforts by RNA-dependent RNA polymerase (RdRp) together with other capsid proteins and genomic RNA. Here we report the near-atomic resolution structure of the RdRp protein VP2 in complex with its cofactor protein VP4 and genomic RNA within an aquareovirus capsid using 200-kV cryoelectron microscopy and symmetry-mismatch reconstruction. The structure of these capsid proteins enabled us to observe the elaborate nonicosahedral structure within the double-layered icosahedral capsid. Our structure shows that the RdRp complex is anchored at the inner surface of the capsid shell and interacts with genomic dsRNA and four of the five asymmetrically arranged N termini of the capsid shell proteins under the fivefold axis, implying roles for these N termini in virus assembly. The binding site of the RNA end at VP2 is different from the RNA cap binding site identified in the crystal structure of orthoreovirus RdRp λ3, although the structures of VP2 and λ3 are almost identical. A loop, which was thought to separate the RNA template and transcript, interacts with an apical domain of the capsid shell protein, suggesting a mechanism for regulating RdRp replication and transcription. A conserved nucleoside triphosphate binding site was localized in our RdRp cofactor protein VP4 structure, and interactions between the VP4 and the genomic RNA were identified.
Validation Report
SummaryFull reportAbout validation report
History
DepositionMay 12, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-6969
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  • Superimposition on EM map
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Structure viewerMolecule:
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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
Polymers1,480,22635
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
Polymers88,813,5632100
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
Polymers7,401,130175
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
Polymers8,881,356210
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
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

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Protein , 4 types, 24 molecules lbfdhjnprtBDFHJLNPRTUVXY

#1: Protein
Outer capsid VP7


Mass: 29844.648 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Grass carp reovirus / Production host: Ctenopharyngodon idella (grass carp) / References: UniProt: Q8JU63
#3: Protein
C-terminus of outer capsid protein VP5 / C-terminus of outer capsid protein VP4


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


Mass: 44606.535 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Grass carp reovirus / Production host: Ctenopharyngodon idella (grass carp) / References: UniProt: Q8JU64
#6: Protein VP3


Mass: 132203.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Grass carp reovirus / Production host: Ctenopharyngodon idella (grass carp) / References: UniProt: Q9E3V8

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Protein/peptide / Antibody / Non-polymers , 3 types, 21 molecules ACEGIKMOQSW

#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 method: isolated from a genetically manipulated source
Source: (gene. exp.) Grass carp reovirus / Production host: Ctenopharyngodon idella (grass carp) / References: UniProt: Q8JU67
#5: Antibody VP1


Mass: 141512.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Grass carp reovirus / Production host: Ctenopharyngodon idella (grass carp) / References: UniProt: Q9E3W0
#7: Chemical
ChemComp-MYR / MYRISTIC ACID / Myristic acid


Mass: 228.371 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C14H28O2

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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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 / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: 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)

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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 / Num. of particles: 41000 / Symmetry type: POINT

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