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- PDB-3k1q: Backbone model of an aquareovirus virion by cryo-electron microsc... -

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Basic information

Entry
Database: PDB / ID: 3k1q
TitleBackbone model of an aquareovirus virion by cryo-electron microscopy and bioinformatics
Components
  • (Outer capsid ...) x 2
  • Core protein VP6
  • VP1
  • VP3A
  • VP3B
KeywordsVIRUS / cryoEM / bioinformatics / structure-based refinement / macromolecular assembly / GCRV virion
Function / homology
Function and homology information


host cell surface binding / viral inner capsid / viral outer capsid / permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane / 7-methylguanosine mRNA capping / viral capsid / mRNA guanylyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity ...host cell surface binding / viral inner capsid / viral outer capsid / permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane / 7-methylguanosine mRNA capping / viral capsid / mRNA guanylyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / RNA helicase / hydrolase activity / GTP binding / ATP binding / metal ion binding
Similarity search - Function
Outer capsid protein VP7 / Outer capsid protein VP7 / Mu1 membrane penetration protein, domain III / Outer capsid protein Mu1/VP4 / Mu1 membrane penetration protein, domain IV / Mu1 membrane penetration protein, domain II / Mu1/VP4 superfamily / Reovirus major virion structural protein Mu-1/Mu-1C (M2) / Sigma1/sigma2, reoviral / Reoviral Sigma1/Sigma2 family ...Outer capsid protein VP7 / Outer capsid protein VP7 / Mu1 membrane penetration protein, domain III / Outer capsid protein Mu1/VP4 / Mu1 membrane penetration protein, domain IV / Mu1 membrane penetration protein, domain II / Mu1/VP4 superfamily / Reovirus major virion structural protein Mu-1/Mu-1C (M2) / Sigma1/sigma2, reoviral / Reoviral Sigma1/Sigma2 family / Reovirus core-spike lambda-2 / Reovirus core-spike protein lambda-2 (L2), C-terminal / Inner capsid protein lambda-1/ VP3 / C2H2-type zinc finger / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Outer capsid VP7 / Core protein VP6 / Putative outer capsid VP4 / RNA helicase / VP1
Similarity search - Component
Biological speciesGrass carp reovirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsCheng, L.P. / Zhu, J. / Hiu, W.H. / Zhang, X.K. / Honig, B. / Fang, Q. / Zhou, Z.H.
Citation
Journal: J Mol Biol / Year: 2010
Title: Backbone model of an aquareovirus virion by cryo-electron microscopy and bioinformatics.
Authors: Lingpeng Cheng / Jiang Zhu / Wong Hoi Hui / Xiaokang Zhang / Barry Honig / Qin Fang / Z Hong Zhou /
Abstract: Grass carp reovirus (GCRV) is a member of the aquareovirus genus in the Reoviridae family and has a capsid with two shells-a transcription-competent core surrounded by a coat. We report a near-atomic- ...Grass carp reovirus (GCRV) is a member of the aquareovirus genus in the Reoviridae family and has a capsid with two shells-a transcription-competent core surrounded by a coat. We report a near-atomic-resolution reconstruction of the GCRV virion by cryo-electron microscopy and single-particle reconstruction. A backbone model of the GCRV virion, including seven conformers of the five capsid proteins making up the 1500 molecules in both the core and the coat, was derived using cryo-electron microscopy density-map-constrained homology modeling and refinement. Our structure clearly showed that the amino-terminal segment of core protein VP3B forms an approximately 120-A-long alpha-helix-rich extension bridging across the icosahedral 2-fold-symmetry-related molecular interface. The presence of this unique structure across this interface and the lack of an external cementing molecule at this location in GCRV suggest a stabilizing role of this extended amino-terminal density. Moreover, part of this amino-terminal extension becomes invisible in the reconstruction of transcription-competent core particles, suggesting its involvement in endogenous viral RNA transcription. Our structure of the VP1 turret represents its open state, and comparison with its related structures at the closed state suggests hinge-like domain movements associated with the mRNA-capping machinery. Overall, this first backbone model of an aquareovirus virion provides a wealth of structural information for understanding the structural basis of GCRV assembly and transcription.
#1: Journal: To be Published
Title: Building Models for Molecular Assemblies by Cryo-electron Microscopy, Homology Modeling and Multi-scale Structure-Based Refinement
Authors: Honig, B.
History
DepositionSep 28, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 14, 2015Group: Database references / Other
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_ref_seq_dif.details

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
  • Imaged by Jmol
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  • Biological unit as icosahedral pentamer
  • Imaged by Jmol
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  • Biological unit as icosahedral 23 hexamer
  • Imaged by Jmol
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  • Deposited structure unit
  • Imaged by Jmol
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VP1
B: VP3A
C: VP3B
D: Core protein VP6
E: Core protein VP6
F: Outer capsid VP7
G: Outer capsid VP7
H: Outer capsid VP7
I: Outer capsid VP5
J: Outer capsid VP5
K: Outer capsid VP5
L: Outer capsid VP7
M: Outer capsid VP7
N: Outer capsid VP7
O: Outer capsid VP5
P: Outer capsid VP5
Q: Outer capsid VP5
R: Outer capsid VP7
S: Outer capsid VP7
T: Outer capsid VP7
U: Outer capsid VP5
V: Outer capsid VP5
W: Outer capsid VP5
X: Outer capsid VP5
Y: Outer capsid VP7


Theoretical massNumber of molelcules
Total (without water)1,449,51625
Polymers1,449,51625
Non-polymers00
Water0
1
A: VP1
B: VP3A
C: VP3B
D: Core protein VP6
E: Core protein VP6
F: Outer capsid VP7
G: Outer capsid VP7
H: Outer capsid VP7
I: Outer capsid VP5
J: Outer capsid VP5
K: Outer capsid VP5
L: Outer capsid VP7
M: Outer capsid VP7
N: Outer capsid VP7
O: Outer capsid VP5
P: Outer capsid VP5
Q: Outer capsid VP5
R: Outer capsid VP7
S: Outer capsid VP7
T: Outer capsid VP7
U: Outer capsid VP5
V: Outer capsid VP5
W: Outer capsid VP5
X: Outer capsid VP5
Y: Outer capsid VP7
x 60


Theoretical massNumber of molelcules
Total (without water)86,970,9881500
Polymers86,970,9881500
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: VP1
B: VP3A
C: VP3B
D: Core protein VP6
E: Core protein VP6
F: Outer capsid VP7
G: Outer capsid VP7
H: Outer capsid VP7
I: Outer capsid VP5
J: Outer capsid VP5
K: Outer capsid VP5
L: Outer capsid VP7
M: Outer capsid VP7
N: Outer capsid VP7
O: Outer capsid VP5
P: Outer capsid VP5
Q: Outer capsid VP5
R: Outer capsid VP7
S: Outer capsid VP7
T: Outer capsid VP7
U: Outer capsid VP5
V: Outer capsid VP5
W: Outer capsid VP5
X: Outer capsid VP5
Y: Outer capsid VP7
x 5


  • icosahedral pentamer
  • 7.25 MDa, 125 polymers
Theoretical massNumber of molelcules
Total (without water)7,247,582125
Polymers7,247,582125
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: VP1
B: VP3A
C: VP3B
D: Core protein VP6
E: Core protein VP6
F: Outer capsid VP7
G: Outer capsid VP7
H: Outer capsid VP7
I: Outer capsid VP5
J: Outer capsid VP5
K: Outer capsid VP5
L: Outer capsid VP7
M: Outer capsid VP7
N: Outer capsid VP7
O: Outer capsid VP5
P: Outer capsid VP5
Q: Outer capsid VP5
R: Outer capsid VP7
S: Outer capsid VP7
T: Outer capsid VP7
U: Outer capsid VP5
V: Outer capsid VP5
W: Outer capsid VP5
X: Outer capsid VP5
Y: Outer capsid VP7
x 6


  • icosahedral 23 hexamer
  • 8.7 MDa, 150 polymers
Theoretical massNumber of molelcules
Total (without water)8,697,099150
Polymers8,697,099150
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
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, 5 molecules ABCDE

#1: Protein VP1


Mass: 141512.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Grass carp reovirus / References: UniProt: Q9E3W0
#2: Protein VP3A


Mass: 112883.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Grass carp reovirus / References: UniProt: Q9E3V8
#3: Protein VP3B


Mass: 130304.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Grass carp reovirus / References: UniProt: Q9E3V8
#4: Protein Core protein VP6


Mass: 44606.535 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Grass carp reovirus / References: UniProt: Q8JU64

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Outer capsid ... , 2 types, 20 molecules FGHLMNRSTYIJKOPQUVWX

#5: Protein
Outer capsid VP7


Mass: 29844.648 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Grass carp reovirus / References: UniProt: Q8JU63
#6: Protein
Outer capsid VP5


Mass: 67715.734 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Grass carp reovirus / References: UniProt: Q8JU67

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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: Aqaurevirus: Grass carp reovirus (GCRV) / Type: VIRUS / Synonym: sputnik
Details of virusHost category: CARP / Type: VIRION
Natural hostOrganism: Ctenopharyngodon idella
Buffer solutionDetails: 10mM phosphate-buffered saline
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Quantifoil holey carbon grids, 2um/1um type
VitrificationCryogen name: ETHANE / Details: Manual pluger freshing into liquid ethane

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Details: The electron beam is carefully monitored to ensure that the beam is just slightly larger than the CCD. See above
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 154380 X / Nominal defocus max: 2300 nm / Nominal defocus min: 800 nm / Cs: 2 mm
Specimen holderTemperature: 77 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 20 e/Å2 / Film or detector model: GENERIC CCD
Image scansNum. digital images: 4000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

CTF correctionDetails: Fully corrected. See Zhou et al., 1999, J. Virol. 73, 3210-3218
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 4.5 Å / Num. of particles: 15000 / Nominal pixel size: 0.97 Å / Actual pixel size: 0.97 Å / Symmetry type: POINT
Atomic model buildingB value: 100
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms101798 0 0 0 101798

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