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- PDB-3iyl: Atomic CryoEM Structure of a Nonenveloped Virus Suggests How Memb... -

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Basic information

Entry
Database: PDB / ID: 3iyl
TitleAtomic CryoEM Structure of a Nonenveloped Virus Suggests How Membrane Penetration Protein is Primed for Cell Entry
Components
  • Core protein VP6
  • Outer capsid VP4
  • VP1
  • VP3
KeywordsVIRUS / Non-enveloped virus / Membrane penetration protein / Autocleavage / Myristol Group / Icosahedral virus
Function / homology
Function and homology information


symbiont entry into host cell via permeabilization of inner membrane / permeabilization of host organelle membrane involved in viral entry into host cell / viral inner capsid / host cell surface binding / viral outer capsid / 7-methylguanosine mRNA capping / viral capsid / mRNA guanylyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity ...symbiont entry into host cell via permeabilization of inner membrane / permeabilization of host organelle membrane involved in viral entry into host cell / viral inner capsid / host cell surface binding / viral outer capsid / 7-methylguanosine mRNA capping / viral capsid / mRNA guanylyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / hydrolase activity / RNA helicase / GTP binding / ATP binding / metal ion binding
Similarity search - Function
Protein mu-1, chain B, domain 3 / Protein mu-1, chain B, domain 3 / Helix Hairpins - #1520 / Membrane penetration protein mu1, Chain B, domain 4 / Reovirus core / Reovirus components fold / Reovirus components / Reovirus components fold / Reovirus components / Outer capsid protein Mu1/VP4 ...Protein mu-1, chain B, domain 3 / Protein mu-1, chain B, domain 3 / Helix Hairpins - #1520 / Membrane penetration protein mu1, Chain B, domain 4 / Reovirus core / Reovirus components fold / Reovirus components / Reovirus components fold / Reovirus components / Outer capsid protein Mu1/VP4 / Mu1 membrane penetration protein, domain IV / Mu1 membrane penetration protein, domain II / Mu1/VP4 superfamily / Mu1 membrane penetration protein, domain III / 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 / 3-Layer(bab) Sandwich / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / Vaccinia Virus protein VP39 / Helix Hairpins / Jelly Rolls / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Immunoglobulins / Immunoglobulin-like fold / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
MYRISTIC ACID / 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: 3.3 Å
AuthorsZhang, X. / Jin, L. / Fang, Q. / Hui, W. / Zhou, Z.H.
CitationJournal: Cell / Year: 2010
Title: 3.3 A cryo-EM structure of a nonenveloped virus reveals a priming mechanism for cell entry.
Authors: Xing Zhang / Lei Jin / Qin Fang / Wong H Hui / Z Hong Zhou /
Abstract: To achieve cell entry, many nonenveloped viruses must transform from a dormant to a primed state. In contrast to the membrane fusion mechanism of enveloped viruses (e.g., influenza virus), this ...To achieve cell entry, many nonenveloped viruses must transform from a dormant to a primed state. In contrast to the membrane fusion mechanism of enveloped viruses (e.g., influenza virus), this membrane penetration mechanism is poorly understood. Here, using single-particle cryo-electron microscopy, we report a 3.3 A structure of the primed, infectious subvirion particle of aquareovirus. The density map reveals side-chain densities of all types of amino acids (except glycine), enabling construction of a full-atom model of the viral particle. Our structure and biochemical results show that priming involves autocleavage of the membrane penetration protein and suggest that Lys84 and Glu76 may facilitate this autocleavage in a nucleophilic attack. We observe a myristoyl group, covalently linked to the N terminus of the penetration protein and embedded in a hydrophobic pocket. These results suggest a well-orchestrated process of nonenveloped virus entry involving autocleavage of the penetration protein prior to exposure of its membrane-insertion finger.
History
DepositionFeb 2, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id / _em_software.name
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list / struct_conn / struct_site
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_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
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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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  • Simplified surface model + fitted atomic model
  • EMDB-5160
  • Imaged by Jmol
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  • Superimposition on EM map
  • EMDB-5160
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Outer capsid VP4
B: Outer capsid VP4
C: Outer capsid VP4
D: Outer capsid VP4
E: Outer capsid VP4
F: Outer capsid VP4
G: Outer capsid VP4
H: Outer capsid VP4
I: Outer capsid VP4
J: Outer capsid VP4
K: Outer capsid VP4
L: Outer capsid VP4
M: Outer capsid VP4
N: Outer capsid VP4
O: Outer capsid VP4
P: Outer capsid VP4
Q: Outer capsid VP4
R: Outer capsid VP4
S: Outer capsid VP4
T: Outer capsid VP4
U: Core protein VP6
V: Core protein VP6
W: VP1
X: VP3
Y: VP3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,870,35135
Polymers1,868,06725
Non-polymers2,28410
Water00
1
A: Outer capsid VP4
B: Outer capsid VP4
C: Outer capsid VP4
D: Outer capsid VP4
E: Outer capsid VP4
F: Outer capsid VP4
G: Outer capsid VP4
H: Outer capsid VP4
I: Outer capsid VP4
J: Outer capsid VP4
K: Outer capsid VP4
L: Outer capsid VP4
M: Outer capsid VP4
N: Outer capsid VP4
O: Outer capsid VP4
P: Outer capsid VP4
Q: Outer capsid VP4
R: Outer capsid VP4
S: Outer capsid VP4
T: Outer capsid VP4
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)112,221,0342100
Polymers112,084,0111500
Non-polymers137,023600
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: Outer capsid VP4
B: Outer capsid VP4
C: Outer capsid VP4
D: Outer capsid VP4
E: Outer capsid VP4
F: Outer capsid VP4
G: Outer capsid VP4
H: Outer capsid VP4
I: Outer capsid VP4
J: Outer capsid VP4
K: Outer capsid VP4
L: Outer capsid VP4
M: Outer capsid VP4
N: Outer capsid VP4
O: Outer capsid VP4
P: Outer capsid VP4
Q: Outer capsid VP4
R: Outer capsid VP4
S: Outer capsid VP4
T: Outer capsid VP4
U: Core protein VP6
V: Core protein VP6
W: VP1
X: VP3
Y: VP3
hetero molecules
x 5


  • icosahedral pentamer
  • 9.35 MDa, 125 polymers
Theoretical massNumber of molelcules
Total (without water)9,351,753175
Polymers9,340,334125
Non-polymers11,41950
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Outer capsid VP4
B: Outer capsid VP4
C: Outer capsid VP4
D: Outer capsid VP4
E: Outer capsid VP4
F: Outer capsid VP4
G: Outer capsid VP4
H: Outer capsid VP4
I: Outer capsid VP4
J: Outer capsid VP4
K: Outer capsid VP4
L: Outer capsid VP4
M: Outer capsid VP4
N: Outer capsid VP4
O: Outer capsid VP4
P: Outer capsid VP4
Q: Outer capsid VP4
R: Outer capsid VP4
S: Outer capsid VP4
T: Outer capsid VP4
U: Core protein VP6
V: Core protein VP6
W: VP1
X: VP3
Y: VP3
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 11.2 MDa, 150 polymers
Theoretical massNumber of molelcules
Total (without water)11,222,103210
Polymers11,208,401150
Non-polymers13,70260
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

#1: Protein
Outer capsid VP4


Mass: 68646.750 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Source: (natural) Grass carp reovirus / References: UniProt: Q8JU67
#2: 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
#3: 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
#4: Protein VP3


Mass: 132203.312 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Grass carp reovirus / References: UniProt: Q9E3V8
#5: Chemical
ChemComp-MYR / MYRISTIC ACID


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

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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: Aquareovirus / Type: VIRUS / Details: The sample was monodisperse
Molecular weightValue: 72 MDa / Experimental value: NO
Details of virusEmpty: NO / Enveloped: NO / Host category: VERTEBRATES / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 7.5 / Details: 10mM PBS Buffer
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: 10mM PBS Buffer
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: METHANE / Temp: 90 K / Humidity: 100 % / Method: Blot for 7-9 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Mar 1, 2009
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 59000 X / Calibrated magnification: 57700 X / Nominal defocus max: 2700 nm / Nominal defocus min: 400 nm / Cs: 2.7 mm
Astigmatism: objective lens astigmatism was corrected at 250,000 times magnification
Camera length: 0 mm
Specimen holderSpecimen holder model: OTHER / Specimen holder type: Eucentric / Temperature: 90 K / Temperature (min): 90 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 25 e/Å2 / Film or detector model: KODAK SO-163 FILM
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1FREALIGN3D reconstruction
2IMIRS3D reconstruction
CTF correctionDetails: Each particle
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: Fourier Space Reconstruction / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 18464 / Symmetry type: POINT
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms80835 0 150 0 80985

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