[English] 日本語
Yorodumi
- PDB-3iyl: Atomic CryoEM Structure of a Nonenveloped Virus Suggests How Memb... -

+
Open data


ID or keywords:

Loading...

no data

-
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 / homologyC2H2-type zinc finger / Zinc finger C2H2-type / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 type domain signature. / Reovirus core-spike protein lambda-2 (L2) / Reovirus major virion structural protein Mu-1/Mu-1C (M2) / Reoviral Sigma1/Sigma2 family / Mu1/VP4 superfamily / Mu1 membrane penetration protein, subdomain 2 / Mu1 membrane penetration protein, subdomain 3 ...C2H2-type zinc finger / Zinc finger C2H2-type / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 type domain signature. / Reovirus core-spike protein lambda-2 (L2) / Reovirus major virion structural protein Mu-1/Mu-1C (M2) / Reoviral Sigma1/Sigma2 family / Mu1/VP4 superfamily / Mu1 membrane penetration protein, subdomain 2 / Mu1 membrane penetration protein, subdomain 3 / Immunoglobulin-like fold / Reovirus core-spike lambda-2 / Outer capsid protein Mu1/VP4 / Sigma1/sigma2, reoviral / 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 / 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
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Feb 2, 2010 / Release: May 12, 2010
RevisionDateData content typeGroupCategoryItemProviderType
1.0May 12, 2010Structure modelrepositoryInitial release
1.1Jul 13, 2011Structure modelVersion format compliance
1.2Jul 18, 2018Structure modelData collectionem_image_scans / em_software_em_software.image_processing_id / _em_software.name

-
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-5160
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-5160
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Polyers1,868,06725
Non-polymers2,28410
Water0
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
Polyers112,084,0111500
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
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
Polyers9,340,334125
Non-polymers11,41950
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
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
Polyers11,208,401150
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

#1: Protein/peptide
Outer capsid VP4


Mass: 68646.750 Da / Num. of mol.: 20 / Source: (natural) Grass carp reovirus / References: UniProt: Q8JU67
#2: Protein/peptide Core protein VP6


Mass: 44606.535 Da / Num. of mol.: 2 / Source: (natural) Grass carp reovirus / References: UniProt: Q8JU64
#3: Protein/peptide VP1


Mass: 141512.156 Da / Num. of mol.: 1 / Source: (natural) Grass carp reovirus / References: UniProt: Q9E3W0
#4: Protein/peptide VP3


Mass: 132203.312 Da / Num. of mol.: 2 / Source: (natural) Grass carp reovirus / References: UniProt: Q9E3V8
#5: 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: Aquareovirus / Type: VIRUS / Details: The sample was monodisperse
Molecular weightValue: 72 MDa / Experimental value: NO
Details of virusEmpty: NO / Enveloped: NO / Virus host category: VERTEBRATES / Virus isolate: STRAIN / Virus type: VIRION
Buffer solutionDetails: 10mM PBS Buffer / pH: 7.5
SpecimenDetails: 10mM PBS Buffer / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: METHANE / Temp: 90 K / Humidity: 100 % / Method: Blot for 7-9 seconds before plunging

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS / Date: Mar 1, 2009
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 59000 / Calibrated magnification: 57700 / 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 kelvins / Temperature (min): 90 kelvins / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
Image recordingElectron dose: 25 e/Å2 / Film or detector model: KODAK SO-163 FILM
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M
Radiation wavelengthRelative weight: 1

-
Processing

EM software
IDNameCategory
1FREALIGN3D reconstruction
2IMIRS3D reconstruction
CTF correctionDetails: Each particle
SymmetryPoint symmetry: I
3D reconstructionMethod: Fourier Space Reconstruction / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 18464 / Symmetry type: POINT
Number of atoms included #LASTProtein: 80835 / Nucleic acid: 0 / Ligand: 150 / Solvent: 0 / Total: 80985

+
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