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- PDB-5a8f: Structure and genome release mechanism of human cardiovirus Saffo... -

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Basic information

Entry
Database: PDB / ID: 5a8f
TitleStructure and genome release mechanism of human cardiovirus Saffold virus-3
Components
  • GENOME POLYPHUMAN SAFFOLD VIRUS-3 VP3 PROTEIN
  • HUMAN SAFFOLD VIRUS-3 VP1
  • HUMAN SAFFOLD VIRUS-3 VP2
KeywordsVIRAL PROTEIN / SAFFOLD / VIRUS / CARDIOVIRUS / PICORNAVIRALES / A / ALTERED / VIRION / PARTICLE / CAPSID / GENOME / RNA / SSRNA
Function / homology
Function and homology information


host cell nucleolus / symbiont-mediated suppression of host mRNA export from nucleus / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / channel activity / monoatomic ion transmembrane transport / RNA helicase activity / RNA helicase ...host cell nucleolus / symbiont-mediated suppression of host mRNA export from nucleus / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / channel activity / monoatomic ion transmembrane transport / RNA helicase activity / RNA helicase / symbiont entry into host cell / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding
Similarity search - Function
Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Picornavirus coat protein / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid ...Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Picornavirus coat protein / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesSAFFOLD VIRUS
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 10.6 Å
AuthorsMullapudi, E. / Novacek, J. / Palkova, L. / Kulich, P. / Lindberg, M. / vanKuppeveld, F.J.M. / Plevka, P.
CitationJournal: J Virol / Year: 2016
Title: Structure and Genome Release Mechanism of the Human Cardiovirus Saffold Virus 3.
Authors: Edukondalu Mullapudi / Jiří Nováček / Lenka Pálková / Pavel Kulich / A Michael Lindberg / Frank J M van Kuppeveld / Pavel Plevka /
Abstract: In order to initiate an infection, viruses need to deliver their genomes into cells. This involves uncoating the genome and transporting it to the cytoplasm. The process of genome delivery is not ...In order to initiate an infection, viruses need to deliver their genomes into cells. This involves uncoating the genome and transporting it to the cytoplasm. The process of genome delivery is not well understood for nonenveloped viruses. We address this gap in our current knowledge by studying the uncoating of the nonenveloped human cardiovirus Saffold virus 3 (SAFV-3) of the family Picornaviridae SAFVs cause diseases ranging from gastrointestinal disorders to meningitis. We present a structure of a native SAFV-3 virion determined to 2.5 Å by X-ray crystallography and an 11-Å-resolution cryo-electron microscopy reconstruction of an "altered" particle that is primed for genome release. The altered particles are expanded relative to the native virus and contain pores in the capsid that might serve as channels for the release of VP4 subunits, N termini of VP1, and the RNA genome. Unlike in the related enteroviruses, pores in SAFV-3 are located roughly between the icosahedral 3- and 5-fold axes at an interface formed by two VP1 and one VP3 subunit. Furthermore, in native conditions many cardioviruses contain a disulfide bond formed by cysteines that are separated by just one residue. The disulfide bond is located in a surface loop of VP3. We determined the structure of the SAFV-3 virion in which the disulfide bonds are reduced. Disruption of the bond had minimal effect on the structure of the loop, but it increased the stability and decreased the infectivity of the virus. Therefore, compounds specifically disrupting or binding to the disulfide bond might limit SAFV infection.
IMPORTANCE: A capsid assembled from viral proteins protects the virus genome during transmission from one cell to another. However, when a virus enters a cell the virus genome has to be released from ...IMPORTANCE: A capsid assembled from viral proteins protects the virus genome during transmission from one cell to another. However, when a virus enters a cell the virus genome has to be released from the capsid in order to initiate infection. This process is not well understood for nonenveloped viruses. We address this gap in our current knowledge by studying the genome release of Human Saffold virus 3 Saffold viruses cause diseases ranging from gastrointestinal disorders to meningitis. We show that before the genome is released, the Saffold virus 3 particle expands, and holes form in the previously compact capsid. These holes serve as channels for the release of the genome and small capsid proteins VP4 that in related enteroviruses facilitate subsequent transport of the virus genome into the cell cytoplasm.
History
DepositionJul 15, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 8, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2016Group: Database references
Revision 1.2Aug 31, 2016Group: Database references
Revision 1.3Aug 30, 2017Group: Data collection / Category: em_software / Item: _em_software.image_processing_id
Revision 1.4Oct 30, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_validate_close_contact / struct_conn / struct_conn_type

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Structure visualization

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  • 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-3097
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  • Superimposition on EM map
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Structure viewerMolecule:
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Assembly

Deposited unit
A: HUMAN SAFFOLD VIRUS-3 VP1
B: GENOME POLYPHUMAN SAFFOLD VIRUS-3 VP3 PROTEIN
C: HUMAN SAFFOLD VIRUS-3 VP2


Theoretical massNumber of molelcules
Total (without water)74,3783
Polymers74,3783
Non-polymers00
Water00
1
A: HUMAN SAFFOLD VIRUS-3 VP1
B: GENOME POLYPHUMAN SAFFOLD VIRUS-3 VP3 PROTEIN
C: HUMAN SAFFOLD VIRUS-3 VP2
x 60


Theoretical massNumber of molelcules
Total (without water)4,462,674180
Polymers4,462,674180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
A: HUMAN SAFFOLD VIRUS-3 VP1
B: GENOME POLYPHUMAN SAFFOLD VIRUS-3 VP3 PROTEIN
C: HUMAN SAFFOLD VIRUS-3 VP2
x 5


  • icosahedral pentamer
  • 372 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)371,89015
Polymers371,89015
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: HUMAN SAFFOLD VIRUS-3 VP1
B: GENOME POLYPHUMAN SAFFOLD VIRUS-3 VP3 PROTEIN
C: HUMAN SAFFOLD VIRUS-3 VP2
x 6


  • icosahedral 23 hexamer
  • 446 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)446,26718
Polymers446,26718
Non-polymers00
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

#1: Protein HUMAN SAFFOLD VIRUS-3 VP1


Mass: 24785.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SAFFOLD VIRUS / References: UniProt: C0MHL9
#2: Protein GENOME POLYPHUMAN SAFFOLD VIRUS-3 VP3 PROTEIN


Mass: 20893.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SAFFOLD VIRUS / References: UniProt: E3TMG9
#3: Protein HUMAN SAFFOLD VIRUS-3 VP2


Mass: 28698.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SAFFOLD VIRUS / References: UniProt: C0MHL9

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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: A PARTICLE OF SAFFOLD VIRUS-3 / Type: VIRUS
Buffer solutionName: 20MM HEPES, 150MM NACL / pH: 7.5 / Details: 20MM HEPES, 150MM NACL
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE
Details: CRYOGEN - LIQUID ETHANE, VITROBOT MARK IV, BLOT FOR 2 SECONDS

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20 / Date: Sep 3, 2014
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 55000 X / Nominal defocus max: 3950 nm / Nominal defocus min: 2330 nm / Cs: 2 mm
Specimen holderTilt angle max: 0 °
Image recordingElectron dose: 20 e/Å2 / Film or detector model: FEI EAGLE (4k x 4k)
Image scansNum. digital images: 264

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Processing

EM software
IDNameVersionCategory
1JALIGNinitial Euler assignment
2Bsoft3D reconstruction
3EMAN23D reconstruction
4J3DR3D reconstruction
CTF correctionDetails: EACH PARTICLE
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: PROJECTION MATCHING, FOURIER METHODS / Resolution: 10.6 Å / Num. of particles: 14028 / Nominal pixel size: 2.2176 Å / Actual pixel size: 2.2176 Å
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3097. (DEPOSITION ID: 13604).
Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL / Details: METHOD--LOCAL CORRELATION
RefinementHighest resolution: 10.6 Å
Refinement stepCycle: LAST / Highest resolution: 10.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5243 0 0 0 5243

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