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- PDB-6odm: Herpes simplex virus type 1 (HSV-1) portal vertex-adjacent capsid... -

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Basic information

Entry
Database: PDB / ID: 6odm
TitleHerpes simplex virus type 1 (HSV-1) portal vertex-adjacent capsid/CATC, asymmetric unit
Components
  • (Capsid vertex component ...) x 2
  • (Triplex capsid protein ...) x 2
  • Large tegument protein deneddylase
  • Major capsid protein
  • Small capsomere-interacting protein
KeywordsVIRAL PROTEIN / tegument / portal / DNA-packaging / capsid
Function / homology
Function and homology information


cysteine-type deubiquitinase activity => GO:0004843 / chromosome organization => GO:0051276 / T=16 icosahedral viral capsid / deNEDDylase activity / viral genome packaging / viral tegument / viral capsid assembly / viral DNA genome replication / viral release from host cell / viral process ...cysteine-type deubiquitinase activity => GO:0004843 / chromosome organization => GO:0051276 / T=16 icosahedral viral capsid / deNEDDylase activity / viral genome packaging / viral tegument / viral capsid assembly / viral DNA genome replication / viral release from host cell / viral process / viral penetration into host nucleus / viral capsid / symbiont-mediated perturbation of host ubiquitin-like protein modification / ubiquitinyl hydrolase 1 / host cell cytoplasm / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / symbiont entry into host cell / host cell nucleus / structural molecule activity / DNA binding
Similarity search - Function
Herpesvirus large tegument protein deneddylase / Herpesvirus UL36 tegument protein / Herpesvirus UL35 / Herpesvirus UL35 family / Large tegument protein deneddylase / Herpesvirus tegument ubiquitin-specific protease (htUSP) domain profile. / Herpesvirus large tegument protein, USP domain / Herpesvirus tegument protein, N-terminal conserved region / Herpesvirus capsid vertex component 1 / Herpesvirus UL17 protein ...Herpesvirus large tegument protein deneddylase / Herpesvirus UL36 tegument protein / Herpesvirus UL35 / Herpesvirus UL35 family / Large tegument protein deneddylase / Herpesvirus tegument ubiquitin-specific protease (htUSP) domain profile. / Herpesvirus large tegument protein, USP domain / Herpesvirus tegument protein, N-terminal conserved region / Herpesvirus capsid vertex component 1 / Herpesvirus UL17 protein / Herpesvirus UL25 / Herpesvirus UL25 family / Herpesvirus capsid protein 2 / Herpesvirus capsid shell protein 1 / Herpesvirus VP23 like capsid protein / Herpesvirus capsid shell protein VP19C / Herpesvirus major capsid protein / Herpesvirus major capsid protein, upper domain superfamily / Herpes virus major capsid protein / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
Large tegument protein deneddylase / Capsid vertex component 2 / Capsid vertex component 1 / Triplex capsid protein 2 / Major capsid protein / Large tegument protein deneddylase / Triplex capsid protein 1 / Small capsomere-interacting protein
Similarity search - Component
Biological speciesHuman herpesvirus 1 strain KOS
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsLiu, Y.T. / Jih, J. / Dai, X.H. / Bi, G.Q. / Zhou, Z.H.
Funding support China, United States, 9items
OrganizationGrant numberCountry
Other government2017YFA0505300 National Key R&D Program of China China
Other government2016YFA0400900 National Key R&D Program of China China
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM071940 United States
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)DE025567 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI094386 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)1S10RR23057 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1U24GM116792 United States
National Science Foundation (NSF, United States)DBI-1338135 United States
National Science Foundation (NSF, United States)DMR-1548924 United States
CitationJournal: Nature / Year: 2019
Title: Cryo-EM structures of herpes simplex virus type 1 portal vertex and packaged genome.
Authors: Yun-Tao Liu / Jonathan Jih / Xinghong Dai / Guo-Qiang Bi / Z Hong Zhou /
Abstract: Herpesviruses are enveloped viruses that are prevalent in the human population and are responsible for diverse pathologies, including cold sores, birth defects and cancers. They are characterized by ...Herpesviruses are enveloped viruses that are prevalent in the human population and are responsible for diverse pathologies, including cold sores, birth defects and cancers. They are characterized by a highly pressurized pseudo-icosahedral capsid-with triangulation number (T) equal to 16-encapsidating a tightly packed double-stranded DNA (dsDNA) genome. A key process in the herpesvirus life cycle involves the recruitment of an ATP-driven terminase to a unique portal vertex to recognize, package and cleave concatemeric dsDNA, ultimately giving rise to a pressurized, genome-containing virion. Although this process has been studied in dsDNA phages-with which herpesviruses bear some similarities-a lack of high-resolution in situ structures of genome-packaging machinery has prevented the elucidation of how these multi-step reactions, which require close coordination among multiple actors, occur in an integrated environment. To better define the structural basis of genome packaging and organization in herpes simplex virus type 1 (HSV-1), we developed sequential localized classification and symmetry relaxation methods to process cryo-electron microscopy (cryo-EM) images of HSV-1 virions, which enabled us to decouple and reconstruct hetero-symmetric and asymmetric elements within the pseudo-icosahedral capsid. Here we present in situ structures of the unique portal vertex, genomic termini and ordered dsDNA coils in the capsid spooled around a disordered dsDNA core. We identify tentacle-like helices and a globular complex capping the portal vertex that is not observed in phages, indicative of herpesvirus-specific adaptations in the DNA-packaging process. Finally, our atomic models of portal vertex elements reveal how the fivefold-related capsid accommodates symmetry mismatch imparted by the dodecameric portal-a longstanding mystery in icosahedral viruses-and inform possible DNA-sequence recognition and headful-sensing pathways involved in genome packaging. This work showcases how to resolve symmetry-mismatched elements in a large eukaryotic virus and provides insights into the mechanisms of herpesvirus genome packaging.
History
DepositionMar 26, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 18, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]

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Structure visualization

Movie
  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-9860
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  • Superimposition on EM map
  • EMDB-9860
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Structure viewerMolecule:
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Assembly

Deposited unit
T: Major capsid protein
W: Major capsid protein
S: Major capsid protein
X: Major capsid protein
L: Small capsomere-interacting protein
P: Small capsomere-interacting protein
E: Small capsomere-interacting protein
F: Small capsomere-interacting protein
5: Triplex capsid protein 1
6: Triplex capsid protein 2
7: Triplex capsid protein 2
C: Capsid vertex component 1
G: Capsid vertex component 2
K: Capsid vertex component 2
O: Large tegument protein deneddylase
B: Large tegument protein deneddylase
D: Triplex capsid protein 1
H: Triplex capsid protein 2
A: Triplex capsid protein 2


Theoretical massNumber of molelcules
Total (without water)1,742,22819
Polymers1,742,22819
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 3 types, 10 molecules TWSXLPEFOB

#1: Protein
Major capsid protein / MCP


Mass: 149303.125 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: P2 MCP subunit of periportal P hexon / Source: (natural) Human herpesvirus 1 strain KOS / Strain: KOS / References: UniProt: H9E925
#2: Protein
Small capsomere-interacting protein


Mass: 12108.655 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Details: Chain E: P1 SCP subunit of periportal P hexon; decorates periportal P1 MCP (chain S) Chain F: P2 SCP subunit of periportal P hexon; decorates periportal P2 MCP (chain T) Chain L: P5 SCP ...Details: Chain E: P1 SCP subunit of periportal P hexon; decorates periportal P1 MCP (chain S) Chain F: P2 SCP subunit of periportal P hexon; decorates periportal P2 MCP (chain T) Chain L: P5 SCP subunit of periportal P hexon; decorates periportal P5 MCP (chain W) Chain P: P6 SCP subunit of periportal P hexon; decorates periportal P6 MCP (chain X)
Source: (natural) Human herpesvirus 1 strain KOS / Strain: KOS / References: UniProt: Q25BW6
#7: Protein Large tegument protein deneddylase


Mass: 329179.500 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: Chain B: left pUL36 subunit of the periportal capsid-associated tegument complex (CATC); each CATC contains two pUL36 subunits Chain O: right pUL36 subunit of the periportal CATC
Source: (natural) Human herpesvirus 1 strain KOS / Strain: KOS
References: UniProt: A0A0B5E3K2, UniProt: I1UYK0*PLUS, ubiquitinyl hydrolase 1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases

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Triplex capsid protein ... , 2 types, 6 molecules 5D67HA

#3: Protein Triplex capsid protein 1


Mass: 50370.363 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Tri1 subunit of periportal triplex Ta / Source: (natural) Human herpesvirus 1 strain KOS / Strain: KOS / References: UniProt: Q1T724
#4: Protein
Triplex capsid protein 2


Mass: 34301.617 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Details: Chain 6: Tri2B subunit of periportal triplex Ta Chain H: Tri2B subunit of periportal triplex Tc
Source: (natural) Human herpesvirus 1 strain KOS / Strain: KOS / References: UniProt: G8H8D9

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Capsid vertex component ... , 2 types, 3 molecules CGK

#5: Protein Capsid vertex component 1


Mass: 74769.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: pUL17 subunit of the periportal capsid-associated tegument complex (CATC); each CATC contains one pUL17 subunit
Source: (natural) Human herpesvirus 1 strain KOS / Strain: KOS / References: UniProt: F8REV0
#6: Protein Capsid vertex component 2


Mass: 62752.777 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: upper pUL25 subunit of the periportal capsid-associated tegument complex (CATC); each CATC contains two pUL25 subunits
Source: (natural) Human herpesvirus 1 strain KOS / Strain: KOS / References: UniProt: D3YPI2

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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: Human herpesvirus 1 strain KOS / Type: VIRUS / Details: Cultured in Vero cells. / Entity ID: all / Source: NATURAL
Molecular weightValue: 200 MDa / Experimental value: NO
Source (natural)Organism: Human herpesvirus 1 strain KOS
Details of virusEmpty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Homo sapiens
Virus shellName: Capsid / Diameter: 1300 nm / Triangulation number (T number): 16
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/1
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Chamber temperature: 298 K
Details: The sample was manually blotted and frozen with a homemade plunger.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 14000 X / Calibrated magnification: 24271 X / Calibrated defocus min: 1000 nm / Calibrated defocus max: 3000 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 79 K
Image recordingAverage exposure time: 13 sec. / Electron dose: 25 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 8000
Image scansSampling size: 2.5 µm / Width: 1440 / Height: 1440 / Movie frames/image: 26

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.13_2998refinement
PHENIX1.13_2998refinement
EM software
IDNameVersionCategory
1EMAN1.09particle selection
2Leginonimage acquisition
4CTFFIND3CTF correction
5RELION2.1CTF correction
8Coot0.8.6.1model fitting
10RELION2.1initial Euler assignment
11RELION2.1final Euler assignment
13RELION2.13D reconstruction
14PHENIX1.13model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 45445
SymmetryPoint symmetry: C5 (5 fold cyclic)
3D reconstructionResolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 42857 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingB value: 100 / Protocol: FLEXIBLE FIT / Space: REAL
Details: Capsid and CATC atomic models from Dai & Zhou, Science 2018 (PDB-6CGR) were docked into the C5 portal vertex map (EMD-9860) and manually refined in Coot to improve fit. Regions demonstrating ...Details: Capsid and CATC atomic models from Dai & Zhou, Science 2018 (PDB-6CGR) were docked into the C5 portal vertex map (EMD-9860) and manually refined in Coot to improve fit. Regions demonstrating major differences were reconstructed ab initio. Models were then iteratively refined between real space refinement in PHENIX and manual refinement in Coot.
RefinementStereochemistry target values: GeoStd + Monomer Library
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.004867127
ELECTRON MICROSCOPYf_angle_d0.921191616
ELECTRON MICROSCOPYf_chiral_restr0.05210360
ELECTRON MICROSCOPYf_plane_restr0.00712197
ELECTRON MICROSCOPYf_dihedral_angle_d4.609640269

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