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- PDB-8tes: Human cytomegalovirus portal vertex, virion configuration 2 (VC2) -

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Basic information

Entry
Database: PDB / ID: 8tes
TitleHuman cytomegalovirus portal vertex, virion configuration 2 (VC2)
Components
  • (Capsid vertex component ...) x 2
  • (Triplex capsid protein ...) x 2
  • Large structural phosphoprotein
  • Large tegument protein deneddylase
  • Major capsid protein
  • Small capsomere-interacting protein
KeywordsVIRUS / tegument / portal / DNA packaging / intracellular transport
Function / homology
Function and homology information


host cell viral assembly compartment / T=16 icosahedral viral capsid / viral tegument / viral DNA genome packaging / viral capsid assembly / host cell cytoplasmic vesicle / chromosome organization / viral process / viral penetration into host nucleus / viral capsid ...host cell viral assembly compartment / T=16 icosahedral viral capsid / viral tegument / viral DNA genome packaging / viral capsid assembly / host cell cytoplasmic vesicle / chromosome organization / viral process / viral penetration into host nucleus / viral capsid / host cell / 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 / host cell perinuclear region of cytoplasm / symbiont entry into host cell / host cell nucleus / structural molecule activity / proteolysis / DNA binding
Similarity search - Function
Herpesvirus UL11/UL32 / Herpesvirus large structural phosphoprotein UL32 / Small capsid protein, Herpesviridae / Small capsid protein of Herpesviridae / 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 UL11/UL32 / Herpesvirus large structural phosphoprotein UL32 / Small capsid protein, Herpesviridae / Small capsid protein of Herpesviridae / 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 shell protein 1 / Herpesvirus capsid shell protein VP19C / Herpesvirus capsid protein 2 / Herpesvirus VP23 like capsid protein / 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 structural phosphoprotein / Capsid vertex component 2 / Triplex capsid protein 2 / Major capsid protein / Triplex capsid protein 1 / Large tegument protein deneddylase / Capsid vertex component 1 / Small capsomere-interacting protein
Similarity search - Component
Biological speciesHuman herpesvirus 5 strain AD169
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.27 Å
AuthorsJih, J. / Liu, Y.T. / Liu, W. / Zhou, H.
Funding support United States, 9items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)DE028583 United States
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)T32AR071307 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P30 AI152501 United States
James B. Pendleton Charitable Trust (to the UCLA AIDS Institute) United States
McCarthy Family Foundation (to the UCLA AIDS Institute) United States
National Institutes of Health/Office of the Director1S10RR23057 United States
National Institutes of Health/Office of the Director1S10OD018111 United States
National Science Foundation (NSF, United States)DBI-1338135 United States
National Science Foundation (NSF, United States)DMR-1548924 United States
CitationJournal: Sci Adv / Year: 2024
Title: The incredible bulk: Human cytomegalovirus tegument architectures uncovered by AI-empowered cryo-EM.
Authors: Jonathan Jih / Yun-Tao Liu / Wei Liu / Z Hong Zhou /
Abstract: The compartmentalization of eukaryotic cells presents considerable challenges to the herpesvirus life cycle. The herpesvirus tegument, a bulky proteinaceous aggregate sandwiched between ...The compartmentalization of eukaryotic cells presents considerable challenges to the herpesvirus life cycle. The herpesvirus tegument, a bulky proteinaceous aggregate sandwiched between herpesviruses' capsid and envelope, is uniquely evolved to address these challenges, yet tegument structure and organization remain poorly characterized. We use deep-learning-enhanced cryogenic electron microscopy to investigate the tegument of human cytomegalovirus virions and noninfectious enveloped particles (NIEPs; a genome packaging-aborted state), revealing a portal-biased tegumentation scheme. We resolve atomic structures of portal vertex-associated tegument (PVAT) and identify multiple configurations of PVAT arising from layered reorganization of pUL77, pUL48 (large tegument protein), and pUL47 (inner tegument protein) assemblies. Analyses show that pUL77 seals the last-packaged viral genome end through electrostatic interactions, pUL77 and pUL48 harbor a head-linker-capsid-binding motif conducive to PVAT reconfiguration, and pUL47/48 dimers form 45-nm-long filaments extending from the portal vertex. These results provide a structural framework for understanding how herpesvirus tegument facilitates and evolves during processes spanning viral genome packaging to delivery.
History
DepositionJul 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Large tegument protein deneddylase
C: Large tegument protein deneddylase
E: Capsid vertex component 2
F: Capsid vertex component 2
G: Capsid vertex component 1
H: Major capsid protein
I: Major capsid protein
J: Major capsid protein
K: Major capsid protein
L: Major capsid protein
M: Major capsid protein
N: Small capsomere-interacting protein
O: Small capsomere-interacting protein
P: Small capsomere-interacting protein
Q: Small capsomere-interacting protein
R: Small capsomere-interacting protein
S: Small capsomere-interacting protein
T: Triplex capsid protein 1
U: Triplex capsid protein 2
V: Triplex capsid protein 2
W: Triplex capsid protein 1
X: Triplex capsid protein 2
Y: Triplex capsid protein 2
Z: Large structural phosphoprotein


Theoretical massNumber of molelcules
Total (without water)2,010,97224
Polymers2,010,97224
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 4 types, 15 molecules ACHIJKLMNOPQRSZ

#1: Protein Large tegument protein deneddylase


Mass: 253541.141 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Human herpesvirus 5 strain AD169
References: UniProt: P16785, ubiquitinyl hydrolase 1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#4: Protein
Major capsid protein / MCP


Mass: 154048.906 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Human herpesvirus 5 strain AD169 / References: UniProt: P16729
#5: Protein
Small capsomere-interacting protein / Smallest capsid protein / SCP


Mass: 8495.924 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Human herpesvirus 5 strain AD169 / References: UniProt: Q7M6N6
#8: Protein Large structural phosphoprotein / 150 kDa matrix phosphoprotein / 150 kDa phosphoprotein / pp150 / Basic phosphoprotein / BPP / ...150 kDa matrix phosphoprotein / 150 kDa phosphoprotein / pp150 / Basic phosphoprotein / BPP / Phosphoprotein UL32 / Tegument protein UL32


Mass: 112829.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human herpesvirus 5 strain AD169 / References: UniProt: P08318

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

#2: Protein Capsid vertex component 2


Mass: 71269.570 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Human herpesvirus 5 strain AD169 / References: UniProt: P16726
#3: Protein Capsid vertex component 1


Mass: 68567.211 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human herpesvirus 5 strain AD169 / References: UniProt: P16799

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Triplex capsid protein ... , 2 types, 6 molecules TWUVXY

#6: Protein Triplex capsid protein 1 / Triplex monomer protein / Tri1


Mass: 33071.270 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Human herpesvirus 5 strain AD169 / References: UniProt: P16783
#7: Protein
Triplex capsid protein 2 / Triplex dimer protein / Tri2


Mass: 34635.750 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Human herpesvirus 5 strain AD169 / References: UniProt: P16728

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Details

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: Human herpesvirus 5 strain AD169 / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Human herpesvirus 5 strain AD169
Details of virusEmpty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Homo sapiens
Virus shellName: Virion capsid / Triangulation number (T number): 16
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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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 FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Image recordingAverage exposure time: 8 sec. / Electron dose: 47.2 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameCategory
1IMODparticle selection
2Topazparticle selection
3RELIONparticle selection
4SerialEMimage acquisition
6CTFFINDCTF correction
9Cootmodel fitting
10UCSF ChimeraXmodel fitting
12PHENIXmodel refinement
13ISOLDEmodel refinement
14RELIONinitial Euler assignment
15RELIONfinal Euler assignment
17RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 367007
SymmetryPoint symmetry: C5 (5 fold cyclic)
3D reconstructionResolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 69628 / Symmetry type: POINT

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