6ODM

Herpes simplex virus type 1 (HSV-1) portal vertex-adjacent capsid/CATC, asymmetric unit

  • Classification: VIRAL PROTEIN
  • Organism(s): Human herpesvirus 1

  • Deposited: 2019-03-26 Released: 2019-06-19 
  • Deposition Author(s): Liu, Y.T., Jih, J., Dai, X.H., Bi, G.Q., Zhou, Z.H.
  • Funding Organization(s): Other government; National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS); National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR); National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID); National Institutes of Health/National Center for Research Resources (NIH/NCRR); National Science Foundation (NSF, United States) 

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.3 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Cryo-EM structures of herpes simplex virus type 1 portal vertex and packaged genome.

Liu, Y.T.Jih, J.Dai, X.Bi, G.Q.Zhou, Z.H.

(2019) Nature 570: 257-261

  • DOI: 10.1038/s41586-019-1248-6
  • Primary Citation of Related Structures:  

  • PubMed 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 a highly pressurized pseudo-icosahedral capsid-with ...

    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 1-3 . 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 4,5 . Although this process has been studied in dsDNA phages 6-9 -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.


    Organizational Affiliation

    Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA. hong.zhou@ucla.edu.,Center for Integrative Imaging, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, China.,Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA.,Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA.,Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA. hong.zhou@ucla.edu.,School of Life Sciences, University of Science and Technology of China, Hefei, China.,California NanoSystems Institute (CNSI), University of California, Los Angeles, Los Angeles, CA, USA.,California NanoSystems Institute (CNSI), University of California, Los Angeles, Los Angeles, CA, USA. hong.zhou@ucla.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Major capsid protein
T, W, S, X
1374Human herpesvirus 1Mutation(s): 0 
Gene Names: UL19 (MCP)
Find proteins for H9E925 (Human herpesvirus 1)
Go to UniProtKB:  H9E925
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Small capsomere-interacting protein
L, P, E, F
112Human herpesvirus 1Mutation(s): 0 
Gene Names: UL35 (SCP)
Find proteins for Q25BW6 (Human herpesvirus 1)
Go to UniProtKB:  Q25BW6
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Triplex capsid protein 1
5, D
465Human herpesvirus 1Mutation(s): 0 
Gene Names: UL38 (TRX1, VP19C)
Find proteins for Q1T724 (Human herpesvirus 1)
Go to UniProtKB:  Q1T724
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Triplex capsid protein 2
6, 7, H, A
318Human herpesvirus 1Mutation(s): 0 
Gene Names: UL18 (TRX2)
Find proteins for G8H8D9 (Human herpesvirus 1)
Go to UniProtKB:  G8H8D9
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Capsid vertex component 1
C
703Human herpesvirus 1Mutation(s): 0 
Gene Names: UL17 (CVC1)
Find proteins for F8REV0 (Human herpesvirus 1)
Go to UniProtKB:  F8REV0
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Capsid vertex component 2
G, K
580Human herpesvirus 1Mutation(s): 0 
Gene Names: UL25 (CVC2)
Find proteins for D3YPI2 (Human herpesvirus 1)
Go to UniProtKB:  D3YPI2
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Large tegument protein deneddylase
O, B
3094Human herpesvirus 1Mutation(s): 0 
Gene Names: UL36
EC: 3.4.19.12, 3.4.22.-
Find proteins for I1UYK0 (Human herpesvirus 1)
Go to UniProtKB:  I1UYK0
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.3 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
phenix.real_space_refinerefinement
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentChina2017YFA0505300 National Key R&D Program of China
Other governmentChina2016YFA0400900 National Key R&D Program of China
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM071940
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)United StatesDE025567
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI094386
National Institutes of Health/National Center for Research Resources (NIH/NCRR)United States1S10RR23057
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1U24GM116792
National Science Foundation (NSF, United States)United StatesDBI-1338135
National Science Foundation (NSF, United States)United StatesDMR-1548924

Revision History 

  • Version 1.0: 2019-06-19
    Type: Initial release
  • Version 1.1: 2019-06-26
    Type: Data collection, Database references
  • Version 1.2: 2019-11-27
    Type: Author supporting evidence
  • Version 1.3: 2019-12-18
    Type: Other