6Q1F

Atomic structure of the Human Herpesvirus 6B Capsid and Capsid-Associated Tegument Complexes


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Atomic structure of the human herpesvirus 6B capsid and capsid-associated tegument complexes.

Zhang, Y.Liu, W.Li, Z.Kumar, V.Alvarez-Cabrera, A.L.Leibovitch, E.C.Cui, Y.Mei, Y.Bi, G.Q.Jacobson, S.Zhou, Z.H.

(2019) Nat Commun 10: 5346-5346

  • DOI: https://doi.org/10.1038/s41467-019-13064-x
  • Primary Citation of Related Structures:  
    6Q1F

  • PubMed Abstract: 

    Human herpesvirus 6B (HHV-6B) belongs to the β-herpesvirus subfamily of the Herpesviridae. To understand capsid assembly and capsid-tegument interactions, here we report atomic structures of HHV-6B capsid and capsid-associated tegument complex (CATC) obtained by cryoEM and sub-particle reconstruction. Compared to other β-herpesviruses, HHV-6B exhibits high similarity in capsid structure but organizational differences in its CATC (pU11 tetramer). 180 "VΛ"-shaped CATCs are observed in HHV-6B, distinguishing from the 255 "Λ"-shaped dimeric CATCs observed in murine cytomegalovirus and the 310 "Δ"-shaped CATCs in human cytomegalovirus. This trend in CATC quantity correlates with the increasing genomes sizes of these β-herpesviruses. Incompatible distances revealed by the atomic structures rationalize the lack of CATC's binding to triplexes Ta, Tc, and Tf in HHV-6B. Our results offer insights into HHV-6B capsid assembly and the roles of its tegument proteins, including not only the β-herpesvirus-specific pU11 and pU14, but also those conserved across all subfamilies of Herpesviridae.


  • Organizational Affiliation

    California NanoSystems Institute, University of California, Los Angeles (UCLA), Los Angeles, CA, 90095-7151, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Major capsid protein1,345Human herpesvirus 6 strain Z29Mutation(s): 0 
Gene Names: MCPU57
UniProt
Find proteins for Q9QJ26 (Human herpesvirus 6B (strain Z29))
Explore Q9QJ26 
Go to UniProtKB:  Q9QJ26
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9QJ26
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Large structural phosphoprotein858Human herpesvirus 6 strain Z29Mutation(s): 0 
Gene Names: U11
UniProt
Find proteins for Q69535 (Human herpesvirus 6B (strain Z29))
Explore Q69535 
Go to UniProtKB:  Q69535
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ69535
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Small capsomere-interacting protein89Human herpesvirus 6 strain Z29Mutation(s): 0 
Gene Names: SCPU32
UniProt
Find proteins for Q9WT32 (Human herpesvirus 6B (strain Z29))
Explore Q9WT32 
Go to UniProtKB:  Q9WT32
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9WT32
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Triplex capsid protein 1SA [auth 5],
TA [auth S],
UA [auth T],
VA [auth U],
WA [auth V]
299Human herpesvirus 6 strain Z29Mutation(s): 0 
Gene Names: TRX1U29
UniProt
Find proteins for Q9WT35 (Human herpesvirus 6B (strain Z29))
Explore Q9WT35 
Go to UniProtKB:  Q9WT35
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9WT35
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Triplex capsid protein 2296Human herpesvirus 6 strain Z29Mutation(s): 0 
Gene Names: TRX2U56
UniProt
Find proteins for Q9QJ27 (Human herpesvirus 6B (strain Z29))
Explore Q9QJ27 
Go to UniProtKB:  Q9QJ27
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9QJ27
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)United StatesDE028583, DE025567
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI094386
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1S10RR23057, 1S10OD018111, and 1U24GM116792
National Science Foundation (NSF, United States)United StatesDBI-1338135 and DMR-1548924

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-11
    Type: Initial release