5VKU

An atomic structure of the human cytomegalovirus (HCMV) capsid with its securing layer of pp150 tegument protein

  • Classification: VIRUS
  • Organism(s): Human herpesvirus 5 strain AD169
  • Mutation(s): No 

  • Deposited: 2017-04-24 Released: 2017-06-28 
  • Deposition Author(s): Yu, X., Jih, J., Jiang, J., Zhou, H.
  • Funding Organization(s): 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: 3.90 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

Atomic structure of the human cytomegalovirus capsid with its securing tegument layer of pp150.

Yu, X., Jih, J., Jiang, J., Zhou, Z.H.

(2017) Science 356

  • DOI: 10.1126/science.aam6892
  • Primary Citation of Related Structures:  
    5VKU

  • PubMed Abstract: 

    • Herpesviruses possess a genome-pressurized capsid. The 235-kilobase genome of human cytomegalovirus (HCMV) is by far the largest of any herpesvirus, yet it has been unclear how its capsid, which is similar in size to those of other herpesviruses, is ...

    Herpesviruses possess a genome-pressurized capsid. The 235-kilobase genome of human cytomegalovirus (HCMV) is by far the largest of any herpesvirus, yet it has been unclear how its capsid, which is similar in size to those of other herpesviruses, is stabilized. Here we report a HCMV atomic structure consisting of the herpesvirus-conserved capsid proteins MCP, Tri1, Tri2, and SCP and the HCMV-specific tegument protein pp150-totaling ~4000 molecules and 62 different conformers. MCPs manifest as a complex of insertions around a bacteriophage HK97 gp5-like domain, which gives rise to three classes of capsid floor-defining interactions; triplexes, composed of two "embracing" Tri2 conformers and a "third-wheeling" Tri1, fasten the capsid floor. HCMV-specific strategies include using hexon channels to accommodate the genome and pp150 helix bundles to secure the capsid via cysteine tetrad-to-SCP interactions. Our structure should inform rational design of countermeasures against HCMV, other herpesviruses, and even HIV/AIDS.

    Organizational Affiliation: 

    California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095-7364, USA.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tegument protein pp1500, 1, 2, 3, 4, 5, 6, 7, 8, 9, v, w, x, y, z285Human herpesvirus 5 strain AD169Mutation(s): 0 
Gene Names: UL32
Find proteins for P08318 (Human cytomegalovirus (strain AD169))
Explore P08318 
Go to UniProtKB:  P08318
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Major capsid proteinA, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P1370Human herpesvirus 5 strain AD169Mutation(s): 0 
Gene Names: MCP, UL86
Find proteins for P16729 (Human cytomegalovirus (strain AD169))
Explore P16729 
Go to UniProtKB:  P16729
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Small capsomere-interacting proteinQ, R, S, T, U, V, W, X, Y, Z, a, b, c, d, e, f75Human herpesvirus 5 strain AD169Mutation(s): 0 
Gene Names: SCP, UL48A
Find proteins for Q7M6N6 (Human cytomegalovirus (strain AD169))
Explore Q7M6N6 
Go to UniProtKB:  Q7M6N6
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Triplex capsid protein 1g, j, m, p, s290Human herpesvirus 5 strain AD169Mutation(s): 0 
Gene Names: TRX1, UL46
Find proteins for P16783 (Human cytomegalovirus (strain AD169))
Explore P16783 
Go to UniProtKB:  P16783
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Triplex capsid protein 2h, i, k, l, n, o, q, r, t, u306Human herpesvirus 5 strain AD169Mutation(s): 0 
Gene Names: TRX2, UL85
Find proteins for P16728 (Human cytomegalovirus (strain AD169))
Explore P16728 
Go to UniProtKB:  P16728
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
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

Revision History 

  • Version 1.0: 2017-06-28
    Type: Initial release
  • Version 1.1: 2017-07-12
    Changes: Database references
  • Version 1.2: 2017-09-13
    Changes: Author supporting evidence, Data collection
  • Version 1.3: 2019-11-27
    Changes: Author supporting evidence, Structure summary