6B1T

Improved cryoEM structure of human adenovirus type 5 with atomic details of minor proteins VI and VII

  • Classification: VIRUS
  • Organism(s): Human adenovirus 5
  • Mutation(s): No 

  • Deposited: 2017-09-18 Released: 2017-09-27 
  • Deposition Author(s): Dai, X.H., Wu, L., Sun, R., Zhou, Z.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 Advancing Translational Sciences (NIH/NCATS), National Institutes of Health/Office of the Director, National Science Foundation (NSF, United States)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Atomic Structures of Minor Proteins VI and VII in Human Adenovirus.

Dai, X.Wu, L.Sun, R.Zhou, Z.H.

(2017) J Virol 91

  • DOI: 10.1128/JVI.00850-17
  • Primary Citation of Related Structures:  
    6B1T

  • PubMed Abstract: 
  • Human adenoviruses (Ad) are double-stranded DNA (dsDNA) viruses associated with infectious diseases, but they are better known as tools for gene delivery and oncolytic anticancer therapy. Atomic structures of Ad provide the basis for the development of antivirals and for engineering efforts toward more effective applications ...

    Human adenoviruses (Ad) are double-stranded DNA (dsDNA) viruses associated with infectious diseases, but they are better known as tools for gene delivery and oncolytic anticancer therapy. Atomic structures of Ad provide the basis for the development of antivirals and for engineering efforts toward more effective applications. Since 2010, atomic models of human Ad5 have been derived independently from photographic film cryo-electron microscopy (cryo-EM) and X-ray crystallography studies, but discrepancies exist concerning the assignment of cement proteins IIIa, VIII, and IX. To clarify these discrepancies, we employed the technology of direct electron counting to obtain a cryo-EM structure of human Ad5 at 3.2-Å resolution. Our improved structure unambiguously confirms our previous cryo-EM models of proteins IIIa, VIII, and IX and explains the likely cause of conflict in the crystallography models. The improved structure also allows the identification of three new components in the cavity of hexon-the cleaved N terminus of precursor protein VI (pVIn), the cleaved N terminus of precursor protein VII (pVIIn2), and mature protein VI. The binding of pVIIn2-and, by extension, that of genome-condensing pVII-to hexons is consistent with the previously proposed dsDNA genome-capsid coassembly for adenoviruses, which resembles that of single-stranded RNA (ssRNA) viruses but differs from the well-established mechanism of pumping dsDNA into a preformed protein capsid exemplified by tailed bacteriophages and herpesviruses. IMPORTANCE Adenovirus is a double-edged sword to humans: it is a widespread pathogen but can be used as a bioengineering tool for anticancer and gene therapies. The atomic structure of the virus provides the basis for antiviral and application developments, but conflicting atomic models for the important cement proteins IIIa, VIII, and IX from conventional/film cryo-EM and X-ray crystallography studies have caused confusion. Using cutting-edge cryo-EM technology with electron counting, we improved the structure of human adenovirus type 5 and confirmed our previous models of cement proteins IIIa, VIII, and IX, thus clarifying the inconsistent structures. The improved structure also reveals atomic details of membrane-lytic protein VI and genome-condensing protein VII and supports the previously proposed genome-capsid coassembly mechanism for adenoviruses.


    Organizational Affiliation

    California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Hexon protein
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H, I, J, K, L
952Human adenovirus 5Mutation(s): 0 
Gene Names: L3
UniProt
Find proteins for P04133 (Human adenovirus C serotype 5)
Explore P04133 
Go to UniProtKB:  P04133
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Penton proteinM571Human adenovirus 5Mutation(s): 0 
Gene Names: L2
UniProt
Find proteins for P12538 (Human adenovirus C serotype 5)
Explore P12538 
Go to UniProtKB:  P12538
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-hexon-linking protein IIIaN585Human adenovirus 5Mutation(s): 0 
Gene Names: L1
UniProt
Find proteins for P12537 (Human adenovirus C serotype 5)
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Go to UniProtKB:  P12537
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-hexon-linking protein VIIIO, P227Human adenovirus 5Mutation(s): 0 
Gene Names: L4
UniProt
Find proteins for P24936 (Human adenovirus C serotype 5)
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Go to UniProtKB:  P24936
Protein Feature View
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Hexon-interlacing proteinQ, R, S, T140Human adenovirus 5Mutation(s): 0 
Gene Names: IX
UniProt
Find proteins for P03281 (Human adenovirus C serotype 5)
Explore P03281 
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  • Reference Sequence
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-protein VIU, V, Y33Human adenovirus 5Mutation(s): 0 
Gene Names: L3
UniProt
Find proteins for P24937 (Human adenovirus C serotype 5)
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Protein Feature View
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-histone-like nucleoproteinW11Human adenovirus 5Mutation(s): 0 
Gene Names: L2
UniProt
Find proteins for P68951 (Human adenovirus C serotype 5)
Explore P68951 
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Protein Feature View
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-protein VIX217Human adenovirus 5Mutation(s): 0 
Gene Names: L3
UniProt
Find proteins for P24937 (Human adenovirus C serotype 5)
Explore P24937 
Go to UniProtKB:  P24937
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



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 Advancing Translational Sciences (NIH/NCATS)United StatesUL1TR001881
National Institutes of Health/Office of the DirectorUnited States1S10OD018111
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  (Full details and data files)

  • Version 1.0: 2017-09-27
    Type: Initial release
  • Version 1.1: 2017-10-04
    Changes: Advisory
  • Version 1.2: 2017-10-18
    Changes: Author supporting evidence, Database references
  • Version 1.3: 2018-07-18
    Changes: Data collection
  • Version 1.4: 2019-04-17
    Changes: Data collection, Database references, Structure summary
  • Version 1.5: 2019-11-27
    Changes: Author supporting evidence