6B1T

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

  • Classification: VIRUS
  • Organism(s): Human adenovirus C serotype 5

  • 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; National Institutes of Health/National Institute of Dental and Craniofacial Research; National Institutes of Health/National Institute Of Allergy and Infectious Diseases; National Institutes of Health/National Center for Advancing Translational Sciences; National Institutes of Health/Office of the Director; National Science Foundation (United States) 

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.2 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 Structures of Minor Proteins VI and VII in the Human Adenovirus.

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

(2017) J. Virol. --: --

  • DOI: 10.1128/JVI.00850-17

  • PubMed Abstract: 
  • Human adenoviruses (Ad) are dsDNA viruses associated with infectious diseases, yet better known as tools for gene delivery and oncolytic anti-cancer therapy. Atomic structures of Ad provide the basis for the development of antivirals and for engineer ...

    Human adenoviruses (Ad) are dsDNA viruses associated with infectious diseases, yet better known as tools for gene delivery and oncolytic anti-cancer therapy. Atomic structures of Ad provide the basis for the development of antivirals and for engineering efforts towards more effective applications. Since 2010, atomic models of human Ad5 have been independently derived from photographic film cryoEM and X-ray crystallography, but discrepancies exist concerning the assignment of cement proteins IIIa, VIII and IX. To clarify these discrepancies, here we have employed the technology of direct electron-counting to obtain a cryoEM structure of human Ad5 at 3.2 Å resolution. Our improved structure unambiguously confirmed our previous cryoEM models of proteins IIIa, VIII and IX and explained the likely cause of conflict in the crystallography models. The improved structure also allows the identification of three new components in the cavities of hexons - 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--by extension that of genome-condensing pVII--to hexons is consistent with the previously proposed dsDNA genome-capsid co-assembly for adenoviruses, which resembles that of ssRNA viruses but differs from the well-established mechanism of pumping dsDNA into a preformed protein capsid, as exemplified by tailed bacteriophages and herpesviruses.IMPORTANCE Adenovirus is a double-edged sword to humans - as a widespread pathogen and a bioengineering tool for anti-cancer and gene therapy. Atomic structure of the virus provides the basis for antiviral and application developments, but conflicting atomic models from conventional/film cryoEM and X-ray crystallography for important cement proteins IIIa, VIII, and IX have caused confusion. Using the cutting-edge cryoEM 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 co-assembly mechanism for adenoviruses.


    Organizational Affiliation

    Department of Microbiology, Immunology, and Molecular GeneticsCalifornia NanoSystems Institute Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hexon protein
A, B, C, D, E, F, G, H, I, J, K, L
952Human adenovirus C serotype 5Mutation(s): 0 
Gene Names: L3
Find proteins for P04133 (Human adenovirus C serotype 5)
Go to UniProtKB:  P04133
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Penton protein
M
571Human adenovirus C serotype 5Mutation(s): 0 
Gene Names: L2
Find proteins for P12538 (Human adenovirus C serotype 5)
Go to UniProtKB:  P12538
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Pre-hexon-linking protein IIIa
N
585Human adenovirus C serotype 5Mutation(s): 0 
Find proteins for P12537 (Human adenovirus C serotype 5)
Go to UniProtKB:  P12537
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Pre-hexon-linking protein VIII
O, P
227Human adenovirus C serotype 5Mutation(s): 0 
Gene Names: L4
Find proteins for P24936 (Human adenovirus C serotype 5)
Go to UniProtKB:  P24936
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Hexon-interlacing protein
Q, R, S, T
140Human adenovirus C serotype 5Mutation(s): 0 
Gene Names: IX
Find proteins for P03281 (Human adenovirus C serotype 5)
Go to UniProtKB:  P03281
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Pre-protein VI
U, V, Y
33Human adenovirus C serotype 5Mutation(s): 0 
Gene Names: L3
Find proteins for P24937 (Human adenovirus C serotype 5)
Go to UniProtKB:  P24937
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Pre-histone-like nucleoprotein
W
11Human adenovirus C serotype 5Mutation(s): 0 
Gene Names: L2
Find proteins for P68951 (Human adenovirus C serotype 5)
Go to UniProtKB:  P68951
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Pre-protein VI
X
217Human adenovirus C serotype 5Mutation(s): 0 
Gene Names: L3
Find proteins for P24937 (Human adenovirus C serotype 5)
Go to UniProtKB:  P24937
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.2 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM071940
National Institutes of Health/National Institute of Dental and Craniofacial ResearchUnited StatesDE025567
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesAI094386
National Institutes of Health/National Center for Advancing Translational SciencesUnited StatesUL1TR001881
National Institutes of Health/Office of the DirectorUnited States1S10OD018111
National Institutes of Health/National Institute of General Medical SciencesUnited States1U24GM116792
National Science Foundation (United States)United StatesDBI-1338135

Revision History 

  • Version 1.0: 2017-09-27
    Type: Initial release
  • Version 1.1: 2017-10-04
    Type: Advisory
  • Version 1.2: 2017-10-18
    Type: Author supporting evidence, Database references
  • Version 1.3: 2018-07-18
    Type: Data collection