5TX1

Cryo-Electron microscopy structure of species-D human adenovirus 26

  • Classification: VIRUS
  • Organism(s): Human adenovirus 26

  • Deposited: 2016-11-15 Released: 2017-05-31 
  • Deposition Author(s): Reddy, V., Yu, X., Veesler, D.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases 

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.7 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Cryo-EM structure of human adenovirus D26 reveals the conservation of structural organization among human adenoviruses.

Yu, X.Veesler, D.Campbell, M.G.Barry, M.E.Asturias, F.J.Barry, M.A.Reddy, V.S.

(2017) Sci Adv 3: e1602670-e1602670

  • DOI: 10.1126/sciadv.1602670

  • PubMed Abstract: 
  • Human adenoviruses (HAdVs) cause acute respiratory, ocular, and gastroenteric diseases and are also frequently used as gene and vaccine delivery vectors. Unlike the archetype human adenovirus C5 (HAdV-C5), human adenovirus D26 (HAdV-D26) belongs to s ...

    Human adenoviruses (HAdVs) cause acute respiratory, ocular, and gastroenteric diseases and are also frequently used as gene and vaccine delivery vectors. Unlike the archetype human adenovirus C5 (HAdV-C5), human adenovirus D26 (HAdV-D26) belongs to species-D HAdVs, which target different cellular receptors, and is differentially recognized by immune surveillance mechanisms. HAdV-D26 is being championed as a lower seroprevalent vaccine and oncolytic vector in preclinical and human clinical studies. To understand the molecular basis for their distinct biological properties and independently validate the structures of minor proteins, we determined the first structure of species-D HAdV at 3.7 Å resolution by cryo-electron microscopy. All the hexon hypervariable regions (HVRs), including HVR1, have been identified and exhibit a distinct organization compared to those of HAdV-C5. Despite the differences in the arrangement of helices in the coiled-coil structures, protein IX molecules form a continuous hexagonal network on the capsid exterior. In addition to the structurally conserved region (3 to 300) of IIIa, we identified an extra helical domain comprising residues 314 to 390 that further stabilizes the vertex region. Multiple (two to three) copies of the cleaved amino-terminal fragment of protein VI (pVIn) are observed in each hexon cavity, suggesting that there could be ≥480 copies of VI present in HAdV-D26. In addition, a localized asymmetric reconstruction of the vertex region provides new details of the three-pronged "claw hold" of the trimeric fiber and its interactions with the penton base. These observations resolve the previous conflicting assignments of the minor proteins and suggest the likely conservation of their organization across different HAdVs.


    Organizational Affiliation

    Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, 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 26Mutation(s): 0 
Gene Names: L3
Find proteins for Q3S8B3 (Human adenovirus 26)
Go to UniProtKB:  Q3S8B3
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Penton
N
497Human adenovirus 26Mutation(s): 0 
Gene Names: L2
Find proteins for A4ZKL2 (Human adenovirus 26)
Go to UniProtKB:  A4ZKL2
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Fiber
O
19Human adenovirus 26Mutation(s): 0 
Find proteins for A4ZKM1 (Human adenovirus 26)
Go to UniProtKB:  A4ZKM1
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
PIIIa
M
388Human adenovirus 26Mutation(s): 0 
Find proteins for A4ZKL1 (Human adenovirus 26)
Go to UniProtKB:  A4ZKL1
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
PIX
P, Q, R, S
134Human adenovirus 26Mutation(s): 0 
Gene Names: IX
Find proteins for A4ZKK7 (Human adenovirus 26)
Go to UniProtKB:  A4ZKK7
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
PVIII
U, V
227Human adenovirus 26Mutation(s): 0 
Gene Names: L4
Find proteins for A4ZKM0 (Human adenovirus 26)
Go to UniProtKB:  A4ZKM0
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
PVI
1, 2, 3, 4, 5, 6, 7, 8, 9
31Human adenovirus 26Mutation(s): 0 
Gene Names: L3
Find proteins for A4ZKL5 (Human adenovirus 26)
Go to UniProtKB:  A4ZKL5
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Unknown
X, Y, Z
10N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
X, Y, Z
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.7 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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 Allergy and Infectious DiseasesUnited StatesAI070771
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesAI103692

Revision History 

  • Version 1.0: 2017-05-31
    Type: Initial release
  • Version 1.1: 2017-09-13
    Type: Author supporting evidence, Data collection
  • Version 1.2: 2018-07-18
    Type: Data collection, Experimental preparation