6CGV

Revised crystal structure of human adenovirus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.427 
  • R-Value Work: 0.422 

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This is version 1.4 of the entry. See complete history


Literature

Revised Crystal Structure of Human Adenovirus Reveals the Limits on Protein IX Quasi-Equivalence and on Analyzing Large Macromolecular Complexes.

Kundhavai Natchiar, S.Venkataraman, S.Mullen, T.M.Nemerow, G.R.Reddy, V.S.

(2018) J Mol Biol 430: 4132-4141

  • DOI: 10.1016/j.jmb.2018.08.011
  • Primary Citation of Related Structures:  
    6CGV

  • PubMed Abstract: 
  • We report the revised crystal structure of a pseudo-typed human adenovirus at 3.8-Å resolution that is consistent with the atomic models of minor proteins determined by cryo-electron microscopy. The diffraction data from multiple crystals were rescaled and merged to increase the data completeness ...

    We report the revised crystal structure of a pseudo-typed human adenovirus at 3.8-Å resolution that is consistent with the atomic models of minor proteins determined by cryo-electron microscopy. The diffraction data from multiple crystals were rescaled and merged to increase the data completeness. The densities for the minor proteins were initially identified in the phase-refined omit maps that were further improved by the phases from docked poly-alanine models to build atomic structures. While the trimeric fiber molecules are disordered due to flexibility and imposition of 5-fold symmetry, the remaining major capsid proteins hexon and penton base are clearly ordered, with the exception of hypervariable region 1 of hexons, the RGD containing loop, and the N-termini of the penton base. The exterior minor protein IX together with the interior minor proteins IIIa and VIII stabilizes the adenovirus virion. A segment of N-terminal pro-peptide of VI is found in the interior cavities of peripentonal hexons, and the rest of VI is disordered. While the triskelion substructures formed by the N-termini of IX conform to excellent quasi 3-fold symmetry, the tetrameric coiled-coils formed by the C-termini and organized in parallel and anti-parallel arrangement do not exhibit any quasi-symmetry. This observation also conveys the pitfalls of using the quasi-equivalence as validation criteria for the structural analysis of extended (non-modular) capsid proteins such as IX. Together, these results remedy certain discrepancies in the previous X-ray model in agreement with the cryo-electron microscopy models.


    Related Citations: 
    • Structures and organization of adenovirus cement proteins provide insights into the role of capsid maturation in virus entry and infection.
      Reddy, V.S., Nemerow, G.R.
      (2014) Proc Natl Acad Sci U S A 111: 11715

    Organizational Affiliation

    Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. Electronic address: reddyv@scripps.edu.



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
949Human 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 proteinM [auth N]571Human 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 IIIaN [auth M]585Human adenovirus 5Mutation(s): 0 
Gene Names: L1
UniProt
Find proteins for P12537 (Human adenovirus C serotype 5)
Explore P12537 
Go to UniProtKB:  P12537
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Hexon-interlacing proteinO [auth P], P [auth Q], Q [auth R], R [auth S]140Human adenovirus 5Mutation(s): 0 
Gene Names: IX
UniProt
Find proteins for P03281 (Human adenovirus C serotype 5)
Explore P03281 
Go to UniProtKB:  P03281
Protein Feature View
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-hexon-linking protein VIIIS [auth U], T [auth V]227Human adenovirus 5Mutation(s): 0 
Gene Names: L4
UniProt
Find proteins for P24936 (Human adenovirus C serotype 5)
Explore P24936 
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Protein Feature View
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  • Reference Sequence
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-protein VIU [auth W]24Human adenovirus 5Mutation(s): 0 
Gene Names: L3
UniProt
Find proteins for P24937 (Human adenovirus C serotype 5)
Explore P24937 
Go to UniProtKB:  P24937
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.427 
  • R-Value Work: 0.422 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 854.245α = 60.38
b = 855.315β = 60.43
c = 865.907γ = 61.98
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01 AI070771

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-25
    Type: Initial release
  • Version 1.1: 2018-09-05
    Changes: Data collection, Database references
  • Version 1.2: 2018-10-24
    Changes: Data collection, Database references
  • Version 1.3: 2019-02-20
    Changes: Author supporting evidence, Data collection
  • Version 1.4: 2019-12-18
    Changes: Author supporting evidence