6CGV

Revised crystal structure of human adenovirus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.8 Å
  • R-Value Free: 0.427 
  • R-Value Work: 0.422 

wwPDB Validation 3D Report Full Report


This is version 1.3 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

  • 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 rescal ...

    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 Immunology and Microbial Sciences, The Scripps Research Institute, La Jolla, CA 92037, USA.,Department of Immunology and Microbial Sciences, The Scripps Research Institute, La Jolla, CA 92037, USA. Electronic address: gnemerow@scripps.edu.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. Electronic address: reddyv@scripps.edu.,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
949Human 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
N
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
M
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
Hexon-interlacing protein
P, Q, R, S
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: 5
MoleculeChainsSequence LengthOrganismDetails
Pre-hexon-linking protein VIII
U, V
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: 6
MoleculeChainsSequence LengthOrganismDetails
Pre-protein VI
W
24Human 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: X-RAY DIFFRACTION
  • Resolution: 3.8 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
HKL-2000data reduction
SCALAdata scaling
REFMACrefinement
PHASERphasing

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 StatesR01 AI070771

Revision History 

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