5G5N | pdb_00005g5n

Structure of the snake adenovirus 1 hexon-interlacing LH3 protein, methylmercury chloride derivative


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.205 (Depositor), 0.212 (DCC) 
  • R-Value Work: 
    0.172 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 
    0.173 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5G5N

This is version 1.3 of the entry. See complete history

Literature

Structure of a Reptilian Adenovirus Reveals a Phage Tailspike Fold Stabilizing a Vertebrate Virus Capsid.

Menendez-Conejero, R.Nguyen, T.H.Singh, A.K.Condezo, G.N.Marschang, R.E.van Raaij, M.J.San Martin, C.

(2017) Structure 25: 1562-1573

  • DOI: https://doi.org/10.1016/j.str.2017.08.007
  • Primary Citation Related Structures: 
    5G5N, 5G5O

  • PubMed Abstract: 

    Although non-human adenoviruses (AdVs) might offer solutions to problems posed by human AdVs as therapeutic vectors, little is known about their basic biology. In particular, there are no structural studies on the complete virion of any AdV with a non-mammalian host. We combine mass spectrometry, cryo-electron microscopy, and protein crystallography to characterize the composition and structure of a snake AdV (SnAdV-1, Atadenovirus genus). SnAdV-1 particles contain the genus-specific proteins LH3, p32k, and LH2, a previously unrecognized structural component. Remarkably, the cementing protein LH3 has a trimeric β helix fold typical of bacteriophage host attachment proteins. The organization of minor coat proteins differs from that in human AdVs, correlating with higher thermostability in SnAdV-1. These findings add a new piece to the intriguing puzzle of virus evolution, hint at the use of cell entry pathways different from those in human AdVs, and will help development of new, thermostable SnAdV-1-based vectors.


  • Organizational Affiliation
    • Departamento de Estructura de Macromoléculas, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, 28049 Madrid, Spain.

Macromolecule Content 

  • Total Structure Weight: 117.06 kDa 
  • Atom Count: 8,019 
  • Modeled Residue Count: 1,022 
  • Deposited Residue Count: 1,059 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
LH3 HEXON-INTERLACING CAPSID PROTEIN
A, B, C
353Snake adenovirus 1Mutation(s): 0 
UniProt
Find proteins for A9CB85 (Snake adenovirus serotype 1)
Explore A9CB85 
Go to UniProtKB:  A9CB85
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA9CB85
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MMC

Query on MMC



Download:Ideal Coordinates CCD File
AA [auth C]
BA [auth C]
G [auth A]
H [auth A]
I [auth A]
AA [auth C],
BA [auth C],
G [auth A],
H [auth A],
I [auth A],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
Z [auth C]
METHYL MERCURY ION
C H3 Hg
DBUXSCUEGJMZAE-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A],
F [auth A],
O [auth B],
Y [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
CA [auth C]
DA [auth C]
EA [auth C]
FA [auth C]
J [auth A]
CA [auth C],
DA [auth C],
EA [auth C],
FA [auth C],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
T [auth B],
U [auth B],
V [auth B],
W [auth B],
X [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.205 (Depositor), 0.212 (DCC) 
  • R-Value Work:  0.172 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 0.173 (Depositor) 
Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 149.259α = 90
b = 149.259β = 90
c = 108.689γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
CRANK2phasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-07
    Type: Initial release
  • Version 1.1: 2017-10-04
    Changes: Database references
  • Version 1.2: 2017-10-11
    Changes: Database references
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references, Derived calculations