4D0U

Crystal structure of the fiber head domain of the Atadenovirus snake adenovirus 1, selenomethionine-derivative

PDB DOI: 10.2210/pdb4D0U/pdb

Classification: VIRAL PROTEIN
Organism(s): Snake adenovirus 1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2014-04-30 Released: 2014-12-17
Deposition Author(s): Singh, A.K., van Raaij, M.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.189
R-Value Work: 0.158
R-Value Observed: 0.159

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Literature

Crystal structure of the fibre head domain of the Atadenovirus Snake Adenovirus 1.

Singh, A.K., Menendez-Conejero, R., San Martin, C., van Raaij, M.J.

(2014) PLoS One 9: e114373-e114373

PubMed: 25486282 Search on PubMedSearch on PubMed Central
DOI: 10.1371/journal.pone.0114373
Primary Citation of Related Structures:
4D0U, 4D0V, 4D1F, 4D1G, 4UMI

PubMed Abstract:

Adenoviruses are non-enveloped icosahedral viruses with trimeric fibre proteins protruding from their vertices. There are five known genera, from which only Mastadenoviruses have been widely studied. Apart from studying adenovirus as a biological model system and with a view to prevent or combat viral infection, there is a major interest in using adenovirus for vaccination, cancer therapy and gene therapy purposes. Adenoviruses from the Atadenovirus genus have been isolated from squamate reptile hosts, ruminants and birds and have a characteristic gene organization and capsid morphology. The carboxy-terminal virus-distal fibre head domains are likely responsible for primary receptor recognition. We determined the high-resolution crystal structure of the Snake Adenovirus 1 (SnAdV-1) fibre head using the multi-wavelength anomalous dispersion (MAD) method. Despite the absence of significant sequence homology, this Atadenovirus fibre head has the same beta-sandwich propeller topology as other adenovirus fibre heads. However, it is about half the size, mainly due to much shorter loops connecting the beta-strands. The detailed structure of the SnAdV-1 fibre head and other animal adenovirus fibre heads, together with the future identification of their natural receptors, may lead to the development of new strategies to target adenovirus vectors to cells of interest.

Related Citations:

Crystallization of the C-terminal domain of the fibre protein from snake adenovirus 1, an atadenovirus.
Singh, A.K., Menendez-Conejero, R., San Martin, C., van Raaij, M.J.
(2013) Acta Crystallogr Sect F Struct Biol Cryst Commun 69: 1374

Physicochemical Properties and Cytopathogenicity of an Adenovirus-Like Agent Isolated from Corn Snake (Elaphe Guttata).
Juhasz, A., Ahne, W.
(1993) Arch Virol 130: 429

Completion of the Genome Analysis of Snake Adenovirus Type 1, a Representative of the Reptilian Lineage within the Novel Genus Atadenovirus.
Farkas, S.L., Harrach, B., Benko, M.
(2008) Virus Res 132: 132

Organizational Affiliation:

Departamento de Estructura de Macromoleculas, Centro Nacional de Biotecnologia (CNB-CSIC), Madrid, Spain; NanoBiomedicine Initiative, Centro Nacional de Biotecnologia (CNB-CSIC), Madrid, Spain.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FIBER PROTEIN	A, B, C, D	145	Snake adenovirus 1	Mutation(s): 2 Gene Names: L5
UniProt
Find proteins for A9CB96 (Snake adenovirus serotype 1) Explore A9CB96 Go to UniProtKB: A9CB96
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A9CB96
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PE8 Query on PE8 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth D] MOL2 format, chain E [auth A] MOL2 format, chain J [auth D]	E [auth A], J [auth D]	3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL C₁₆ H₃₄ O₉ GLZWNFNQMJAZGY-UHFFFAOYSA-N		Ligand Interaction
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain H [auth C] SDF format, chain I [auth C] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth C] MOL2 format, chain I [auth C]	F [auth B], G [auth B], H [auth C], I [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Ligand Interaction

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.189
R-Value Work: 0.158
R-Value Observed: 0.159
Space Group: I 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 149.54	α = 90
b = 149.54	β = 90
c = 149.54	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
autoSHARP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Deposited Date: 2014-04-30
Released Date: 2014-12-17

Deposition Author(s):

Singh, A.K.

van Raaij, M.J.

Revision History (Full details and data files)

Version 1.0: 2014-12-17
Type: Initial release
Version 1.1: 2015-03-04
Changes: Database references
Version 1.2: 2015-04-29
Changes: Data collection
Version 1.3: 2018-01-17
Changes: Database references
Version 2.0: 2018-12-19
Changes: Atomic model, Data collection, Derived calculations