8OFU

Human adenovirus type 53 fiber-knob protein

PDB DOI: https://doi.org/10.2210/pdb8OFU/pdb

Classification: VIRAL PROTEIN
Organism(s): Human adenovirus 53
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-03-16 Released: 2023-09-20
Deposition Author(s): Rizkallah, P.J., Parker, A.L., Mundy, R.M., Baker, A.T.
Funding Organization(s): Medical Research Council (MRC, United Kingdom), Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.61 Å
R-Value Free: 0.213
R-Value Work: 0.191
R-Value Observed: 0.192

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Broad sialic acid usage amongst species D human adenovirus.

Mundy, R.M., Baker, A.T., Bates, E.A., Cunliffe, T.G., Teijeira-Crespo, A., Moses, E., Rizkallah, P.J., Parker, A.L.

(2023) Npj Viruses 1: 1-1

PubMed: 38665237 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s44298-023-00001-5
Primary Citation of Related Structures:
8OFP, 8OFQ, 8OFR, 8OFS, 8OFT, 8OFU, 8OFV

PubMed Abstract:
Human adenoviruses (HAdV) are widespread pathogens causing usually mild infections. The Species D (HAdV-D) cause gastrointestinal tract infections and epidemic keratoconjunctivitis (EKC). Despite being significant pathogens, knowledge around HAdV-D mechanism of cell infection is lacking. Sialic acid (SA) usage has been proposed as a cell infection mechanism for EKC causing HAdV-D. Here we highlight an important role for SA engagement by many HAdV-D. We provide apo state crystal structures of 7 previously undetermined HAdV-D fiber-knob proteins, and structures of HAdV-D25, D29, D30 and D53 fiber-knob proteins in complex with SA. Biologically, we demonstrate that removal of cell surface SA reduced infectivity of HAdV-C5 vectors pseudotyped with HAdV-D fiber-knob proteins, whilst engagement of the classical HAdV receptor CAR was variable. Our data indicates variable usage of SA and CAR across HAdV-D. Better defining these interactions will enable improved development of antivirals and engineering of the viruses into refined therapeutic vectors.

Organizational Affiliation

Division of Cancer & Genetics, Cardiff University School of Medicine, Cardiff, CF14 4XN UK.

Macromolecule Content

Total Structure Weight: 129.84 kDa
Atom Count: 10,039
Modelled Residue Count: 1,112
Deposited Residue Count: 1,128
Unique protein chains: 1

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, E A, B, C, D, E, F	188	Human adenovirus 53	Mutation(s): 0 Gene Names: L5
UniProt
Find proteins for E5RWD1 (Human adenovirus 53) Explore E5RWD1 Go to UniProtKB: E5RWD1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	E5RWD1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain EA [auth D] SDF format, chain MA [auth F] SDF format, chain NA [auth F] SDF format, chain W [auth C] SDF format, chain X [auth C] MOL2 format, chain EA [auth D] MOL2 format, chain MA [auth F] MOL2 format, chain NA [auth F] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] mmCIF format, chain EA [auth D] mmCIF format, chain MA [auth F] mmCIF format, chain NA [auth F] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C]	EA [auth D], MA [auth F], NA [auth F], W [auth C], X [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain EA [auth D] Focus chain MA [auth F] Focus chain NA [auth F] Focus chain W [auth C] Focus chain X [auth C] Interactions & Density Focus chain EA [auth D] Focus chain MA [auth F] Focus chain NA [auth F] Focus chain W [auth C] Focus chain X [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain FA [auth E] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain JA [auth F] SDF format, chain KA [auth F] SDF format, chain N [auth B] SDF format, chain U [auth C] MOL2 format, chain FA [auth E] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain JA [auth F] MOL2 format, chain KA [auth F] MOL2 format, chain N [auth B] MOL2 format, chain U [auth C] mmCIF format, chain FA [auth E] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain JA [auth F] mmCIF format, chain KA [auth F] mmCIF format, chain N [auth B] mmCIF format, chain U [auth C]	FA [auth E] G [auth A] H [auth A] JA [auth F] KA [auth F] FA [auth E], G [auth A], H [auth A], JA [auth F], KA [auth F], N [auth B], U [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain FA [auth E] Focus chain G [auth A] Focus chain H [auth A] Focus chain JA [auth F] Focus chain KA [auth F] Focus chain N [auth B] Focus chain U [auth C] Interactions & Density Focus chain FA [auth E] Focus chain G [auth A] Focus chain H [auth A] Focus chain JA [auth F] Focus chain KA [auth F] Focus chain N [auth B] Focus chain U [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain DA [auth D] SDF format, chain I [auth A] SDF format, chain M [auth A] SDF format, chain O [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain GA [auth E] SDF format, chain HA [auth E] SDF format, chain IA [auth E] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain LA [auth F] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain V [auth C] SDF format, chain Y [auth D] SDF format, chain Z [auth D] MOL2 format, chain AA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain M [auth A] MOL2 format, chain O [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain GA [auth E] MOL2 format, chain HA [auth E] MOL2 format, chain IA [auth E] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth F] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain V [auth C] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D] mmCIF format, chain AA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain M [auth A] mmCIF format, chain O [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain GA [auth E] mmCIF format, chain HA [auth E] mmCIF format, chain IA [auth E] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth F] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain V [auth C] mmCIF format, chain Y [auth D] mmCIF format, chain Z [auth D]	AA [auth D] BA [auth D] CA [auth D] DA [auth D] GA [auth E] AA [auth D], BA [auth D], CA [auth D], DA [auth D], GA [auth E], HA [auth E], I [auth A], IA [auth E], J [auth A], K [auth A], L [auth A], LA [auth F], M [auth A], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], V [auth C], Y [auth D], Z [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain GA [auth E] Focus chain HA [auth E] Focus chain I [auth A] Focus chain IA [auth E] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth F] Focus chain M [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain V [auth C] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain GA [auth E] Focus chain HA [auth E] Focus chain I [auth A] Focus chain IA [auth E] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth F] Focus chain M [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain V [auth C] Focus chain Y [auth D] Focus chain Z [auth D]