8OFV | pdb_00008ofv

Human adenovirus type 53 fiber-knob protein complexed with sialic acid

PDB DOI: https://doi.org/10.2210/pdb8OFV/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: 1.77 Å
R-Value Free:
0.228 (Depositor), 0.198 (DCC)
R-Value Work:
0.208 (Depositor)
R-Value Observed:
0.209 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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 PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s44298-023-00001-5
Primary Citation 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: 260.9 kDa
Atom Count: 19,866
Modeled Residue Count: 2,214
Deposited Residue Count: 2,268
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 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, G, H, I, J, K, L	189	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	E5RWD1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SIA Query on SIA Download:Ideal Coordinates CCD File SDF format, chain BB [auth L] MOL2 format, chain BB [auth L] mmCIF format, chain BB [auth L]	BB [auth L]	N-acetyl-alpha-neuraminic acid C₁₁ H₁₉ N O₉ SQVRNKJHWKZAKO-YRMXFSIDSA-N		Interactions Focus chain BB [auth L] Interactions & Density Focus chain BB [auth L]
SLB (Subject of Investigation/LOI) Query on SLB Download:Ideal Coordinates CCD File SDF format, chain HA [auth F] MOL2 format, chain HA [auth F] mmCIF format, chain HA [auth F]	HA [auth F]	N-acetyl-beta-neuraminic acid C₁₁ H₁₉ N O₉ SQVRNKJHWKZAKO-PFQGKNLYSA-N		Interactions Focus chain HA [auth F] Interactions & Density Focus chain HA [auth F]
P4G Query on P4G Download:Ideal Coordinates CCD File SDF format, chain AB [auth L] SDF format, chain GA [auth F] SDF format, chain NA [auth G] SDF format, chain OA [auth G] SDF format, chain V [auth B] SDF format, chain VA [auth I] SDF format, chain W [auth B] SDF format, chain XA [auth K] SDF format, chain Y [auth C] SDF format, chain Z [auth C] SDF format, chain ZA [auth L] MOL2 format, chain AB [auth L] MOL2 format, chain GA [auth F] MOL2 format, chain NA [auth G] MOL2 format, chain OA [auth G] MOL2 format, chain V [auth B] MOL2 format, chain VA [auth I] MOL2 format, chain W [auth B] MOL2 format, chain XA [auth K] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] MOL2 format, chain ZA [auth L] mmCIF format, chain AB [auth L] mmCIF format, chain GA [auth F] mmCIF format, chain NA [auth G] mmCIF format, chain OA [auth G] mmCIF format, chain V [auth B] mmCIF format, chain VA [auth I] mmCIF format, chain W [auth B] mmCIF format, chain XA [auth K] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C] mmCIF format, chain ZA [auth L]	AB [auth L] GA [auth F] NA [auth G] OA [auth G] V [auth B] AB [auth L], GA [auth F], NA [auth G], OA [auth G], V [auth B], VA [auth I], W [auth B], XA [auth K], Y [auth C], Z [auth C], ZA [auth L]	1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE C₈ H₁₈ O₃ RRQYJINTUHWNHW-UHFFFAOYSA-N		Interactions Focus chain AB [auth L] Focus chain GA [auth F] Focus chain NA [auth G] Focus chain OA [auth G] Focus chain V [auth B] Focus chain VA [auth I] Focus chain W [auth B] Focus chain XA [auth K] Focus chain Y [auth C] Focus chain Z [auth C] Focus chain ZA [auth L] Interactions & Density Focus chain AB [auth L] Focus chain GA [auth F] Focus chain NA [auth G] Focus chain OA [auth G] Focus chain V [auth B] Focus chain VA [auth I] Focus chain W [auth B] Focus chain XA [auth K] Focus chain Y [auth C] Focus chain Z [auth C] Focus chain ZA [auth L]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain CA [auth E] SDF format, chain DA [auth E] SDF format, chain FA [auth F] SDF format, chain LA [auth G] SDF format, chain M [auth A] SDF format, chain MA [auth G] SDF format, chain Q [auth B] SDF format, chain QA [auth H] SDF format, chain R [auth B] SDF format, chain RA [auth H] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain UA [auth I] SDF format, chain WA [auth K] SDF format, chain X [auth C] SDF format, chain TA [auth I] MOL2 format, chain BA [auth E] MOL2 format, chain CA [auth E] MOL2 format, chain DA [auth E] MOL2 format, chain FA [auth F] MOL2 format, chain LA [auth G] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth G] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth H] MOL2 format, chain R [auth B] MOL2 format, chain RA [auth H] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain UA [auth I] MOL2 format, chain WA [auth K] MOL2 format, chain X [auth C] MOL2 format, chain TA [auth I] mmCIF format, chain BA [auth E] mmCIF format, chain CA [auth E] mmCIF format, chain DA [auth E] mmCIF format, chain FA [auth F] mmCIF format, chain LA [auth G] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth G] mmCIF format, chain Q [auth B] mmCIF format, chain QA [auth H] mmCIF format, chain R [auth B] mmCIF format, chain RA [auth H] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain UA [auth I] mmCIF format, chain WA [auth K] mmCIF format, chain X [auth C] mmCIF format, chain TA [auth I]	BA [auth E] CA [auth E] DA [auth E] FA [auth F] LA [auth G] BA [auth E], CA [auth E], DA [auth E], FA [auth F], LA [auth G], M [auth A], MA [auth G], Q [auth B], QA [auth H], R [auth B], RA [auth H], S [auth B], T [auth B], TA [auth I], U [auth B], UA [auth I], WA [auth K], X [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain BA [auth E] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain FA [auth F] Focus chain LA [auth G] Focus chain M [auth A] Focus chain MA [auth G] Focus chain Q [auth B] Focus chain QA [auth H] Focus chain R [auth B] Focus chain RA [auth H] Focus chain S [auth B] Focus chain T [auth B] Focus chain TA [auth I] Focus chain U [auth B] Focus chain UA [auth I] Focus chain WA [auth K] Focus chain X [auth C] Interactions & Density Focus chain BA [auth E] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain FA [auth F] Focus chain LA [auth G] Focus chain M [auth A] Focus chain MA [auth G] Focus chain Q [auth B] Focus chain QA [auth H] Focus chain R [auth B] Focus chain RA [auth H] Focus chain S [auth B] Focus chain T [auth B] Focus chain TA [auth I] Focus chain U [auth B] Focus chain UA [auth I] Focus chain WA [auth K] Focus chain X [auth C]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain EA [auth F] SDF format, chain JA [auth G] SDF format, chain KA [auth G] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain PA [auth H] SDF format, chain SA [auth I] SDF format, chain YA [auth L] SDF format, chain N [auth B] SDF format, chain IA [auth G] MOL2 format, chain AA [auth E] MOL2 format, chain EA [auth F] MOL2 format, chain JA [auth G] MOL2 format, chain KA [auth G] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain PA [auth H] MOL2 format, chain SA [auth I] MOL2 format, chain YA [auth L] MOL2 format, chain N [auth B] MOL2 format, chain IA [auth G] mmCIF format, chain AA [auth E] mmCIF format, chain EA [auth F] mmCIF format, chain JA [auth G] mmCIF format, chain KA [auth G] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain PA [auth H] mmCIF format, chain SA [auth I] mmCIF format, chain YA [auth L] mmCIF format, chain N [auth B] mmCIF format, chain IA [auth G]	AA [auth E] EA [auth F] IA [auth G] JA [auth G] KA [auth G] AA [auth E], EA [auth F], IA [auth G], JA [auth G], KA [auth G], N [auth B], O [auth B], P [auth B], PA [auth H], SA [auth I], YA [auth L]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain EA [auth F] Focus chain IA [auth G] Focus chain JA [auth G] Focus chain KA [auth G] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain PA [auth H] Focus chain SA [auth I] Focus chain YA [auth L] Interactions & Density Focus chain AA [auth E] Focus chain EA [auth F] Focus chain IA [auth G] Focus chain JA [auth G] Focus chain KA [auth G] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain PA [auth H] Focus chain SA [auth I] Focus chain YA [auth L]