8OFR | pdb_00008ofr

Human adenovirus type 25 fiber-knob protein complexed with sialic acid

PDB DOI: https://doi.org/10.2210/pdb8OFR/pdb

Classification: VIRAL PROTEIN
Organism(s): Human adenovirus 25
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: 2.51 Å
R-Value Free:
0.239 (Depositor), 0.240 (DCC)
R-Value Work:
0.221 (Depositor), 0.220 (DCC)
R-Value Observed:
0.222 (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 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: 515.4 kDa
Atom Count: 35,979
Modelled Residue Count: 4,302
Deposited Residue Count: 4,464
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	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X	186	Human adenovirus 25	Mutation(s): 0 Gene Names: L5
UniProt
Find proteins for M0QUM1 (Human adenovirus 25) Explore M0QUM1 Go to UniProtKB: M0QUM1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	M0QUM1
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SLB (Subject of Investigation/LOI) Query on SLB Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain EA [auth G] SDF format, chain FA [auth H] SDF format, chain HA [auth J] SDF format, chain IA [auth K] SDF format, chain JA [auth L] SDF format, chain KA [auth M] SDF format, chain NA [auth P] SDF format, chain OA [auth Q] SDF format, chain RA [auth T] SDF format, chain SA [auth U] SDF format, chain VA [auth X] SDF format, chain Y [auth A] SDF format, chain Z [auth B] SDF format, chain BA [auth D] SDF format, chain CA [auth E] SDF format, chain DA [auth F] SDF format, chain GA [auth I] SDF format, chain LA [auth N] SDF format, chain MA [auth O] SDF format, chain PA [auth R] SDF format, chain QA [auth S] SDF format, chain TA [auth V] SDF format, chain UA [auth W] MOL2 format, chain AA [auth C] MOL2 format, chain EA [auth G] MOL2 format, chain FA [auth H] MOL2 format, chain HA [auth J] MOL2 format, chain IA [auth K] MOL2 format, chain JA [auth L] MOL2 format, chain KA [auth M] MOL2 format, chain NA [auth P] MOL2 format, chain OA [auth Q] MOL2 format, chain RA [auth T] MOL2 format, chain SA [auth U] MOL2 format, chain VA [auth X] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth B] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth E] MOL2 format, chain DA [auth F] MOL2 format, chain GA [auth I] MOL2 format, chain LA [auth N] MOL2 format, chain MA [auth O] MOL2 format, chain PA [auth R] MOL2 format, chain QA [auth S] MOL2 format, chain TA [auth V] MOL2 format, chain UA [auth W] mmCIF format, chain AA [auth C] mmCIF format, chain EA [auth G] mmCIF format, chain FA [auth H] mmCIF format, chain HA [auth J] mmCIF format, chain IA [auth K] mmCIF format, chain JA [auth L] mmCIF format, chain KA [auth M] mmCIF format, chain NA [auth P] mmCIF format, chain OA [auth Q] mmCIF format, chain RA [auth T] mmCIF format, chain SA [auth U] mmCIF format, chain VA [auth X] mmCIF format, chain Y [auth A] mmCIF format, chain Z [auth B] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth E] mmCIF format, chain DA [auth F] mmCIF format, chain GA [auth I] mmCIF format, chain LA [auth N] mmCIF format, chain MA [auth O] mmCIF format, chain PA [auth R] mmCIF format, chain QA [auth S] mmCIF format, chain TA [auth V] mmCIF format, chain UA [auth W]	AA [auth C] BA [auth D] CA [auth E] DA [auth F] EA [auth G] AA [auth C], BA [auth D], CA [auth E], DA [auth F], EA [auth G], FA [auth H], GA [auth I], HA [auth J], IA [auth K], JA [auth L], KA [auth M], LA [auth N], MA [auth O], NA [auth P], OA [auth Q], PA [auth R], QA [auth S], RA [auth T], SA [auth U], TA [auth V], UA [auth W], VA [auth X], Y [auth A], Z [auth B]	N-acetyl-beta-neuraminic acid C₁₁ H₁₉ N O₉ SQVRNKJHWKZAKO-PFQGKNLYSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth D] Focus chain CA [auth E] Focus chain DA [auth F] Focus chain EA [auth G] Focus chain FA [auth H] Focus chain GA [auth I] Focus chain HA [auth J] Focus chain IA [auth K] Focus chain JA [auth L] Focus chain KA [auth M] Focus chain LA [auth N] Focus chain MA [auth O] Focus chain NA [auth P] Focus chain OA [auth Q] Focus chain PA [auth R] Focus chain QA [auth S] Focus chain RA [auth T] Focus chain SA [auth U] Focus chain TA [auth V] Focus chain UA [auth W] Focus chain VA [auth X] Focus chain Y [auth A] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth D] Focus chain CA [auth E] Focus chain DA [auth F] Focus chain EA [auth G] Focus chain FA [auth H] Focus chain GA [auth I] Focus chain HA [auth J] Focus chain IA [auth K] Focus chain JA [auth L] Focus chain KA [auth M] Focus chain LA [auth N] Focus chain MA [auth O] Focus chain NA [auth P] Focus chain OA [auth Q] Focus chain PA [auth R] Focus chain QA [auth S] Focus chain RA [auth T] Focus chain SA [auth U] Focus chain TA [auth V] Focus chain UA [auth W] Focus chain VA [auth X] Focus chain Y [auth A] Focus chain Z [auth B]