8OLC | pdb_00008olc

SA11 Rotavirus Trypsinized Triple Layered Particle

PDB DOI: https://doi.org/10.2210/pdb8OLC/pdb
EM Map EMD-16955: EMDB EMDataResource

Classification: VIRUS
Organism(s): Rotavirus
Expression System: Chlorocebus aethiops
Mutation(s): No

Deposited: 2023-03-30 Released: 2024-09-25
Deposition Author(s): Asensio-Cob, D., Perez-Mata, C., Gomez-Blanco, J., Vargas, J., Rodriguez, J.M., Luque, D.
Funding Organization(s): Spanish Ministry of Science, Innovation, and Universities

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.48 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structural determinants of rotavirus proteolytic activation.

Asensio-Cob, D., Mata, C.P., Gomez-Blanco, J., Vargas, J., Rodriguez, J.M., Luque, D.

(2025) PLoS Pathog 21: e1013063-e1013063

PubMed: 40794814 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1371/journal.ppat.1013063
Primary Citation of Related Structures:
8OLB, 8OLC, 8OLE, 8QTZ

PubMed Abstract:
The infectivity of rotavirus (RV), the leading cause of childhood diarrhea, hinges on the activation of viral particles through the proteolysis of the spike protein by trypsin-like proteases in the host intestinal lumen. In order to determine the structural basis of trypsin activation, we have used cryogenic electron microscopy (cryo-EM) and advanced image processing methods to compare uncleaved and cleaved RV particles. We find that the conformation of the non-proteolyzed spike is constrained by the position of loops that surround its structure, linking the lectin domains of the spike head to its body. The proteolysis of these loops removes this structural constraint, thereby enabling the spike to undergo the necessary conformational changes required for cell membrane penetration. Thus, these loops function as regulatory elements to ensure that the spike protein is activated precisely when and where it is needed to facilitate a successful infection.

Organizational Affiliation

Department of Molecular Medicine, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Ontario, Canada.

Macromolecule Content

Total Structure Weight: 1,277.02 kDa
Atom Count: 82,143
Modeled Residue Count: 10,266
Deposited Residue Count: 11,163
Unique protein chains: 3

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer capsid glycoprotein VP7	A [auth c] B [auth d] C [auth e] D [auth f] E [auth g] A [auth c], B [auth d], C [auth e], D [auth f], E [auth g], F [auth h], G [auth i], H [auth j], I [auth k], J [auth l], K [auth m], L [auth n], M [auth o]	326	Rotavirus	Mutation(s): 0 Gene Names: VP7, VP1
UniProt
Find proteins for A0A060IEQ1 (Rotavirus A) Explore A0A060IEQ1 Go to UniProtKB: A0A060IEQ1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A060IEQ1
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain D [auth f] Focus chain H [auth j] Focus chain J [auth l]
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Intermediate capsid protein VP6	N [auth C] O [auth D] P [auth E] Q [auth F] R [auth G] N [auth C], O [auth D], P [auth E], Q [auth F], R [auth G], S [auth H], T [auth I], U [auth J], V [auth K], W [auth L], X [auth M], Y [auth N], Z [auth O]	397	Rotavirus	Mutation(s): 0 Gene Names: VP6
UniProt
Find proteins for A2T3S6 (Rotavirus A) Explore A2T3S6 Go to UniProtKB: A2T3S6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A2T3S6
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Inner capsid protein VP2	AA [auth A], BA [auth B]	882	Rotavirus	Mutation(s): 0 Gene Names: VP2
UniProt
Find proteins for A2T3R1 (Rotavirus A) Explore A2T3R1 Go to UniProtKB: A2T3R1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A2T3R1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download Ideal Coordinates CCD File SDF format, chain DA [auth d] SDF format, chain DB [auth m] SDF format, chain JB [auth o] SDF format, chain KA [auth f] SDF format, chain PA [auth h] SDF format, chain XA [auth k] SDF format, chain UA [auth j] SDF format, chain HA [auth e] SDF format, chain GB [auth n] SDF format, chain AB [auth l] MOL2 format, chain DA [auth d] MOL2 format, chain DB [auth m] MOL2 format, chain JB [auth o] MOL2 format, chain KA [auth f] MOL2 format, chain PA [auth h] MOL2 format, chain XA [auth k] MOL2 format, chain UA [auth j] MOL2 format, chain HA [auth e] MOL2 format, chain GB [auth n] MOL2 format, chain AB [auth l] mmCIF format, chain DA [auth d] mmCIF format, chain DB [auth m] mmCIF format, chain JB [auth o] mmCIF format, chain KA [auth f] mmCIF format, chain PA [auth h] mmCIF format, chain XA [auth k] mmCIF format, chain UA [auth j] mmCIF format, chain HA [auth e] mmCIF format, chain GB [auth n] mmCIF format, chain AB [auth l]	AB [auth l] DA [auth d] DB [auth m] GB [auth n] HA [auth e] AB [auth l], DA [auth d], DB [auth m], GB [auth n], HA [auth e], JB [auth o], KA [auth f], PA [auth h], UA [auth j], XA [auth k]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth l] Focus chain DA [auth d] Focus chain DB [auth m] Focus chain GB [auth n] Focus chain HA [auth e] Focus chain JB [auth o] Focus chain KA [auth f] Focus chain PA [auth h] Focus chain UA [auth j] Focus chain XA [auth k] Interactions & Density Focus chain AB [auth l] Focus chain DA [auth d] Focus chain DB [auth m] Focus chain GB [auth n] Focus chain HA [auth e] Focus chain JB [auth o] Focus chain KA [auth f] Focus chain PA [auth h] Focus chain UA [auth j] Focus chain XA [auth k]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain NB [auth F] SDF format, chain OB [auth I] SDF format, chain QB [auth O] SDF format, chain PB [auth L] SDF format, chain MB [auth C] MOL2 format, chain NB [auth F] MOL2 format, chain OB [auth I] MOL2 format, chain QB [auth O] MOL2 format, chain PB [auth L] MOL2 format, chain MB [auth C] mmCIF format, chain NB [auth F] mmCIF format, chain OB [auth I] mmCIF format, chain QB [auth O] mmCIF format, chain PB [auth L] mmCIF format, chain MB [auth C]	MB [auth C], NB [auth F], OB [auth I], PB [auth L], QB [auth O]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain MB [auth C] Focus chain NB [auth F] Focus chain OB [auth I] Focus chain PB [auth L] Focus chain QB [auth O] Interactions & Density Focus chain MB [auth C] Focus chain NB [auth F] Focus chain OB [auth I] Focus chain PB [auth L] Focus chain QB [auth O]
CA (Subject of Investigation/LOI) Query on CA Download Ideal Coordinates CCD File SDF format, chain EB [auth m] SDF format, chain GA [auth d] SDF format, chain IA [auth e] SDF format, chain IB [auth n] SDF format, chain LA [auth f] SDF format, chain NA [auth g] SDF format, chain QA [auth h] SDF format, chain WA [auth j] SDF format, chain YA [auth k] SDF format, chain ZA [auth k] SDF format, chain VA [auth j] SDF format, chain TA [auth i] SDF format, chain SA [auth i] SDF format, chain RA [auth h] SDF format, chain OA [auth g] SDF format, chain MA [auth f] SDF format, chain LB [auth o] SDF format, chain KB [auth o] SDF format, chain JA [auth e] SDF format, chain HB [auth n] SDF format, chain FB [auth m] SDF format, chain FA [auth d] SDF format, chain EA [auth d] SDF format, chain CB [auth l] SDF format, chain CA [auth c] SDF format, chain BB [auth l] MOL2 format, chain EB [auth m] MOL2 format, chain GA [auth d] MOL2 format, chain IA [auth e] MOL2 format, chain IB [auth n] MOL2 format, chain LA [auth f] MOL2 format, chain NA [auth g] MOL2 format, chain QA [auth h] MOL2 format, chain WA [auth j] MOL2 format, chain YA [auth k] MOL2 format, chain ZA [auth k] MOL2 format, chain VA [auth j] MOL2 format, chain TA [auth i] MOL2 format, chain SA [auth i] MOL2 format, chain RA [auth h] MOL2 format, chain OA [auth g] MOL2 format, chain MA [auth f] MOL2 format, chain LB [auth o] MOL2 format, chain KB [auth o] MOL2 format, chain JA [auth e] MOL2 format, chain HB [auth n] MOL2 format, chain FB [auth m] MOL2 format, chain FA [auth d] MOL2 format, chain EA [auth d] MOL2 format, chain CB [auth l] MOL2 format, chain CA [auth c] MOL2 format, chain BB [auth l] mmCIF format, chain EB [auth m] mmCIF format, chain GA [auth d] mmCIF format, chain IA [auth e] mmCIF format, chain IB [auth n] mmCIF format, chain LA [auth f] mmCIF format, chain NA [auth g] mmCIF format, chain QA [auth h] mmCIF format, chain WA [auth j] mmCIF format, chain YA [auth k] mmCIF format, chain ZA [auth k] mmCIF format, chain VA [auth j] mmCIF format, chain TA [auth i] mmCIF format, chain SA [auth i] mmCIF format, chain RA [auth h] mmCIF format, chain OA [auth g] mmCIF format, chain MA [auth f] mmCIF format, chain LB [auth o] mmCIF format, chain KB [auth o] mmCIF format, chain JA [auth e] mmCIF format, chain HB [auth n] mmCIF format, chain FB [auth m] mmCIF format, chain FA [auth d] mmCIF format, chain EA [auth d] mmCIF format, chain CB [auth l] mmCIF format, chain CA [auth c] mmCIF format, chain BB [auth l]	BB [auth l] CA [auth c] CB [auth l] EA [auth d] EB [auth m] BB [auth l], CA [auth c], CB [auth l], EA [auth d], EB [auth m], FA [auth d], FB [auth m], GA [auth d], HB [auth n], IA [auth e], IB [auth n], JA [auth e], KB [auth o], LA [auth f], LB [auth o], MA [auth f], NA [auth g], OA [auth g], QA [auth h], RA [auth h], SA [auth i], TA [auth i], VA [auth j], WA [auth j], YA [auth k], ZA [auth k]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain BB [auth l] Focus chain CA [auth c] Focus chain CB [auth l] Focus chain EA [auth d] Focus chain EB [auth m] Focus chain FA [auth d] Focus chain FB [auth m] Focus chain GA [auth d] Focus chain HB [auth n] Focus chain IA [auth e] Focus chain IB [auth n] Focus chain JA [auth e] Focus chain KB [auth o] Focus chain LA [auth f] Focus chain LB [auth o] Focus chain MA [auth f] Focus chain NA [auth g] Focus chain OA [auth g] Focus chain QA [auth h] Focus chain RA [auth h] Focus chain SA [auth i] Focus chain TA [auth i] Focus chain VA [auth j] Focus chain WA [auth j] Focus chain YA [auth k] Focus chain ZA [auth k] Interactions & Density Focus chain BB [auth l] Focus chain CA [auth c] Focus chain CB [auth l] Focus chain EA [auth d] Focus chain EB [auth m] Focus chain FA [auth d] Focus chain FB [auth m] Focus chain GA [auth d] Focus chain HB [auth n] Focus chain IA [auth e] Focus chain IB [auth n] Focus chain JA [auth e] Focus chain KB [auth o] Focus chain LA [auth f] Focus chain LB [auth o] Focus chain MA [auth f] Focus chain NA [auth g] Focus chain OA [auth g] Focus chain QA [auth h] Focus chain RA [auth h] Focus chain SA [auth i] Focus chain TA [auth i] Focus chain VA [auth j] Focus chain WA [auth j] Focus chain YA [auth k] Focus chain ZA [auth k]