8OLC

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 1.1 of the entry. See complete history.

Literature

Structural basis of rotavirus spike proteolytic activation

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

To be published.

Macromolecule Content

Total Structure Weight: 1,277.02 kDa
Atom Count: 82,143
Modelled 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 AB [auth l] SDF format, chain DA [auth d] SDF format, chain DB [auth m] SDF format, chain GB [auth n] SDF format, chain HA [auth e] SDF format, chain JB [auth o] SDF format, chain KA [auth f] SDF format, chain PA [auth h] SDF format, chain UA [auth j] SDF format, chain XA [auth k] MOL2 format, chain AB [auth l] MOL2 format, chain DA [auth d] MOL2 format, chain DB [auth m] MOL2 format, chain GB [auth n] MOL2 format, chain HA [auth e] MOL2 format, chain JB [auth o] MOL2 format, chain KA [auth f] MOL2 format, chain PA [auth h] MOL2 format, chain UA [auth j] MOL2 format, chain XA [auth k] mmCIF format, chain AB [auth l] mmCIF format, chain DA [auth d] mmCIF format, chain DB [auth m] mmCIF format, chain GB [auth n] mmCIF format, chain HA [auth e] mmCIF format, chain JB [auth o] mmCIF format, chain KA [auth f] mmCIF format, chain PA [auth h] mmCIF format, chain UA [auth j] mmCIF format, chain XA [auth k]	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 MB [auth C] SDF format, chain NB [auth F] SDF format, chain OB [auth I] SDF format, chain PB [auth L] SDF format, chain QB [auth O] MOL2 format, chain MB [auth C] MOL2 format, chain NB [auth F] MOL2 format, chain OB [auth I] MOL2 format, chain PB [auth L] MOL2 format, chain QB [auth O] mmCIF format, chain MB [auth C] mmCIF format, chain NB [auth F] mmCIF format, chain OB [auth I] mmCIF format, chain PB [auth L] mmCIF format, chain QB [auth O]	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 BB [auth l] SDF format, chain CA [auth c] SDF format, chain CB [auth l] SDF format, chain EA [auth d] SDF format, chain EB [auth m] SDF format, chain FA [auth d] SDF format, chain FB [auth m] SDF format, chain GA [auth d] SDF format, chain HB [auth n] SDF format, chain IA [auth e] SDF format, chain IB [auth n] SDF format, chain JA [auth e] SDF format, chain KB [auth o] SDF format, chain LA [auth f] SDF format, chain LB [auth o] SDF format, chain MA [auth f] SDF format, chain NA [auth g] SDF format, chain OA [auth g] SDF format, chain QA [auth h] SDF format, chain RA [auth h] SDF format, chain SA [auth i] SDF format, chain TA [auth i] SDF format, chain VA [auth j] SDF format, chain WA [auth j] SDF format, chain YA [auth k] SDF format, chain ZA [auth k] MOL2 format, chain BB [auth l] MOL2 format, chain CA [auth c] MOL2 format, chain CB [auth l] MOL2 format, chain EA [auth d] MOL2 format, chain EB [auth m] MOL2 format, chain FA [auth d] MOL2 format, chain FB [auth m] MOL2 format, chain GA [auth d] MOL2 format, chain HB [auth n] MOL2 format, chain IA [auth e] MOL2 format, chain IB [auth n] MOL2 format, chain JA [auth e] MOL2 format, chain KB [auth o] MOL2 format, chain LA [auth f] MOL2 format, chain LB [auth o] MOL2 format, chain MA [auth f] MOL2 format, chain NA [auth g] MOL2 format, chain OA [auth g] MOL2 format, chain QA [auth h] MOL2 format, chain RA [auth h] MOL2 format, chain SA [auth i] MOL2 format, chain TA [auth i] MOL2 format, chain VA [auth j] MOL2 format, chain WA [auth j] MOL2 format, chain YA [auth k] MOL2 format, chain ZA [auth k] mmCIF format, chain BB [auth l] mmCIF format, chain CA [auth c] mmCIF format, chain CB [auth l] mmCIF format, chain EA [auth d] mmCIF format, chain EB [auth m] mmCIF format, chain FA [auth d] mmCIF format, chain FB [auth m] mmCIF format, chain GA [auth d] mmCIF format, chain HB [auth n] mmCIF format, chain IA [auth e] mmCIF format, chain IB [auth n] mmCIF format, chain JA [auth e] mmCIF format, chain KB [auth o] mmCIF format, chain LA [auth f] mmCIF format, chain LB [auth o] mmCIF format, chain MA [auth f] mmCIF format, chain NA [auth g] mmCIF format, chain OA [auth g] mmCIF format, chain QA [auth h] mmCIF format, chain RA [auth h] mmCIF format, chain SA [auth i] mmCIF format, chain TA [auth i] mmCIF format, chain VA [auth j] mmCIF format, chain WA [auth j] mmCIF format, chain YA [auth k] mmCIF format, chain ZA [auth k]	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]