6YL3

High resolution cryo-EM structure of urease from the pathogen Yersinia enterocolitica

PDB DOI: https://doi.org/10.2210/pdb6YL3/pdb
EM Map EMD-10835: EMDB EMDataResource

Classification: METAL BINDING PROTEIN
Organism(s): Yersinia enterocolitica W22703
Mutation(s): No

Deposited: 2020-04-06 Released: 2020-05-06
Deposition Author(s): Righetto, R.D., Anton, L., Adaixo, R., Jakob, R., Zivanov, J., Mahi, M.A., Ringler, P., Schwede, T., Maier, T., Stahlberg, H.
Funding Organization(s): Swiss National Science Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 1.98 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

High-resolution cryo-EM structure of urease from the pathogen Yersinia enterocolitica.

Righetto, R.D., Anton, L., Adaixo, R., Jakob, R.P., Zivanov, J., Mahi, M.A., Ringler, P., Schwede, T., Maier, T., Stahlberg, H.

(2020) Nat Commun 11: 5101-5101

PubMed: 33037208 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41467-020-18870-2
Primary Citation of Related Structures:
6YL3

PubMed Abstract:
Urease converts urea into ammonia and carbon dioxide and makes urea available as a nitrogen source for all forms of life except animals. In human bacterial pathogens, ureases also aid in the invasion of acidic environments such as the stomach by raising the surrounding pH. Here, we report the structure of urease from the pathogen Yersinia enterocolitica at 2 Å resolution from cryo-electron microscopy. Y. enterocolitica urease is a dodecameric assembly of a trimer of three protein chains, ureA, ureB and ureC. The high data quality enables detailed visualization of the urease bimetal active site and of the impact of radiation damage. The obtained structure is of sufficient quality to support drug development efforts.

Organizational Affiliation

Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, Mattenstrasse 26, CH-4058, Basel, Switzerland.

Macromolecule Content

Total Structure Weight: 1,042.17 kDa
Atom Count: 77,112
Modelled Residue Count: 9,552
Deposited Residue Count: 9,636
Unique protein chains: 3

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Urease subunit gamma	A BA [auth 2] D EA [auth 5] G A, BA [auth 2], D, EA [auth 5], G, HA [auth 8], J, M, P, S, V [auth W], Y [auth Z]	100	Yersinia enterocolitica W22703	Mutation(s): 0 EC: 3.5.1.5
UniProt
Find proteins for F4MWM9 (Yersinia enterocolitica W22703) Explore F4MWM9 Go to UniProtKB: F4MWM9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	F4MWM9
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Urease subunit beta	B CA [auth 3] E FA [auth 6] H B, CA [auth 3], E, FA [auth 6], H, IA [auth 9], K, N, Q, T, W [auth X], Z [auth 0]	132	Yersinia enterocolitica W22703	Mutation(s): 0 EC: 3.5.1.5
UniProt
Find proteins for F4MWM8 (Yersinia enterocolitica W22703) Explore F4MWM8 Go to UniProtKB: F4MWM8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	F4MWM8
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Urease subunit alpha	AA [auth 1] C DA [auth 4] F GA [auth 7] AA [auth 1], C, DA [auth 4], F, GA [auth 7], I, JA [auth U], L, O, R, U [auth V], X [auth Y]	571	Yersinia enterocolitica W22703	Mutation(s): 0 EC: 3.5.1.5
UniProt
Find proteins for F4MWM7 (Yersinia enterocolitica W22703) Explore F4MWM7 Go to UniProtKB: F4MWM7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	F4MWM7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NI Query on NI Download Ideal Coordinates CCD File SDF format, chain AB [auth 1] SDF format, chain BB [auth 1] SDF format, chain CB [auth 4] SDF format, chain DB [auth 4] SDF format, chain EB [auth 7] SDF format, chain FB [auth 7] SDF format, chain GB [auth U] SDF format, chain HB [auth U] SDF format, chain KA [auth C] SDF format, chain LA [auth C] SDF format, chain MA [auth F] SDF format, chain NA [auth F] SDF format, chain OA [auth I] SDF format, chain PA [auth I] SDF format, chain QA [auth L] SDF format, chain RA [auth L] SDF format, chain SA [auth O] SDF format, chain TA [auth O] SDF format, chain UA [auth R] SDF format, chain VA [auth R] SDF format, chain WA [auth V] SDF format, chain XA [auth V] SDF format, chain YA [auth Y] SDF format, chain ZA [auth Y] MOL2 format, chain AB [auth 1] MOL2 format, chain BB [auth 1] MOL2 format, chain CB [auth 4] MOL2 format, chain DB [auth 4] MOL2 format, chain EB [auth 7] MOL2 format, chain FB [auth 7] MOL2 format, chain GB [auth U] MOL2 format, chain HB [auth U] MOL2 format, chain KA [auth C] MOL2 format, chain LA [auth C] MOL2 format, chain MA [auth F] MOL2 format, chain NA [auth F] MOL2 format, chain OA [auth I] MOL2 format, chain PA [auth I] MOL2 format, chain QA [auth L] MOL2 format, chain RA [auth L] MOL2 format, chain SA [auth O] MOL2 format, chain TA [auth O] MOL2 format, chain UA [auth R] MOL2 format, chain VA [auth R] MOL2 format, chain WA [auth V] MOL2 format, chain XA [auth V] MOL2 format, chain YA [auth Y] MOL2 format, chain ZA [auth Y]	AB [auth 1] BB [auth 1] CB [auth 4] DB [auth 4] EB [auth 7] AB [auth 1], BB [auth 1], CB [auth 4], DB [auth 4], EB [auth 7], FB [auth 7], GB [auth U], HB [auth U], KA [auth C], LA [auth C], MA [auth F], NA [auth F], OA [auth I], PA [auth I], QA [auth L], RA [auth L], SA [auth O], TA [auth O], UA [auth R], VA [auth R], WA [auth V], XA [auth V], YA [auth Y], ZA [auth Y]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain AB [auth 1] Focus chain BB [auth 1] Focus chain CB [auth 4] Focus chain DB [auth 4] Focus chain EB [auth 7] Focus chain FB [auth 7] Focus chain GB [auth U] Focus chain HB [auth U] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain MA [auth F] Focus chain NA [auth F] Focus chain OA [auth I] Focus chain PA [auth I] Focus chain QA [auth L] Focus chain RA [auth L] Focus chain SA [auth O] Focus chain TA [auth O] Focus chain UA [auth R] Focus chain VA [auth R] Focus chain WA [auth V] Focus chain XA [auth V] Focus chain YA [auth Y] Focus chain ZA [auth Y] Interactions & Density Focus chain AB [auth 1] Focus chain BB [auth 1] Focus chain CB [auth 4] Focus chain DB [auth 4] Focus chain EB [auth 7] Focus chain FB [auth 7] Focus chain GB [auth U] Focus chain HB [auth U] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain MA [auth F] Focus chain NA [auth F] Focus chain OA [auth I] Focus chain PA [auth I] Focus chain QA [auth L] Focus chain RA [auth L] Focus chain SA [auth O] Focus chain TA [auth O] Focus chain UA [auth R] Focus chain VA [auth R] Focus chain WA [auth V] Focus chain XA [auth V] Focus chain YA [auth Y] Focus chain ZA [auth Y]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX Query on KCX	AA [auth 1] C DA [auth 4] F GA [auth 7] AA [auth 1], C, DA [auth 4], F, GA [auth 7], I, JA [auth U], L, O, R, U [auth V], X [auth Y]	L-PEPTIDE LINKING	C₇ H₁₄ N₂ O₄		LYS