8WCI

Cryo-EM structure of the inhibitor-bound Vo complex from Enterococcus hirae

PDB DOI: https://doi.org/10.2210/pdb8WCI/pdb
EM Map EMD-37440: EMDB EMDataResource

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Enterococcus hirae ATCC 9790
Expression System: Escherichia coli
Mutation(s): No
Membrane Protein: Yes PDBTM

Deposited: 2023-09-12 Released: 2024-10-09
Deposition Author(s): Suzuki, K., Mikuriya, S., Adachi, N., Kawasaki, M., Senda, T., Moriya, T., Murata, T.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Agency for Medical Research and Development (AMED)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.20 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Novel Inhibitor of Na+-Transporting V-ATPase Suppresses VRE Colonization in Mice and Reveals the High-Resolution Structure of the Na+ Transport Pathway

Suzuki, K., Goto, Y., Otomo, A., Shimizu, K., Abe, S., Moriyama, K., Yasuda, S., Hashimoto, Y., Kurushima, J., Mikuriya, S., Imai, F.L., Adachi, N., Kawasaki, M., Sato, Y., Ogasawara, S., Iwata, I., Senda, T., Ikeguchi, M., Tomita, H., Iino, R., Moriya, T., Murata, T.

To be published.

Macromolecule Content

Total Structure Weight: 244.73 kDa
Atom Count: 14,876
Modelled Residue Count: 1,903
Deposited Residue Count: 2,232
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type sodium ATPase subunit K	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	156	Enterococcus hirae ATCC 9790	Mutation(s): 0 Gene Names: ntpK, ntpN, EHR_08240 Membrane Entity: Yes
UniProt
Find proteins for P43457 (Enterococcus hirae (strain ATCC 9790 / DSM 20160 / JCM 8729 / LMG 6399 / NBRC 3181 / NCIMB 6459 / NCDO 1258 / NCTC 12367 / WDCM 00089 / R)) Explore P43457 Go to UniProtKB: P43457
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P43457
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type sodium ATPase subunit I	K [auth P]	672	Enterococcus hirae ATCC 9790	Mutation(s): 0 Gene Names: ntpI Membrane Entity: Yes
UniProt
Find proteins for P43439 (Enterococcus hirae (strain ATCC 9790 / DSM 20160 / JCM 8729 / LMG 6399 / NBRC 3181 / NCIMB 6459 / NCDO 1258 / NCTC 12367 / WDCM 00089 / R)) Explore P43439 Go to UniProtKB: P43439
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P43439
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CDL Query on CDL Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain P [auth D] SDF format, chain S [auth F] SDF format, chain U [auth H] SDF format, chain W [auth I] MOL2 format, chain L [auth A] MOL2 format, chain P [auth D] MOL2 format, chain S [auth F] MOL2 format, chain U [auth H] MOL2 format, chain W [auth I] mmCIF format, chain L [auth A] mmCIF format, chain P [auth D] mmCIF format, chain S [auth F] mmCIF format, chain U [auth H] mmCIF format, chain W [auth I]	L [auth A], P [auth D], S [auth F], U [auth H], W [auth I]	CARDIOLIPIN C₈₁ H₁₅₆ O₁₇ P₂ XVTUQDWPJJBEHJ-KZCWQMDCSA-L		Interactions Focus chain L [auth A] Focus chain P [auth D] Focus chain S [auth F] Focus chain U [auth H] Focus chain W [auth I] Interactions & Density Focus chain L [auth A] Focus chain P [auth D] Focus chain S [auth F] Focus chain U [auth H] Focus chain W [auth I]
W3K (Subject of Investigation/LOI) Query on W3K Download Ideal Coordinates CCD File SDF format, chain Z [auth P] MOL2 format, chain Z [auth P] mmCIF format, chain Z [auth P]	Z [auth P]	N,N-dimethyl-4-(5-methyl-1H-benzimidazol-2-yl)aniline C₁₆ H₁₇ N₃ DCBQWCSRVVGWAN-UHFFFAOYSA-N		Interactions Focus chain Z [auth P] Interactions & Density Focus chain Z [auth P]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain N [auth B] SDF format, chain O [auth D] SDF format, chain Q [auth E] SDF format, chain R [auth F] SDF format, chain T [auth G] SDF format, chain V [auth H] SDF format, chain X [auth I] SDF format, chain Y [auth J] MOL2 format, chain M [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth D] MOL2 format, chain Q [auth E] MOL2 format, chain R [auth F] MOL2 format, chain T [auth G] MOL2 format, chain V [auth H] MOL2 format, chain X [auth I] MOL2 format, chain Y [auth J] mmCIF format, chain M [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth D] mmCIF format, chain Q [auth E] mmCIF format, chain R [auth F] mmCIF format, chain T [auth G] mmCIF format, chain V [auth H] mmCIF format, chain X [auth I] mmCIF format, chain Y [auth J]	M [auth A] N [auth B] O [auth D] Q [auth E] R [auth F] M [auth A], N [auth B], O [auth D], Q [auth E], R [auth F], T [auth G], V [auth H], X [auth I], Y [auth J]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth D] Focus chain Q [auth E] Focus chain R [auth F] Focus chain T [auth G] Focus chain V [auth H] Focus chain X [auth I] Focus chain Y [auth J] Interactions & Density Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth D] Focus chain Q [auth E] Focus chain R [auth F] Focus chain T [auth G] Focus chain V [auth H] Focus chain X [auth I] Focus chain Y [auth J]