7MD2

The F1 region of ammocidin-bound Saccharomyces cerevisiae ATP synthase

PDB DOI: https://doi.org/10.2210/pdb7MD2/pdb
EM Map EMD-23763: EMDB EMDataResource

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Saccharomyces cerevisiae
Mutation(s): No

Deposited: 2021-04-03 Released: 2021-08-11
Deposition Author(s): Guo, H., Rubinstein, J.L.
Funding Organization(s): Canadian Institutes of Health Research (CIHR), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Cancer Institute (NIH/NCI), National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.10 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

A Family of Glycosylated Macrolides Selectively Target Energetic Vulnerabilities in Leukemia

Reisman, B.J., Guo, H., Ramsey, H.E., Wright, M.T., Reinfeld, B.I., Ferrell, P.B., Sulikowski, G.A., Rathmell, W.K., Savona, M.R., Plate, L., Rubinstein, J.L., Bachmann, B.O.

(2021) bioRxiv

DOI: https://doi.org/10.1101/2021.05.31.445492

Macromolecule Content

Total Structure Weight: 358.69 kDa
Atom Count: 23,474
Modelled Residue Count: 3,115
Deposited Residue Count: 3,303
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit alpha	A, B, C	510	Saccharomyces cerevisiae	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit beta	D, E, F	478	Saccharomyces cerevisiae	Mutation(s): 0 EC: 7.1.2.2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit gamma	G	278	Saccharomyces cerevisiae	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit epsilon, mitochondrial	H	61	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P21306 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P21306 Go to UniProtKB: P21306
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P21306
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZHD (Subject of Investigation/LOI) Query on ZHD Download Ideal Coordinates CCD File SDF format, chain P [auth G] MOL2 format, chain P [auth G] mmCIF format, chain P [auth G]	P [auth G]	(3~{E},5~{Z},7~{E},9~{R},10~{S},11~{E},13~{E},15~{E},17~{R},18~{S},20~{S})-20-[(1~{R})-1-[(2~{S},3~{R},4~{R},5~{S},6~{R})-5-[(2~{S},4~{S},5~{S},6~{R})-5-[(2~{S},4~{R},5~{R},6~{R})-4,6-dimethyl-4,5-bis(oxidanyl)oxan-2-yl]oxy-6-methyl-4-oxidanyl-oxan-2-yl]oxy-3-methoxy-6-(3-methoxypropyl)-5-methyl-2,4-bis(oxidanyl)oxan-2-yl]ethyl]-5,18-dimethoxy-3,7,9,11,13,15-hexamethyl-10-[(2~{R},3~{S},4~{R},5~{R},6~{S})-6-methyl-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-17-oxidanyl-1-oxacycloicosa-3,5,7,11,13,15-hexaen-2-one C₅₉ H₉₆ O₂₂ QVIWDCUKIZPUBD-RSDTUZBPSA-N		Interactions Focus chain P [auth G] Interactions & Density Focus chain P [auth G]
ATP Query on ATP Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain M [auth C] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain M [auth C] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B] mmCIF format, chain M [auth C]	I [auth A], K [auth B], M [auth C]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Interactions & Density Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain O [auth F] MOL2 format, chain O [auth F] mmCIF format, chain O [auth F]	O [auth F]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain O [auth F] Interactions & Density Focus chain O [auth F]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain L [auth B] SDF format, chain N [auth C] MOL2 format, chain J [auth A] MOL2 format, chain L [auth B] MOL2 format, chain N [auth C] mmCIF format, chain J [auth A] mmCIF format, chain L [auth B] mmCIF format, chain N [auth C]	J [auth A], L [auth B], N [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain L [auth B] Focus chain N [auth C] Interactions & Density Focus chain J [auth A] Focus chain L [auth B] Focus chain N [auth C]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	2.12
MODEL REFINEMENT	cryoSPARC	2.12

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2021-08-11

Deposition Author(s):

Guo, H.

Rubinstein, J.L.

Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	PJT162186
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01 GM092218
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R01 CA226833
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35 GM133552
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	K23 HL138291
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	T32 GM065086
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	T32 GM007347
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	F30 CA236131