9Z5O | pdb_00009z5o

Cryo-EM of the sarco(endo)plasmic reticulum calcium ATPase (SERCA) in presence of calcium and compound UM-52 (bound)

PDB DOI: https://doi.org/10.2210/pdb9Z5O/pdb
EM Map EMD-73820: EMDB EMDataResource

Classification: HYDROLASE
Organism(s): Oryctolagus cuniculus
Mutation(s): No

Deposited: 2025-11-12 Released: 2026-11-04
Deposition Author(s): Nguyen, V.H., Primeau, J.O., Cruz-Cortes, C., Lemieux, M.J., Espinoza-Fonseca, L.M., Young, H.S.
Funding Organization(s): Canadian Institutes of Health Research (CIHR), Other private

Experimental Data Snapshot

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

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9Z5O

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

Literature

Cryo-EM reveals a transmembrane allosteric site and activation mechanism for the SERCA calcium pump

Nguyen, V.H., Primeau, J.O., Cruz-Cortes, C., Lemeiux, M.J., Espinoza-Fonseca, M., Young, H.S.

To be published.

Macromolecule Content

Total Structure Weight: 109.99 kDa
Atom Count: 7,691
Modeled Residue Count: 993
Deposited Residue Count: 994
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sarcoplasmic/endoplasmic reticulum calcium ATPase 1	A	994	Oryctolagus cuniculus	Mutation(s): 0 EC: 3.6.3.8 (PDB Primary Data), 7.2.2.10 (UniProt)
UniProt
Find proteins for P04191 (Oryctolagus cuniculus) Go to UniProtKB: P04191
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04191-2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1C01 (Subject of Investigation/LOI) Query on A1C01 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	5-{2-[(5-phenylpentyl)oxy]ethyl}-2,3-dihydro-1-benzofuran C₂₁ H₂₆ O₂ YQUZEOHHLVGFGD-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
CA (Subject of Investigation/LOI) Query on CA Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

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	4.6.2
MODEL REFINEMENT	PHENIX	1.21_5207

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-11-04

Deposition Author(s):

Cruz-Cortes, C.

Espinoza-Fonseca, L.M.

Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	--
Other private		--

Revision History (Full details and data files)

Version 1.0: 2026-11-04
Type: Initial release