9S3U | pdb_00009s3u

Down class, Primed-state RyR1 with activating ligand mixture (Calcium/ACP/Caffeine) in the native membrane

PDB DOI: https://doi.org/10.2210/pdb9S3U/pdb
EM Map EMD-54552: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Oryctolagus cuniculus
Mutation(s): No

Deposited: 2025-07-25 Released: 2026-08-12
Deposition Author(s): Mikirtumov, V.
Funding Organization(s): German Research Foundation (DFG), Helmholtz Association

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.77 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 9S3U

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

Literature

Activation of RyR1 in native membranes

Mikirtumov, V., Golusik, S., Sprink, T., Balyschew, N., Yang, W., Kotecha, A., Kudryashev, M.

To be published.

Macromolecule Content

Total Structure Weight: 2,311.51 kDa
Atom Count: 143,680
Modeled Residue Count: 18,044
Deposited Residue Count: 20,580
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ryanodine receptor 1	A, B, C, D	5,037	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for P11716 (Oryctolagus cuniculus) Explore P11716 Go to UniProtKB: P11716
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P11716
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase FKBP1A	E, F, G, H	108	Oryctolagus cuniculus	Mutation(s): 0 EC: 5.2.1.8
UniProt
Find proteins for P62943 (Oryctolagus cuniculus) Explore P62943 Go to UniProtKB: P62943
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62943
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 4.77 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	5
MODEL REFINEMENT	ISOLDE

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-08-12

Deposition Author(s):

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	KU3221/3-1
Helmholtz Association	Germany	--

Revision History (Full details and data files)

Version 1.0: 2026-08-12
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.