9R8O | pdb_00009r8o

Primed-state RyR1 in 0.05% POPC micelles, in complex with a nanobody and FKBP

• PDB DOI: https://doi.org/10.2210/pdb9R8O/pdb
• EM Map EMD-53834: EMDB EMDataResource

• Classification: TRANSPORT PROTEIN
• Organism(s): Lama glama, Oryctolagus cuniculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-05-16 Released: 2025-09-17 
• Deposition Author(s): Li, C., Efremov, R.G.
• Funding Organization(s): Research Foundation - Flanders (FWO), European Research Council (ERC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Open-state RyR1 in 0.05% POPC micelles, in complex with a nanobody and FKBP

Li, C., Efremov, R.G.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Hetero 12-mer - A4B4C4 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 2,395.16 kDa 
• Atom Count: 145,532 
• Modeled Residue Count: 18,224 
• Deposited Residue Count: 21,040 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody 9657	A [auth K], D [auth A], G [auth D], J [auth G]	126	Lama glama	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase FKBP1B	B [auth L], E [auth B], H [auth E], K [auth H]	107	Oryctolagus cuniculus	Mutation(s): 0  EC: 5.2.1.8
UniProt
Find proteins for Q8HYX6 (Oryctolagus cuniculus) Explore Q8HYX6  Go to UniProtKB:  Q8HYX6

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Ryanodine receptor 1	C [auth J], F [auth C], I [auth F], L [auth I]	5,027	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for P11716 (Oryctolagus cuniculus) Explore P11716  Go to UniProtKB:  P11716

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
POV (Subject of Investigation/LOI)	AA [auth C], AB [auth F], BB [auth F], CB [auth I], DB [auth I], EA [auth C], EB [auth I], FA [auth C], FB [auth I], GA [auth C], GB [auth I], HA [auth C], IA [auth C], JA [auth C], KB [auth I], LA [auth C], LB [auth I], MA [auth C], MB [auth I], NA [auth C], NB [auth I], OA [auth F], OB [auth I], P [auth J], PA [auth F], Q [auth J], R [auth J], S [auth J], T [auth J], TA [auth F], UA [auth F], V [auth J], VA [auth F], W [auth J], WA [auth F], X [auth J], XA [auth F], Y [auth J], Z [auth C], ZA [auth F]	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate C42 H82 N O8 P WTJKGGKOPKCXLL-PFDVCBLKSA-N
ATP (Subject of Investigation/LOI)	BA [auth C], HB [auth I], M [auth J], QA [auth F]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
CFF (Subject of Investigation/LOI)	CA [auth C], IB [auth I], N [auth J], RA [auth F]	CAFFEINE C8 H10 N4 O2 RYYVLZVUVIJVGH-UHFFFAOYSA-N
ZN	KA [auth C], PB [auth I], U [auth J], YA [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA (Subject of Investigation/LOI)	DA [auth C], JB [auth I], O [auth J], SA [auth F]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.31

Structure Validation

Currently 9R8O does not have a validation slider image.

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-17 
Deposition Author(s): Li, C., Efremov, R.G.

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Funding Organization	Location	Grant Number
Research Foundation - Flanders (FWO)	Belgium	G0H5916N
Research Foundation - Flanders (FWO)	Belgium	G054617N
European Research Council (ERC)	European Union	726436

Revision History  

• Version 1.0: 2025-09-17
  Type: Initial release