9RCW | pdb_00009rcw

Primed-state RyR1 in 0.01% POPC micelles, in complex with a nanobody and FKBP12

PDB DOI: https://doi.org/10.2210/pdb9RCW/pdb
EM Map EMD-53924: EMDB EMDataResource

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

Deposited: 2025-05-30 Released: 2025-09-17
Deposition Author(s): Li, C., Efremov, R.G.
Funding Organization(s): Research Foundation - Flanders (FWO), European Research Council (ERC)

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

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

Literature

Primed-state RyR1 in 0.01% POPC micelles, in complex with a nanobody and FKBP

Li, C., Efremov, R.G.

To be published.

Macromolecule Content

Total Structure Weight: 2,383 kDa
Atom Count: 144,632
Modeled Residue Count: 18,204
Deposited Residue Count: 21,040
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody 9657	A [auth H], D [auth K], G [auth D], J [auth B]	126	Lama glama	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: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase FKBP1B	B [auth I], E [auth L], H [auth E], K [auth F]	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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8HYX6
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Ryanodine receptor 1	C [auth G], F [auth J], I [auth C], L [auth A]	5,027	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for P11716 (Oryctolagus cuniculus) Explore P11716 Go to UniProtKB: P11716
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P11716
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
POV (Subject of Investigation/LOI) Query on POV Download Ideal Coordinates CCD File SDF format, chain ZA [auth A] SDF format, chain YA [auth A] SDF format, chain XA [auth A] SDF format, chain WA [auth A] SDF format, chain W [auth J] SDF format, chain VA [auth A] SDF format, chain V [auth G] SDF format, chain UA [auth A] SDF format, chain U [auth G] SDF format, chain T [auth G] SDF format, chain S [auth G] SDF format, chain R [auth G] SDF format, chain Q [auth G] SDF format, chain PA [auth C] SDF format, chain OA [auth C] SDF format, chain NA [auth C] SDF format, chain MA [auth C] SDF format, chain LA [auth C] SDF format, chain KA [auth C] SDF format, chain FA [auth J] SDF format, chain EA [auth J] SDF format, chain DA [auth J] SDF format, chain CA [auth J] SDF format, chain BA [auth J] MOL2 format, chain ZA [auth A] MOL2 format, chain YA [auth A] MOL2 format, chain XA [auth A] MOL2 format, chain WA [auth A] MOL2 format, chain W [auth J] MOL2 format, chain VA [auth A] MOL2 format, chain V [auth G] MOL2 format, chain UA [auth A] MOL2 format, chain U [auth G] MOL2 format, chain T [auth G] MOL2 format, chain S [auth G] MOL2 format, chain R [auth G] MOL2 format, chain Q [auth G] MOL2 format, chain PA [auth C] MOL2 format, chain OA [auth C] MOL2 format, chain NA [auth C] MOL2 format, chain MA [auth C] MOL2 format, chain LA [auth C] MOL2 format, chain KA [auth C] MOL2 format, chain FA [auth J] MOL2 format, chain EA [auth J] MOL2 format, chain DA [auth J] MOL2 format, chain CA [auth J] MOL2 format, chain BA [auth J] mmCIF format, chain ZA [auth A] mmCIF format, chain YA [auth A] mmCIF format, chain XA [auth A] mmCIF format, chain WA [auth A] mmCIF format, chain W [auth J] mmCIF format, chain VA [auth A] mmCIF format, chain V [auth G] mmCIF format, chain UA [auth A] mmCIF format, chain U [auth G] mmCIF format, chain T [auth G] mmCIF format, chain S [auth G] mmCIF format, chain R [auth G] mmCIF format, chain Q [auth G] mmCIF format, chain PA [auth C] mmCIF format, chain OA [auth C] mmCIF format, chain NA [auth C] mmCIF format, chain MA [auth C] mmCIF format, chain LA [auth C] mmCIF format, chain KA [auth C] mmCIF format, chain FA [auth J] mmCIF format, chain EA [auth J] mmCIF format, chain DA [auth J] mmCIF format, chain CA [auth J] mmCIF format, chain BA [auth J]	BA [auth J] CA [auth J] DA [auth J] EA [auth J] FA [auth J] BA [auth J], CA [auth J], DA [auth J], EA [auth J], FA [auth J], KA [auth C], LA [auth C], MA [auth C], NA [auth C], OA [auth C], PA [auth C], Q [auth G], R [auth G], S [auth G], T [auth G], U [auth G], UA [auth A], V [auth G], VA [auth A], W [auth J], WA [auth A], XA [auth A], YA [auth A], ZA [auth A]	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate C₄₂ H₈₂ N O₈ P WTJKGGKOPKCXLL-PFDVCBLKSA-N		Interactions Focus chain BA [auth J] Focus chain CA [auth J] Focus chain DA [auth J] Focus chain EA [auth J] Focus chain FA [auth J] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain Q [auth G] Focus chain R [auth G] Focus chain S [auth G] Focus chain T [auth G] Focus chain U [auth G] Focus chain UA [auth A] Focus chain V [auth G] Focus chain VA [auth A] Focus chain W [auth J] Focus chain WA [auth A] Focus chain XA [auth A] Focus chain YA [auth A] Focus chain ZA [auth A] Interactions & Density Focus chain BA [auth J] Focus chain CA [auth J] Focus chain DA [auth J] Focus chain EA [auth J] Focus chain FA [auth J] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain Q [auth G] Focus chain R [auth G] Focus chain S [auth G] Focus chain T [auth G] Focus chain U [auth G] Focus chain UA [auth A] Focus chain V [auth G] Focus chain VA [auth A] Focus chain W [auth J] Focus chain WA [auth A] Focus chain XA [auth A] Focus chain YA [auth A] Focus chain ZA [auth A]
ATP (Subject of Investigation/LOI) Query on ATP Download Ideal Coordinates CCD File SDF format, chain Y [auth J] SDF format, chain RA [auth A] SDF format, chain N [auth G] SDF format, chain HA [auth C] MOL2 format, chain Y [auth J] MOL2 format, chain RA [auth A] MOL2 format, chain N [auth G] MOL2 format, chain HA [auth C] mmCIF format, chain Y [auth J] mmCIF format, chain RA [auth A] mmCIF format, chain N [auth G] mmCIF format, chain HA [auth C]	HA [auth C], N [auth G], RA [auth A], Y [auth J]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain HA [auth C] Focus chain N [auth G] Focus chain RA [auth A] Focus chain Y [auth J] Interactions & Density Focus chain HA [auth C] Focus chain N [auth G] Focus chain RA [auth A] Focus chain Y [auth J]
CFF (Subject of Investigation/LOI) Query on CFF Download Ideal Coordinates CCD File SDF format, chain Z [auth J] SDF format, chain SA [auth A] SDF format, chain O [auth G] SDF format, chain IA [auth C] MOL2 format, chain Z [auth J] MOL2 format, chain SA [auth A] MOL2 format, chain O [auth G] MOL2 format, chain IA [auth C] mmCIF format, chain Z [auth J] mmCIF format, chain SA [auth A] mmCIF format, chain O [auth G] mmCIF format, chain IA [auth C]	IA [auth C], O [auth G], SA [auth A], Z [auth J]	CAFFEINE C₈ H₁₀ N₄ O₂ RYYVLZVUVIJVGH-UHFFFAOYSA-N		Interactions Focus chain IA [auth C] Focus chain O [auth G] Focus chain SA [auth A] Focus chain Z [auth J] Interactions & Density Focus chain IA [auth C] Focus chain O [auth G] Focus chain SA [auth A] Focus chain Z [auth J]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain X [auth J] SDF format, chain QA [auth A] SDF format, chain M [auth G] SDF format, chain GA [auth C] MOL2 format, chain X [auth J] MOL2 format, chain QA [auth A] MOL2 format, chain M [auth G] MOL2 format, chain GA [auth C] mmCIF format, chain X [auth J] mmCIF format, chain QA [auth A] mmCIF format, chain M [auth G] mmCIF format, chain GA [auth C]	GA [auth C], M [auth G], QA [auth A], X [auth J]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain GA [auth C] Focus chain M [auth G] Focus chain QA [auth A] Focus chain X [auth J] Interactions & Density Focus chain GA [auth C] Focus chain M [auth G] Focus chain QA [auth A] Focus chain X [auth J]
CA (Subject of Investigation/LOI) Query on CA Download Ideal Coordinates CCD File SDF format, chain TA [auth A] SDF format, chain P [auth G] SDF format, chain JA [auth C] SDF format, chain AA [auth J] MOL2 format, chain TA [auth A] MOL2 format, chain P [auth G] MOL2 format, chain JA [auth C] MOL2 format, chain AA [auth J] mmCIF format, chain TA [auth A] mmCIF format, chain P [auth G] mmCIF format, chain JA [auth C] mmCIF format, chain AA [auth J]	AA [auth J], JA [auth C], P [auth G], TA [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AA [auth J] Focus chain JA [auth C] Focus chain P [auth G] Focus chain TA [auth A] Interactions & Density Focus chain AA [auth J] Focus chain JA [auth C] Focus chain P [auth G] Focus chain TA [auth A]

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
MODEL REFINEMENT	PHENIX	1.21.2_5419

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2025-09-17

Deposition Author(s):

Li, C.

Efremov, R.G.

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