9HEQ | pdb_00009heq

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

PDB DOI: https://doi.org/10.2210/pdb9HEQ/pdb
EM Map EMD-52091: EMDB EMDataResource

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

Deposited: 2024-11-14 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: 3.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Currently 9HEQ does not have a validation slider image.

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

Literature

Open-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: 2,395.16 kDa
Atom Count: 145,440
Modeled Residue Count: 18,208
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
Ryanodine receptor 1	A, C, G, J	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

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody 9657	B, D, H, K	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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase FKBP1B	E, F, I, L	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

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

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.31

Structure Validation

View Full Validation Report

Currently 9HEQ 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.

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