9HEO | pdb_00009heo

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Lipids modulate the open probability of RyR1 under cryo-EM conditions.

Li, C.Efremov, R.G.

(2025) Structure 33: 2029-2040.e3

  • DOI: https://doi.org/10.1016/j.str.2025.09.003
  • Primary Citation Related Structures: 
    9HEO, 9HEQ, 9R8O, 9RCW

  • PubMed Abstract: 

    Ryanodine receptors (RyRs) are intracellular tetrameric ion channels responsible for Ca 2+ release from the sarcoplasmic and endoplasmic reticulum. Ryanodine receptor 1 (RyR1) isoform, critical for muscle contraction, has been studied most extensively. While cryoelectron microscopy (cryo-EM) has been instrumental in revealing near-atomic details of RyR gating mechanisms, the open probability of RyR1 under cryo-EM conditions is notably lower than that observed in electrophysiological studies. Here, we present a cryo-EM study examining the open probability of RyR1 solubilized in CHAPS with varying lipid concentrations. We found that increasing lipid concentration from 0.001% to 0.05% raised the RyR1 open probability from 16% to 84%, whereas RyR1 reconstituted into lipid nanodiscs remained closed. We modeled 72 lipid molecules in the map reconstructed at the highest lipid concentration. These findings demonstrate the important role of lipids in modulating the open fraction of solubilized RyR1 channels under cryo-EM conditions and suggest optimal lipid mimetics for structural studies of RyR1 gating.


  • Organizational Affiliation
    • Center for Structural Biology, Vlaams Instituut voor Biotechnologie, 1050 Brussels, Belgium; Structural Biology Brussels, Department of Bioengineering Sciences, VUB, 1050 Brussels, Belgium.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ryanodine receptor 1
A, C, G, J
5,027Oryctolagus cuniculusMutation(s): 0 
Gene Names: RYR1
UniProt
Find proteins for P11716 (Oryctolagus cuniculus)
Explore P11716 
Go to UniProtKB:  P11716
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11716
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nanobody 9657
B, D, H, K
126Lama glamaMutation(s): 0 
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase FKBP1B
E, F, I, L
107Oryctolagus cuniculusMutation(s): 0 
Gene Names: FKBP1BFKBP12.6
EC: 5.2.1.8
UniProt
Find proteins for Q8HYX6 (Oryctolagus cuniculus)
Explore Q8HYX6 
Go to UniProtKB:  Q8HYX6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8HYX6
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
POV (Subject of Investigation/LOI)
Query on POV

Download Ideal Coordinates CCD File 
AA [auth A]
AB [auth C]
AC [auth J]
BA [auth A]
BB [auth C]
AA [auth A],
AB [auth C],
AC [auth J],
BA [auth A],
BB [auth C],
BC [auth J],
CA [auth A],
CB [auth C],
CC [auth J],
DA [auth A],
DB [auth C],
DC [auth J],
EA [auth A],
EB [auth G],
EC [auth J],
FA [auth A],
FB [auth G],
FC [auth J],
GA [auth A],
GB [auth G],
GC [auth J],
HA [auth A],
IA [auth C],
JA [auth C],
KA [auth C],
LB [auth G],
LC [auth J],
MB [auth G],
MC [auth J],
NB [auth G],
NC [auth J],
OB [auth G],
OC [auth J],
PA [auth C],
PB [auth G],
PC [auth J],
Q [auth A],
QA [auth C],
QB [auth G],
QC [auth J],
R [auth A],
RA [auth C],
RB [auth G],
RC [auth J],
S [auth A],
SA [auth C],
SB [auth G],
SC [auth J],
T [auth A],
TA [auth C],
TB [auth G],
TC [auth J],
U [auth A],
UA [auth C],
UB [auth G],
UC [auth J],
V [auth A],
VA [auth C],
VB [auth G],
VC [auth J],
W [auth A],
WA [auth C],
WB [auth G],
X [auth A],
XA [auth C],
XB [auth G],
Y [auth A],
YA [auth C],
YB [auth G],
Z [auth A],
ZA [auth C],
ZB [auth G]
(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)
Query on ATP

Download Ideal Coordinates CCD File 
IB [auth G],
IC [auth J],
MA [auth C],
N [auth A]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
CFF (Subject of Investigation/LOI)
Query on CFF

Download Ideal Coordinates CCD File 
JB [auth G],
JC [auth J],
NA [auth C],
O [auth A]
CAFFEINE
C8 H10 N4 O2
RYYVLZVUVIJVGH-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
HB [auth G],
HC [auth J],
LA [auth C],
M [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA (Subject of Investigation/LOI)
Query on CA

Download Ideal Coordinates CCD File 
KB [auth G],
KC [auth J],
OA [auth C],
P [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.31

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Research Foundation - Flanders (FWO)BelgiumG0H5916N
Research Foundation - Flanders (FWO)BelgiumG054617N
European Research Council (ERC)European Union726436

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-17
    Type: Initial release
  • Version 1.1: 2026-04-01
    Changes: Data collection, Database references