8RRT

Structure of rabbit RyR1 reconstituted into lipid liposomes in open state in complex with FKBP and Nb9657


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Rapid small-scale nanobody-assisted purification of ryanodine receptors for cryo-EM.

Li, C.Willegems, K.Uchanski, T.Pardon, E.Steyaert, J.Efremov, R.G.

(2024) J Biol Chem : 107734-107734

  • DOI: https://doi.org/10.1016/j.jbc.2024.107734
  • Primary Citation of Related Structures:  
    8RRS, 8RRT, 8RRU, 8RRV, 8RRW, 8RRX, 8RS0

  • PubMed Abstract: 

    Ryanodine receptors (RyRs) are large Ca 2+ release channels residing in the endoplasmic or sarcoplasmic reticulum membrane. Three isoforms of RyRs have been identified in mammals, the disfunction of which has been associated with a series of life-threatening diseases. The need for large amounts of native tissue or eukaryotic cell cultures limits advances in structural studies of RyRs. Here, we report a method that utilizes nanobodies to purify RyRs from only 5 mg of total protein. The purification process, from isolated membranes to cryo-EM grade protein, is achieved within 4 h on the bench, yielding protein usable for cryo-EM analysis. This is demonstrated by solving the structures of rabbit RyR1, solubilized in detergent, reconstituted into lipid nanodiscs or liposomes, and bovine RyR2 reconstituted in nanodisc, and mouse RyR2 in detergent. The reported method facilitates structural studies of RyRs directed toward drug development and is useful in cases where the amount of starting material is limited.


  • Organizational Affiliation

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ryanodine receptor 1A [auth B],
B [auth E],
C [auth G],
D [auth J]
5,027Oryctolagus cuniculusMutation(s): 0 
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
Peptidyl-prolyl cis-trans isomerase FKBP1BE [auth A],
F [auth D],
G [auth H],
H [auth I]
107Oryctolagus cuniculusMutation(s): 0 
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
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Nanobody 9657I [auth C],
J [auth F],
K,
L [auth M]
137Vicugna pacosMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
N [auth B],
R [auth E],
V [auth G],
Z [auth J]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
CFF (Subject of Investigation/LOI)
Query on CFF

Download Ideal Coordinates CCD File 
AA [auth J],
O [auth B],
S [auth E],
W [auth G]
CAFFEINE
C8 H10 N4 O2
RYYVLZVUVIJVGH-UHFFFAOYSA-N
ZN
Query on ZN

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M [auth B],
Q [auth E],
U [auth G],
Y [auth J]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA (Subject of Investigation/LOI)
Query on CA

Download Ideal Coordinates CCD File 
BA [auth J],
P [auth B],
T [auth E],
X [auth G]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.60 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: 2024-10-09
    Type: Initial release