Biological Assembly 1  

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Global Symmetry: Cyclic - C4  (3D View)
Global Stoichiometry: Hetero 8-mer - A4B4 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 2048453.88 
• Atom Count: 111160 
• Residue Count: 18824 
• Unique protein chains: 2

3J8H

Structure of the rabbit ryanodine receptor RyR1 in complex with FKBP12 at 3.8 Angstrom resolution

• DOI: 10.2210/pdb3J8H/pdb
• EMDataResource: EMD-2807

• Classification: TRANSPORT PROTEIN/ISOMERASE
• Organism(s): Oryctolagus cuniculus
• Expression System: Escherichia coli


• Deposited: 2014-10-26 Released: 2014-12-10 
• Deposition Author(s): Yan, Z., Bai, X., Yan, C., Wu, J., Scheres, S.H.W., Shi, Y., Yan, N.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.8 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of the rabbit ryanodine receptor RyR1 at near-atomic resolution.

Yan, Z., Bai, X.C., Yan, C., Wu, J., Li, Z., Xie, T., Peng, W., Yin, C.C., Li, X., Scheres, S.H., Shi, Y., Yan, N.

(2015) Nature 517: 50-55

• PubMed: 25517095 
• DOI: 10.1038/nature14063


• PubMed Abstract: 
  

The ryanodine receptors (RyRs) are high-conductance intracellular Ca(2+) channels that play a pivotal role in the excitation-contraction coupling of skeletal and cardiac muscles. RyRs are the largest known ion channels, with a homotetrameric organization and approximately 5,000 residues in each protomer. Here we report the structure of the rabbit RyR1 in complex with its modulator FKBP12 at an overall resolution of 3.8 Å, determined by single-particle electron cryomicroscopy. Three previously uncharacterized domains, named central, handle and helical domains, display the armadillo repeat fold. These domains, together with the amino-terminal domain, constitute a network of superhelical scaffold for binding and propagation of conformational changes. The channel domain exhibits the voltage-gated ion channel superfamily fold with distinct features. A negative-charge-enriched hairpin loop connecting S5 and the pore helix is positioned above the entrance to the selectivity-filter vestibule. The four elongated S6 segments form a right-handed helical bundle that closes the pore at the cytoplasmic border of the membrane. Allosteric regulation of the pore by the cytoplasmic domains is mediated through extensive interactions between the central domains and the channel domain. These structural features explain high ion conductance by RyRs and the long-range allosteric regulation of channel activities.

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Organizational Affiliation: 

State Key Laboratory of Bio-membrane and Membrane Biotechnology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Ryanodine receptor 1	A, C, E, G	4599	Oryctolagus cuniculus	Mutation(s): 0  Gene Names: RYR1
Membrane protein mpstruc	Group:  TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group:  Channels: Calcium Ion-Selective	Protein:  RyR1 ryanodine receptor, closed state in complex with FKBP12. Cryo-EM structure
Find proteins for P11716 (Oryctolagus cuniculus) Go to Gene View: RYR1 Go to UniProtKB:  P11716

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Peptidyl-prolyl cis-trans isomerase FKBP1A	B, D, F, H	107	Oryctolagus cuniculus	Mutation(s): 0  Gene Names: FKBP1A (FKBP1, FKBP12) EC: 5.2.1.8
Membrane protein mpstruc	Group:  TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group:  Channels: Calcium Ion-Selective	Protein:  RyR1 ryanodine receptor, closed state in complex with FKBP12. Cryo-EM structure
Find proteins for P62943 (Oryctolagus cuniculus) Go to Gene View: FKBP1A Go to UniProtKB:  P62943

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	A, C, E, G	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
UNK	A, C, E, G	L-PEPTIDE LINKING	C4 H9 N O2		--

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.8 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-10-26 
• Released Date: 2014-12-10 
• Deposition Author(s): Yan, Z., Bai, X., Yan, C., Wu, J., Scheres, S.H.W., Shi, Y., Yan, N.

Revision History 

• Version 1.0: 2014-12-10
  Type: Initial release
• Version 1.1: 2014-12-17
  Type: Advisory
• Version 1.2: 2015-01-21
  Type: Structure summary
• Version 1.3: 2015-02-25
  Type: Database references
• Version 1.4: 2018-07-18
  Type: Data collection