5T15

Structural basis for gating and activation of RyR1 (30 uM Ca2+ dataset, all particles)


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural Basis for Gating and Activation of RyR1.

des Georges, A.Clarke, O.B.Zalk, R.Yuan, Q.Condon, K.J.Grassucci, R.A.Hendrickson, W.A.Marks, A.R.Frank, J.

(2016) Cell 167: 145-157.e17

  • DOI: 10.1016/j.cell.2016.08.075
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The type-1 ryanodine receptor (RyR1) is an intracellular calcium (Ca(2+)) release channel required for skeletal muscle contraction. Here, we present cryo-EM reconstructions of RyR1 in multiple functional states revealing the structural basis of chann ...

    The type-1 ryanodine receptor (RyR1) is an intracellular calcium (Ca(2+)) release channel required for skeletal muscle contraction. Here, we present cryo-EM reconstructions of RyR1 in multiple functional states revealing the structural basis of channel gating and ligand-dependent activation. Binding sites for the channel activators Ca(2+), ATP, and caffeine were identified at interdomain interfaces of the C-terminal domain. Either ATP or Ca(2+) alone induces conformational changes in the cytoplasmic assembly ("priming"), without pore dilation. In contrast, in the presence of all three activating ligands, high-resolution reconstructions of open and closed states of RyR1 were obtained from the same sample, enabling analyses of conformational changes associated with gating. Gating involves global conformational changes in the cytosolic assembly accompanied by local changes in the transmembrane domain, which include bending of the S6 transmembrane segment and consequent pore dilation, displacement, and deformation of the S4-S5 linker and conformational changes in the pseudo-voltage-sensor domain.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Howard Hughes Medical Institute, Columbia University, New York, NY 10032, USA; Department of Biological Sciences, Columbia University, New York, NY 10032, USA. Electronic address: jf2192@cumc.columbia.edu.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peptidyl-prolyl cis-trans isomerase FKBP1B
A, F, H, J
108Homo sapiensMutation(s): 0 
Gene Names: FKBP1BFKBP12.6FKBP1LFKBP9OTK4
EC: 5.2.1.8
Find proteins for P68106 (Homo sapiens)
Go to UniProtKB:  P68106
NIH Common Fund Data Resources
PHAROS  P68106

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ryanodine receptor 1,Ryanodine receptor 1,Ryanodine receptor 1,Ryanodine receptor 1,Ryanodine receptor 1,Ryanodine receptor 1,Ryanodine receptor 1
B, E, G, I
4676Oryctolagus cuniculusMutation(s): 0 
Find proteins for P11716 (Oryctolagus cuniculus)
Go to UniProtKB:  P11716
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
B, E, G, I
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
B, E, G, I
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

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

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)United StatesR01AR060037
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesR01HL061503
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesU54GM095315
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM29169

Revision History 

  • Version 1.0: 2016-10-12
    Type: Initial release
  • Version 1.1: 2016-10-26
    Changes: Refinement description
  • Version 1.2: 2017-09-13
    Changes: Author supporting evidence, Data collection
  • Version 1.3: 2018-07-18
    Changes: Data collection
  • Version 1.4: 2019-12-04
    Changes: Author supporting evidence