5TAL

Structure of rabbit RyR1 (Caffeine/ATP/Ca2+ dataset, class 1&2)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.3 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 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
  • Primary Citation of Related Structures:  

  • 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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peptidyl-prolyl cis-trans isomerase FKBP1B
F, A, H, J
108Homo sapiensMutation(s): 0 
Gene Names: FKBP1B (FKBP12.6, FKBP1L, FKBP9, OTK4)
EC: 5.2.1.8
Find proteins for P68106 (Homo sapiens)
Go to Gene View: FKBP1B
Go to UniProtKB:  P68106
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ryanodine receptor 1
B, G, I, E
4416Oryctolagus cuniculusMutation(s): 0 
Gene Names: RYR1
Find proteins for P11716 (Oryctolagus cuniculus)
Go to Gene View: RYR1
Go to UniProtKB:  P11716
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
B, E, G, I
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
ZN
Query on ZN

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

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Download CCD File 
B, E, G, I
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CFF
Query on CFF

Download SDF File 
Download CCD File 
B, E, G, I
CAFFEINE
3,7-DIHYDRO-1,3,7-TRIMETHYL-1H-PURINE-2,6-DIONE
C8 H10 N4 O2
RYYVLZVUVIJVGH-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
B, E, G, I
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.3 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-10-12
    Type: Initial release
  • Version 1.1: 2016-10-26
    Type: Refinement description
  • Version 1.2: 2018-07-18
    Type: Data collection