6OWW

Crystal structure of a Human Cardiac Calsequestrin Filament Complexed with Ytterbium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.84 Å
  • R-Value Free: 0.340 
  • R-Value Work: 0.290 
  • R-Value Observed: 0.292 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Literature

The structure of a calsequestrin filament reveals mechanisms of familial arrhythmia.

Titus, E.W.Deiter, F.H.Shi, C.Wojciak, J.Scheinman, M.Jura, N.Deo, R.C.

(2020) Nat Struct Mol Biol 27: 1142-1151

  • DOI: https://doi.org/10.1038/s41594-020-0510-9
  • Primary Citation of Related Structures:  
    6OWV, 6OWW

  • PubMed Abstract: 

    Mutations in the calcium-binding protein calsequestrin cause the highly lethal familial arrhythmia catecholaminergic polymorphic ventricular tachycardia (CPVT). In vivo, calsequestrin multimerizes into filaments, but there is not yet an atomic-resolution structure of a calsequestrin filament. We report a crystal structure of a human cardiac calsequestrin filament with supporting mutational analysis and in vitro filamentation assays. We identify and characterize a new disease-associated calsequestrin mutation, S173I, that is located at the filament-forming interface, and further show that a previously reported dominant disease mutation, K180R, maps to the same surface. Both mutations disrupt filamentation, suggesting that disease pathology is due to defects in multimer formation. An ytterbium-derivatized structure pinpoints multiple credible calcium sites at filament-forming interfaces, explaining the atomic basis of calsequestrin filamentation in the presence of calcium. Our study thus provides a unifying molecular mechanism through which dominant-acting calsequestrin mutations provoke lethal arrhythmias.


  • Organizational Affiliation

    Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA. erron.titus@ucsf.edu.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Calsequestrin-2
A, B, C, D, E
A, B, C, D, E, F, G, H
387Homo sapiensMutation(s): 0 
Gene Names: CASQ2
UniProt & NIH Common Fund Data Resources
Find proteins for O14958 (Homo sapiens)
Explore O14958 
Go to UniProtKB:  O14958
PHAROS:  O14958
GTEx:  ENSG00000118729 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14958
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
YB (Subject of Investigation/LOI)
Query on YB

Download Ideal Coordinates CCD File 
AA [auth C]
AB [auth E]
BA [auth C]
BB [auth F]
CA [auth C]
AA [auth C],
AB [auth E],
BA [auth C],
BB [auth F],
CA [auth C],
CB [auth F],
DA [auth C],
DB [auth F],
EA [auth C],
EB [auth F],
FA [auth C],
FB [auth F],
GA [auth C],
GB [auth F],
HA [auth C],
HB [auth F],
I [auth A],
IA [auth C],
J [auth A],
JA [auth D],
JB [auth G],
K [auth A],
KA [auth D],
KB [auth G],
L [auth A],
LA [auth D],
LB [auth G],
M [auth A],
MA [auth D],
MB [auth G],
N [auth A],
NA [auth D],
NB [auth G],
O [auth A],
OA [auth D],
OB [auth G],
P [auth A],
PA [auth D],
PB [auth G],
Q [auth A],
QA [auth D],
QB [auth G],
RB [auth H],
S [auth B],
SA [auth E],
SB [auth H],
T [auth B],
TA [auth E],
TB [auth H],
U [auth B],
UA [auth E],
UB [auth H],
V [auth B],
VA [auth E],
VB [auth H],
W [auth B],
WA [auth E],
WB [auth H],
X [auth B],
XA [auth E],
Y [auth B],
YA [auth E],
ZA [auth E]
YTTERBIUM (III) ION
Yb
AWSFICBXMUKWSK-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
IB [auth F],
R [auth A],
RA [auth D],
XB [auth H],
Z [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.832α = 90
b = 86.015β = 89.91
c = 214.34γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Blu-Icedata collection
ELVESdata processing
DIALSdata reduction
DIALSdata scaling
PHASERphasing
Cootmodel building

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesF30HL137329
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesT32GM007618
American Heart AssociationUnited States17IRG33460152
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesDP2HL123228

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-08
    Type: Initial release
  • Version 1.1: 2020-10-14
    Changes: Database references, Derived calculations
  • Version 1.2: 2020-10-21
    Changes: Database references
  • Version 1.3: 2020-12-16
    Changes: Database references
  • Version 1.4: 2023-10-11
    Changes: Data collection, Database references, Refinement description