5OC9 | pdb_00005oc9

Crystal Structure of human TMEM16K / Anoctamin 10


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 
    0.245 (Depositor), 0.262 (DCC) 
  • R-Value Work: 
    0.228 (Depositor), 0.242 (DCC) 
  • R-Value Observed: 
    0.229 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

The structural basis of lipid scrambling and inactivation in the endoplasmic reticulum scramblase TMEM16K.

Bushell, S.R.Pike, A.C.W.Falzone, M.E.Rorsman, N.J.G.Ta, C.M.Corey, R.A.Newport, T.D.Christianson, J.C.Scofano, L.F.Shintre, C.A.Tessitore, A.Chu, A.Wang, Q.Shrestha, L.Mukhopadhyay, S.M.M.Love, J.D.Burgess-Brown, N.A.Sitsapesan, R.Stansfeld, P.J.Huiskonen, J.T.Tammaro, P.Accardi, A.Carpenter, E.P.

(2019) Nat Commun 10: 3956-3956

  • DOI: https://doi.org/10.1038/s41467-019-11753-1
  • Primary Citation Related Structures: 
    5OC9, 6R65, 6R7X, 6R7Y, 6R7Z

  • PubMed Abstract: 

    Membranes in cells have defined distributions of lipids in each leaflet, controlled by lipid scramblases and flip/floppases. However, for some intracellular membranes such as the endoplasmic reticulum (ER) the scramblases have not been identified. Members of the TMEM16 family have either lipid scramblase or chloride channel activity. Although TMEM16K is widely distributed and associated with the neurological disorder autosomal recessive spinocerebellar ataxia type 10 (SCAR10), its location in cells, function and structure are largely uncharacterised. Here we show that TMEM16K is an ER-resident lipid scramblase with a requirement for short chain lipids and calcium for robust activity. Crystal structures of TMEM16K show a scramblase fold, with an open lipid transporting groove. Additional cryo-EM structures reveal extensive conformational changes from the cytoplasmic to the ER side of the membrane, giving a state with a closed lipid permeation pathway. Molecular dynamics simulations showed that the open-groove conformation is necessary for scramblase activity.


  • Organizational Affiliation
    • Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK.

Macromolecule Content 

  • Total Structure Weight: 160.75 kDa 
  • Atom Count: 10,138 
  • Modeled Residue Count: 1,223 
  • Deposited Residue Count: 1,334 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Anoctamin-10
A, B
667Homo sapiensMutation(s): 0 
Gene Names: ANO10TMEM16K
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NW15 (Homo sapiens)
Explore Q9NW15 
Go to UniProtKB:  Q9NW15
PHAROS:  Q9NW15
GTEx:  ENSG00000160746 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NW15
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
79M

Query on 79M



Download:Ideal Coordinates CCD File
AA [auth B]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
AA [auth B],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
S [auth B],
T [auth B],
U [auth B],
V [auth B],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
(2R)-2,3-dihydroxypropyl (7Z)-hexadec-7-enoate
C19 H36 O4
OWGMAJRKMYGYBQ-HJCTWCACSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
O [auth B]
P [auth B]
C [auth A],
D [auth A],
E [auth A],
O [auth B],
P [auth B],
Q [auth B],
R [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free:  0.245 (Depositor), 0.262 (DCC) 
  • R-Value Work:  0.228 (Depositor), 0.242 (DCC) 
  • R-Value Observed: 0.229 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.15α = 90
b = 153.59β = 90
c = 218.78γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
MrBUMPphasing
MR-Rosettaphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-25
    Type: Initial release
  • Version 1.1: 2019-06-12
    Changes: Data collection, Structure summary
  • Version 1.2: 2019-11-20
    Changes: Database references
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description