Cryo-EM structure of calcium-bound nhTMEM16 lipid scramblase in nanodisc (open state)

Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Stepwise activation mechanism of the scramblase nhTMEM16 revealed by cryo-EM.

Kalienkova, V.Clerico Mosina, V.Bryner, L.Oostergetel, G.T.Dutzler, R.Paulino, C.

(2019) Elife 8

  • DOI: https://doi.org/10.7554/eLife.44364
  • Primary Citation of Related Structures:  
    6QM4, 6QM5, 6QM6, 6QM9, 6QMA, 6QMB

  • PubMed Abstract: 

    Scramblases catalyze the movement of lipids between both leaflets of a bilayer. Whereas the X-ray structure of the protein nhTMEM16 has previously revealed the architecture of a Ca 2+ -dependent lipid scramblase, its regulation mechanism has remained elusive. Here, we have used cryo-electron microscopy and functional assays to address this question. Ca 2+ -bound and Ca 2+ -free conformations of nhTMEM16 in detergent and lipid nanodiscs illustrate the interactions with its environment and they reveal the conformational changes underlying its activation. In this process, Ca 2+ binding induces a stepwise transition of the catalytic subunit cavity, converting a closed cavity that is shielded from the membrane in the absence of ligand, into a polar furrow that becomes accessible to lipid headgroups in the Ca 2+ -bound state. Additionally, our structures demonstrate how nhTMEM16 distorts the membrane at both entrances of the subunit cavity, thereby decreasing the energy barrier for lipid movement.

  • Organizational Affiliation

    Department of Biochemistry, University of Zurich, Zurich, Switzerland.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Predicted protein
A, B
735Fusarium vanettenii 77-13-4Mutation(s): 0 
Gene Names: NECHADRAFT_66456
Membrane Entity: Yes 
Find proteins for C7Z7K1 (Fusarium vanettenii (strain ATCC MYA-4622 / CBS 123669 / FGSC 9596 / NRRL 45880 / 77-13-4))
Explore C7Z7K1 
Go to UniProtKB:  C7Z7K1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC7Z7K1
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
European Research CouncilSwitzerland339116, AnoBest.
Netherlands Organisation for Scientific ResearchNetherlands740.018.016

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-06
    Type: Initial release
  • Version 1.1: 2019-03-20
    Changes: Author supporting evidence, Data collection
  • Version 1.2: 2019-12-18
    Changes: Other
  • Version 1.3: 2024-05-15
    Changes: Data collection, Database references