6QMB

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


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 1.2 of the entry. See complete history


Literature

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: 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 ...

    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 Structural Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Predicted proteinA, B735Fusarium vanettenii 77-13-4Mutation(s): 0 
Gene Names: NECHADRAFT_66456
Membrane Entity: Yes 
UniProt
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
Protein Feature View
Expand
  • Reference Sequence
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
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