6HDB

Crystal structure of the potassium channel MtTMEM175 with zinc


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.275 
  • R-Value Observed: 0.276 

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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Structural basis for ion selectivity in TMEM175 K+channels.

Brunner, J.D.Jakob, R.P.Schulze, T.Neldner, Y.Moroni, A.Thiel, G.Maier, T.Schenck, S.

(2020) Elife 9

  • DOI: https://doi.org/10.7554/eLife.53683
  • Primary Citation of Related Structures:  
    6HD8, 6HD9, 6HDA, 6HDB, 6HDC, 6SWR

  • PubMed Abstract: 

    The TMEM175 family constitutes recently discovered K + channels that are important for autophagosome turnover and lysosomal pH regulation and are associated with the early onset of Parkinson Disease. TMEM175 channels lack a P-loop selectivity filter, a hallmark of all known K + channels, raising the question how selectivity is achieved. Here, we report the X-ray structure of a closed bacterial TMEM175 channel in complex with a nanobody fusion-protein disclosing bound K + ions. Our analysis revealed that a highly conserved layer of threonine residues in the pore conveys a basal K + selectivity. An additional layer comprising two serines in human TMEM175 increases selectivity further and renders this channel sensitive to 4-aminopyridine and Zn 2+ . Our findings suggest that large hydrophobic side chains occlude the pore, forming a physical gate, and that channel opening by iris-like motions simultaneously relocates the gate and exposes the otherwise concealed selectivity filter to the pore lumen.


  • Organizational Affiliation

    Department of Biochemistry, University of Zürich, Zürich, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nanobody,Maltose/maltodextrin-binding periplasmic protein486Lama glamaEscherichia coli K-12
This entity is chimeric
Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0AEX9 (Escherichia coli (strain K12))
Explore P0AEX9 
Go to UniProtKB:  P0AEX9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AEX9
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
TMEM175255Marivirga tractuosa DSM 4126Mutation(s): 0 
Gene Names: Ftrac_2467
Membrane Entity: Yes 
UniProt
Find proteins for E4TN31 (Marivirga tractuosa (strain ATCC 23168 / DSM 4126 / NBRC 15989 / NCIMB 1408 / VKM B-1430 / H-43))
Explore E4TN31 
Go to UniProtKB:  E4TN31
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE4TN31
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
C
2N/A
Glycosylation Resources
GlyTouCan:  G07411ON
GlyCosmos:  G07411ON
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.275 
  • R-Value Observed: 0.276 
  • Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.92α = 90
b = 131.92β = 90
c = 132.79γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-28
    Type: Initial release
  • Version 1.1: 2019-09-04
    Changes: Data collection
  • Version 1.2: 2019-09-18
    Changes: Data collection, Database references
  • Version 1.3: 2020-04-15
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2024-01-17
    Changes: Data collection, Database references, Refinement description, Structure summary