6SWR | pdb_00006swr

Crystal structure of the lysosomal potassium channel MtTMEM175 T38A mutant soaked with zinc


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 
    0.299 (Depositor), 0.323 (DCC) 
  • R-Value Work: 
    0.269 (Depositor), 0.297 (DCC) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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This is version 2.3 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 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.

Macromolecule Content 

  • Total Structure Weight: 167.18 kDa 
  • Atom Count: 10,944 
  • Modeled Residue Count: 1,372 
  • Deposited Residue Count: 1,482 
  • Unique protein chains: 2

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Nanobody, Maltose/maltodextrin-binding periplasmic protein,Maltodextrin-binding protein,Maltose/maltodextrin-binding periplasmic proteinA,
C [auth D]
486Lama glamaEscherichia coli K-12
This entity is chimeric
Mutation(s): 0 
Gene Names: malEb4034JW3994
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:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Uncharacterized proteinB,
D [auth E]
255Marivirga 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

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Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranoseE [auth C],
F
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: 3.20 Å
  • R-Value Free:  0.299 (Depositor), 0.323 (DCC) 
  • R-Value Work:  0.269 (Depositor), 0.297 (DCC) 
Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 129.788α = 90
b = 131.611β = 90
c = 151.771γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-15
    Type: Initial release
  • Version 1.1: 2020-04-22
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2020-09-30
    Changes: Database references, Structure summary
  • Version 2.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description
  • Version 2.3: 2024-11-20
    Changes: Structure summary