6HD8

Crystal structure of the potassium channel MtTMEM175 in complex with a Nanobody-MBP fusion protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 

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This is version 2.0 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: 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 ...

    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.


    Related Citations: 
    • 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.
      (2019) Biorxiv --: --

    Organizational Affiliation

    Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nanobody,Maltose/maltodextrin-binding periplasmic proteinA486Lama 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
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
TMEM175B255Marivirga 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
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranoseC 2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G07411ON
GlyCosmos:  G07411ON
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LMT
Query on LMT

Download Ideal Coordinates CCD File 
D [auth B]DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
 Ligand Interaction
K
Query on K

Download Ideal Coordinates CCD File 
E [auth B],
F [auth B]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 3
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900001
Query on PRD_900001
Calpha-maltoseOligosaccharide / Nutrient Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 
  • Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.21α = 90
b = 131.21β = 90
c = 132.59γ = 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