8QJ3

Receptor Sd-Amt1 (OFF-state)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

How sensor Amt-like proteins integrate ammonium signals.

Pfluger, T.Gschell, M.Zhang, L.Shnitsar, V.Zabadne, A.J.Zierep, P.Gunther, S.Einsle, O.Andrade, S.L.A.

(2024) Sci Adv 10: eadm9441-eadm9441

  • DOI: https://doi.org/10.1126/sciadv.adm9441
  • Primary Citation of Related Structures:  
    8QJ3, 8QJ4, 8QPF

  • PubMed Abstract: 

    Unlike aquaporins or potassium channels, ammonium transporters (Amts) uniquely discriminate ammonium from potassium and water. This feature has certainly contributed to their repurposing as ammonium receptors during evolution. Here, we describe the ammonium receptor Sd-Amt1, where an Amt module connects to a cytoplasmic diguanylate cyclase transducer module via an HAMP domain. Structures of the protein with and without bound ammonium were determined to 1.7- and 1.9-Ångstrom resolution, depicting the ON and OFF states of the receptor and confirming the presence of a binding site for two ammonium cations that is pivotal for signal perception and receptor activation. The transducer domain was disordered in the crystals, and an AlphaFold2 prediction suggests that the helices linking both domains are flexible. While the sensor domain retains the trimeric fold formed by all Amt family members, the HAMP domains interact as pairs and serve to dimerize the transducer domain upon activation.


  • Organizational Affiliation

    Faculty of Chemistry and Pharmacy, Institute for Biochemistry, University Freiburg, Albertstr. 21, 79104 Freiburg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ammonium transporter
A, B
644Shewanella denitrificans OS217Mutation(s): 0 
Gene Names: Sden_0766
Membrane Entity: Yes 
UniProt
Find proteins for Q12R70 (Shewanella denitrificans (strain OS217 / ATCC BAA-1090 / DSM 15013))
Explore Q12R70 
Go to UniProtKB:  Q12R70
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12R70
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.757α = 90
b = 114.757β = 90
c = 278.565γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
HKL-2000data reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyAN-676/3
German Research Foundation (DFG)GermanyGRK-2202

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-12
    Type: Initial release