Ammonium Transporter Amt-1 from A. fulgidus (AS)

Experimental Data Snapshot

  • Resolution: 1.54 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.154 

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This is version 1.3 of the entry. See complete history


Crystal structure of the archaeal ammonium transporter Amt-1 from Archaeoglobus fulgidus

Andrade, S.L.Dickmanns, A.Ficner, R.Einsle, O.

(2005) Proc Natl Acad Sci U S A 102: 14994-14999

  • DOI: https://doi.org/10.1073/pnas.0506254102
  • Primary Citation of Related Structures:  
    2B2F, 2B2H, 2B2I, 2B2J

  • PubMed Abstract: 

    Ammonium transporters (Amts) are integral membrane proteins found in all kingdoms of life that fulfill an essential function in the uptake of reduced nitrogen for biosynthetic purposes. Amt-1 is one of three Amts encoded in the genome of the hyperthermophilic archaeon Archaeoglobus fulgidus. The crystal structure of Amt-1 shows a compact trimer with 11 transmembrane helices per monomer and a central channel for substrate conduction in each monomer, similar to the known crystal structure of AmtB from Escherichia coli. Xenon derivatization has been used to identify apolar regions of Amt-1, emphasizing not only the hydrophobicity of the substrate channel but also the unexpected presence of extensive internal cavities that should be detrimental for protein stability. The substrates ammonium and methylammonium have been used for cocrystallization experiments with Amt-1, but the identification of binding sites that are distinct from water positions is not unambiguous. The well ordered cytoplasmic C terminus of the protein in the Amt-1 structure has allowed for the construction of a docking model between Amt-1 and a homology model for its physiological interaction partner, the P(II) protein GlnB-1. In this model, GlnB-1 binds tightly to the cytoplasmic face of the transporter, effectively blocking conduction through the three individual substrate channels.

  • Organizational Affiliation

    Institut für Mikrobiologie und Genetik, Abteilung Molekulare Strukturbiologie, Georg-August-Universität, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. susana.andrade@bio.uni-goettingen.de

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ammonium transporter399Archaeoglobus fulgidusMutation(s): 0 
Gene Names: amt1
Membrane Entity: Yes 
Find proteins for O29285 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16))
Explore O29285 
Go to UniProtKB:  O29285
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO29285
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.54 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.154 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.408α = 90
b = 111.408β = 90
c = 136.644γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-10-11
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2023-10-25
    Changes: Data collection, Database references, Refinement description