1U7G

Crystal Structure of Ammonia Channel AmtB from E. Coli

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.133 
  • R-Value Observed: 0.137 

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This is version 1.4 of the entry. See complete history. 


Literature

Mechanism of ammonia transport by Amt/MEP/Rh: structure of AmtB at 1.35 A

Khademi, S., O'Connell III, J., Remis, J., Robles-Colmenares, Y., Miercke, L.J.W., Stroud, R.M.

(2004) Science 305: 1587-1594

  • DOI: 10.1126/science.1101952
  • Primary Citation of Related Structures:  
    1U77, 1U7C, 1U7G

  • PubMed Abstract: 

    • The first structure of an ammonia channel from the Amt/MEP/Rh protein superfamily, determined to 1.35 angstrom resolution, shows it to be a channel that spans the membrane 11 times. Two structurally similar halves span the membrane with opposite polarity ...

    The first structure of an ammonia channel from the Amt/MEP/Rh protein superfamily, determined to 1.35 angstrom resolution, shows it to be a channel that spans the membrane 11 times. Two structurally similar halves span the membrane with opposite polarity. Structures with and without ammonia or methyl ammonia show a vestibule that recruits NH4+/NH3, a binding site for NH4+, and a 20 angstrom-long hydrophobic channel that lowers the NH4+ pKa to below 6 and conducts NH3. Favorable interactions for NH3 are seen within the channel and use conserved histidines. Reconstitution of AmtB into vesicles shows that AmtB conducts uncharged NH3.

    Organizational Affiliation: 

    Department of Biochemistry and Biophysics, S412C Genentech Hall, University of California-San Francisco, 600 16th Street, San Francisco, CA 94143-2240, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Probable ammonium transporterA385Escherichia coliMutation(s): 14 
Gene Names: amtB
Membrane Entity: Yes 
UniProt
Find proteins for P69681 (Escherichia coli (strain K12))
Explore P69681 
Go to UniProtKB:  P69681
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP69681
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BOG
Query on BOG
Download Ideal Coordinates CCD File 
B [auth A]octyl beta-D-glucopyranoside
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N		 Ligand Interaction
NH4
Query on NH4
Download Ideal Coordinates CCD File 
C [auth A]AMMONIUM ION
H4 N
QGZKDVFQNNGYKY-UHFFFAOYSA-O		 Ligand Interaction
NH3
Query on NH3
Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A]		AMMONIA
H3 N
QGZKDVFQNNGYKY-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE		A L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.133 
  • R-Value Observed: 0.137 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.541α = 90
b = 96.541β = 90
c = 94.622γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
SHELXrefinement
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-09-21
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.4: 2021-10-20
    Changes: Database references, Structure summary