Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 40.80 kDa 
• Atom Count: 3286 
• Modelled Residue Count: 383 
• Deposited Residue Count: 385 
• Unique protein chains: 1

1U7G

Crystal Structure of Ammonia Channel AmtB from E. Coli

• DOI: 10.2210/pdb1U7G/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2004-08-03 Released: 2004-09-21 
• Deposition Author(s): Khademi, S., O'Connell III, J., Remis, J., Robles-Colmenares, Y., Miercke, L.J.W., Stroud, R.M.

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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 

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

• PubMed: 15361618 
• DOI: 10.1126/science.1101952
• Primary Citation of Related Structures:  
  1U7G, 1U7C, 1U77


• 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. 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.

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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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable ammonium transporter	A	385	Escherichia coli	Mutation(s): 14  Gene Names: amtB
Membrane protein Mpstruc	Group:  TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group:  Channels: Amt/Mep/Rh proteins	Protein:  AmtB ammonia channel (mutant)
Find proteins for P69681 (Escherichia coli (strain K12)) Explore P69681  Go to UniProtKB:  P69681

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BOG	B [auth A]	octyl beta-D-glucopyranoside C14 H28 O6 HEGSGKPQLMEBJL-RKQHYHRCSA-N
NH4	C [auth A]	AMMONIUM ION H4 N QGZKDVFQNNGYKY-UHFFFAOYSA-O
NH3	D [auth A], E [auth A], F [auth A]	AMMONIA H3 N QGZKDVFQNNGYKY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

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 = 96.541	α = 90
b = 96.541	β = 90
c = 94.622	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
SHELX	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-08-03 
• Released Date: 2004-09-21 
Deposition Author(s): Khademi, S., O'Connell III, J., Remis, J., Robles-Colmenares, Y., Miercke, L.J.W., Stroud, R.M.

Revision History  

• 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