1U7C | pdb_00001u7c

Crystal Structure of AmtB from E.Coli with Methyl Ammonium.

• PDB DOI: https://doi.org/10.2210/pdb1U7C/pdb

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


• 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.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.205 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.204 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

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: https://doi.org/10.1126/science.1101952
• Primary Citation 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. 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.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 40.47 kDa 
• Atom Count: 3,139 
• Modeled Residue Count: 383 
• Deposited Residue Count: 385 
• Unique protein chains: 1

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 Entity: Yes
UniProt
Find proteins for P69681 (Escherichia coli (strain K12)) Explore P69681  Go to UniProtKB:  P69681

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NME	B [auth A]	METHYLAMINE C H5 N BAVYZALUXZFZLV-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: 1.85 Å
• R-Value Free:  0.205 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.204 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.7	α = 90
b = 95.7	β = 90
c = 94.6	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• 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: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.4: 2023-08-23
  Changes: Data collection, Refinement description
• Version 1.5: 2023-11-15
  Changes: Data collection
• Version 1.6: 2024-11-13
  Changes: Structure summary