1U7G

Crystal Structure of Ammonia Channel AmtB from E. Coli

PDB DOI: https://doi.org/10.2210/pdb1U7G/pdb

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

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: 1.40 Å
R-Value Free: 0.168
R-Value Work: 0.133
R-Value Observed: 0.137

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.6 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

PubMed: 15361618 Search on PubMed
DOI: https://doi.org/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. 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.

Macromolecule Content

Total Structure Weight: 40.8 kDa
Atom Count: 3,286
Modelled Residue Count: 383
Deposited Residue Count: 385
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P69681
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BOG Query on BOG Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	octyl beta-D-glucopyranoside C₁₄ H₂₈ O₆ HEGSGKPQLMEBJL-RKQHYHRCSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
NH4 Query on NH4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	AMMONIUM ION H₄ N QGZKDVFQNNGYKY-UHFFFAOYSA-O		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
NH3 Query on NH3 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A]	D [auth A], E [auth A], F [auth A]	AMMONIA H₃ N QGZKDVFQNNGYKY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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

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Ligand Structure Quality Assessment

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 (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
Version 1.5: 2023-08-23
Changes: Data collection, Refinement description
Version 1.6: 2023-11-15
Changes: Data collection