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1U7G|pdb_00001u7g
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 (Depositor), 0.160 (DCC)
- R-Value Work: 0.133 (Depositor), 0.120 (DCC)
- R-Value Observed: 0.137 (Depositor)
Starting Model:experimental
View more details
Download MendeleyMechanism 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.
- Department of Biochemistry and Biophysics, S412C Genentech Hall, University of California-San Francisco, 600 16th Street, San Francisco, CA 94143-2240, USA.
Organizational Affiliation:
Explore in 3D: Structure |Sequence Annotations |Electron Density |Validation Report |Ligand Interaction (BOG) |Predict Membrane
Global Symmetry: Cyclic - C3 (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3
Find Similar Assemblies
Biological assembly 1 assigned by authors and generated by PISA,PQS (software)
Macromolecule Content
- Total Structure Weight: 40.8 kDa
- Atom Count: 3,286
- Modeled Residue Count: 383
- Deposited Residue Count: 385
- Unique protein chains: 1
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Probable ammonium transporter | 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 AnnotationsExpand | |||||
| |||||
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| BOG Query on BOG Download Ideal Coordinates CCD File | B [auth A] | octyl beta-D-glucopyranoside C14 H28 O6 HEGSGKPQLMEBJL-RKQHYHRCSA-N |  | ||
| NH4 Query on NH4 Download Ideal Coordinates CCD File | C [auth A] | AMMONIUM ION H4 N QGZKDVFQNNGYKY-UHFFFAOYSA-O |  | ||
| NH3 Query on NH3 Download Ideal Coordinates CCD File | 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 Query on MSE | A | L-PEPTIDE LINKING | C5 H11 N O2 Se |  | MET |
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.40 Å
- R-Value Free: 0.168 (Depositor), 0.160 (DCC)
- R-Value Work: 0.133 (Depositor), 0.120 (DCC)
- R-Value Observed: 0.137 (Depositor)
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 96.541 | α = 90 |
| b = 96.541 | β = 90 |
| c = 94.622 | γ = 120 |
| Software Name | Purpose |
|---|---|
| DENZO | data reduction |
| SCALEPACK | data scaling |
| CNS | refinement |
| SHELX | refinement |
| CNS | phasing |
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 - Version 1.7: 2024-10-16
Changes: Structure summary
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RCSB PDB Core Operations are funded by theU.S. National Science Foundation (DBI-2321666), theUS Department of Energy (DE-SC0019749), and theNational Cancer Institute,National Institute of Allergy and Infectious Diseases, andNational Institute of General Medical Sciences of theNational Institutes of Health under grant R01GM157729.