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- PDB-8qpf: Ammonium Transporter Amt1 from Shewanella denitrificans -

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Basic information

Entry
Database: PDB / ID: 8qpf
TitleAmmonium Transporter Amt1 from Shewanella denitrificans
ComponentsAmmonium transporter
KeywordsTRANSPORT PROTEIN / Ammonium Transporter Amt1
Function / homology
Function and homology information


ammonium homeostasis / ammonium channel activity / plasma membrane
Similarity search - Function
Ammonium transporter / Ammonium transporter AmtB-like domain / Ammonium Transporter Family / Ammonium/urea transporter / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / Nucleotide cyclase / Reverse transcriptase/Diguanylate cyclase domain
Similarity search - Domain/homology
Ammonium transporter
Similarity search - Component
Biological speciesShewanella denitrificans (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.53 Å
AuthorsGschell, M. / Zhang, L. / Einsle, O. / Andrade, S.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)AN-676/3 Germany
German Research Foundation (DFG)GRK-2202 Germany
CitationJournal: Sci Adv / Year: 2024
Title: How sensor Amt-like proteins integrate ammonium signals.
Authors: Tobias Pflüger / Mathias Gschell / Lin Zhang / Volodymyr Shnitsar / Annas J Zabadné / Paul Zierep / Stefan Günther / Oliver Einsle / Susana L A Andrade /
Abstract: Unlike aquaporins or potassium channels, ammonium transporters (Amts) uniquely discriminate ammonium from potassium and water. This feature has certainly contributed to their repurposing as ammonium ...Unlike aquaporins or potassium channels, ammonium transporters (Amts) uniquely discriminate ammonium from potassium and water. This feature has certainly contributed to their repurposing as ammonium receptors during evolution. Here, we describe the ammonium receptor Sd-Amt1, where an Amt module connects to a cytoplasmic diguanylate cyclase transducer module via an HAMP domain. Structures of the protein with and without bound ammonium were determined to 1.7- and 1.9-Ångstrom resolution, depicting the ON and OFF states of the receptor and confirming the presence of a binding site for two ammonium cations that is pivotal for signal perception and receptor activation. The transducer domain was disordered in the crystals, and an AlphaFold2 prediction suggests that the helices linking both domains are flexible. While the sensor domain retains the trimeric fold formed by all Amt family members, the HAMP domains interact as pairs and serve to dimerize the transducer domain upon activation.
History
DepositionOct 1, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ammonium transporter
B: Ammonium transporter
C: Ammonium transporter


Theoretical massNumber of molelcules
Total (without water)219,0663
Polymers219,0663
Non-polymers00
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Ammonium transporter


Mass: 73021.875 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella denitrificans (bacteria) / Gene: Sden_0766 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: Q12R70
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: homotrimer Amt1 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Shewanella denitrificans (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: DARK FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 2.53 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 477507 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0059099
ELECTRON MICROSCOPYf_angle_d0.81512372
ELECTRON MICROSCOPYf_dihedral_angle_d4.9561227
ELECTRON MICROSCOPYf_chiral_restr0.051440
ELECTRON MICROSCOPYf_plane_restr0.0071533

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