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- EMDB-18549: Ammonium Transporter Amt1 from Shewanella denitrificans -

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Basic information

Entry
Database: EMDB / ID: EMD-18549
TitleAmmonium Transporter Amt1 from Shewanella denitrificans
Map dataunsharpened map
Sample
  • Complex: homotrimer Amt1
    • Protein or peptide: Ammonium transporter
  • Ligand: water
KeywordsAmmonium Transporter Amt1 / TRANSPORT PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.53 Å
AuthorsGschell M / Zhang L / Einsle O / Andrade S
Funding support Germany, 2 items
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, 2023-
Header (metadata) releaseJun 12, 2024-
Map releaseJun 12, 2024-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18549.png

Downloads & links

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Map

FileDownload / File: emd_18549.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationunsharpened map
Voxel sizeX=Y=Z: 0.84 Å
Density
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.27450183 - 0.46589074
Average (Standard dev.)0.0013840041 (±0.025808003)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 168.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: sharpened map

Fileemd_18549_additional_1.map
Annotationsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_18549_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_18549_half_map_2.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : homotrimer Amt1

EntireName: homotrimer Amt1
Components
  • Complex: homotrimer Amt1
    • Protein or peptide: Ammonium transporter
  • Ligand: water

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Supramolecule #1: homotrimer Amt1

SupramoleculeName: homotrimer Amt1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Shewanella denitrificans (bacteria)

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Macromolecule #1: Ammonium transporter

MacromoleculeName: Ammonium transporter / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Shewanella denitrificans (bacteria)
Molecular weightTheoretical: 73.021875 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSESFLLNLW ILLCACLVLI MQAGFTCFES GNVRNKNSVN VALKNVSDFC VCAVCYWAFG YALMYGNSID GIVGANGFFY STTTNSHET SFFLFQLMFC CTSATIISGA VAERMRFTGY ILVTLLAASL IYPLFGHWAW GGRILGSETS TPGWLEQLGF I DFAGATVV ...String:
MSESFLLNLW ILLCACLVLI MQAGFTCFES GNVRNKNSVN VALKNVSDFC VCAVCYWAFG YALMYGNSID GIVGANGFFY STTTNSHET SFFLFQLMFC CTSATIISGA VAERMRFTGY ILVTLLAASL IYPLFGHWAW GGRILGSETS TPGWLEQLGF I DFAGATVV HSVGGWMALA CVLIIGPRLG RFNNKHGVNQ IFGDNLPLTA LGTFLLFLGW FGFNGGSYGK IDDMLSSVFV NT ALGGTFG GFVVLLICIW QQSLLSIRFV LNGVLAGLVA ITASANSISS IDAATIGGIS GALSFFATIL LEKCKIDDVV SVV PVHLIG GIWGTLALAI FADGQYFIAG NSRVDQFLIQ LLGVVTCGIF AFGLPYMLIR LLNRVYPLRV SPRVEILGLN FGEF GLKSE TFNFLKQMRK NKNSHKNKQA VSVDFFSDIG LIEAEYNAFL EVINLQQRQA DINSHRLSRL AKTDHLTRLN NRLGF DECY DSEWLRMRRE KKPFSLLLID IDHFKLYNDH YGHPRGDQCL QQVALVLAST AKRPADCCAR VGGEEFAILL PDTDSE AGE KIANDINIRL KALEIPHLSS PIMPYVTVSI GIATLTPERY DSLDQAYLYQ CADDALYSAK QAGRNGVKAV IIDEAHE QT KKLDENLYFQ GFEHHHHHH

UniProtKB: Ammonium transporter

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Macromolecule #2: water

MacromoleculeName: water / type: ligand / ID: 2 / Number of copies: 202 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: DARK FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.53 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 477507
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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