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- EMDB-60548: Cryo-EM structure of TmaT-TMA complexes -

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Basic information

Entry
Database: EMDB / ID: EMD-60548
TitleCryo-EM structure of TmaT-TMA complexes
Map data
Sample
  • Complex: sodium-trimethylamine symporter TmaT binding with TMA
    • Protein or peptide: Trimethylamine transporter
  • Ligand: N,N-dimethylmethanamine
KeywordsTMA / ELECTRON TRANSPORT
Function / homologyBCCT transporter family / BCCT, betaine/carnitine/choline family transporter / transmembrane transporter activity / plasma membrane / Trimethylamine transporter
Function and homology information
Biological speciesMyroides profundi (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.09 Å
AuthorsChao G
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: mBio / Year: 2025
Title: Structural basis of a microbial trimethylamine transporter.
Authors: Chao Gao / Hai-Tao Ding / Kang Li / Hai-Yan Cao / Ning Wang / Zeng-Tian Gu / Qing Wang / Mei-Ling Sun / Xiu-Lan Chen / Yin Chen / Yu-Zhong Zhang / Hui-Hui Fu / Chun-Yang Li /
Abstract: Trimethylamine (TMA), a simple trace biogenic amine resulting from the decomposition of proteins and other macromolecules, is ubiquitous in nature. It is found in the human gut as well as in various ...Trimethylamine (TMA), a simple trace biogenic amine resulting from the decomposition of proteins and other macromolecules, is ubiquitous in nature. It is found in the human gut as well as in various terrestrial and marine ecosystems. While the role of TMA in promoting cardiovascular diseases and depolarizing olfactory sensory neurons in humans has only recently been explored, many microbes are well known for their ability to utilize TMA as a carbon, nitrogen, and energy source. Here, we report the first structure of a TMA transporter, TmaT, originally identified from a marine bacterium. TmaT is a member of the betaine-choline-carnitine transporter family, and we show that TmaT is an Na/TMA symporter, which possessed high specificity and binding affinity toward TMA. Furthermore, the structures of TmaT and two TmaT-TMA complexes were solved by cryo-EM. TmaT forms a homotrimer structure in solution. Each TmaT monomer has 12 transmembrane helices, and the TMA transport channel is formed by a four-helix bundle. TMA can move between different aromatic boxes, which provides the structural basis of TmaT importing TMA. When TMA is bound in location I, residues Trp146, Trp151, Tyr154, and Trp326 form an aromatic box to accommodate TMA. Moreover, Met105 also plays an important role in the binding of TMA. When TMA is transferred to location II, it is bound in the aromatic box formed by Trp325, Trp326, and Trp329. Based on our results, we proposed the TMA transport mechanism by TmaT. This study provides novel insights into TMA transport across biological membranes.
IMPORTANCE: The volatile trimethylamine (TMA) plays an important role in promoting cardiovascular diseases and depolarizing olfactory sensory neurons in humans and serves as a key nutrient source for ...IMPORTANCE: The volatile trimethylamine (TMA) plays an important role in promoting cardiovascular diseases and depolarizing olfactory sensory neurons in humans and serves as a key nutrient source for a variety of ubiquitous marine microbes. While the TMA transporter TmaT has been identified from a marine bacterium, the structure of TmaT and the molecular mechanism involved in TMA transport remain unclear. In this study, we elucidated the high-resolution cryo-EM structures of TmaT and TmaT-TMA complexes and revealed the TMA binding and transport mechanisms by structural and biochemical analyses. The results advance our understanding of the TMA transport processes across biological membranes.
History
DepositionJun 14, 2024-
Header (metadata) releaseNov 6, 2024-
Map releaseNov 6, 2024-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60548.png

Downloads & links

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Map

FileDownload / File: emd_60548.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 256 pix.
= 271.36 Å		1.06 Å/pix.
x 256 pix.
= 271.36 Å		1.06 Å/pix.
x 256 pix.
= 271.36 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.31
Minimum - Maximum-1.1800587 - 1.9030557
Average (Standard dev.)0.0042946953 (±0.047624603)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 271.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_60548_half_map_1.map
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Half map: #1

Fileemd_60548_half_map_2.map
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Sample components

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Entire : sodium-trimethylamine symporter TmaT binding with TMA

EntireName: sodium-trimethylamine symporter TmaT binding with TMA
Components
  • Complex: sodium-trimethylamine symporter TmaT binding with TMA
    • Protein or peptide: Trimethylamine transporter
  • Ligand: N,N-dimethylmethanamine

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Supramolecule #1: sodium-trimethylamine symporter TmaT binding with TMA

SupramoleculeName: sodium-trimethylamine symporter TmaT binding with TMA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Myroides profundi (bacteria)

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Macromolecule #1: Trimethylamine transporter

MacromoleculeName: Trimethylamine transporter / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Myroides profundi (bacteria)
Molecular weightTheoretical: 59.955051 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MFKKLLDNKN LVINPPVFIT SILLIVALIL TCVLFPEKVG VWFPAAQLAV TSNFGWFFVV TVNVILIFAI YLAFSKFGRI RLGGDDAEP EFTKASWFAM LFSTGMGIGI MFFSIAEPVS HFFNTPRPVD TDIEAAVQAM QFTSLHWGLH AWGIYAMVGL A LAFFGFNR ...String:
MFKKLLDNKN LVINPPVFIT SILLIVALIL TCVLFPEKVG VWFPAAQLAV TSNFGWFFVV TVNVILIFAI YLAFSKFGRI RLGGDDAEP EFTKASWFAM LFSTGMGIGI MFFSIAEPVS HFFNTPRPVD TDIEAAVQAM QFTSLHWGLH AWGIYAMVGL A LAFFGFNR KLPMTFRSLF YPFWGERIHG WWGHIIDILS ALATVFGLST SLGLGVIQIT AGLEYLYGWE ISPMMQAGII LF VIGIATI SVFSGLDKGV KILSNANMYI AASFMLLIFI LGPTLFIMKG YVENTGAYLA NFIDISTWND TYLGSGWQNV WTI FYWAWW IAWSPFVGSF IARISKGRTV KEFVLGVLIV PGLITLLWMN VFGGSALHTI LSGDVTMIAA VKADVSTALF VFLE NFPFT KFLSIVAIIL IFSFFITSSD SGSLVVDNIT SGSNGESPVW QRVFWSFAQG IIAIVLLWGG GLDALQTAVI ITGLP FAVI LLVMCYSLQK GLKEELAKSS KKAKSKEEKS YKEIIAELLD EPQSKHHHHH HHHHH

UniProtKB: Trimethylamine transporter

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Macromolecule #2: N,N-dimethylmethanamine

MacromoleculeName: N,N-dimethylmethanamine / type: ligand / ID: 2 / Number of copies: 3 / Formula: KEN
Molecular weightTheoretical: 59.11 Da
Chemical component information

ChemComp-KEN:
N,N-dimethylmethanamine

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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: 8
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: 50.23 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: 4D-STEM / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.09 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 148358
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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