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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: To Be Published
Title: Cryo-EM structure of TmaT-TMA complexes
Authors: Chao G
History
DepositionJun 14, 2024-
Header (metadata) releaseNov 6, 2024-
Map releaseNov 6, 2024-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing 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

Size
Brightness
Contrast
Others
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

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
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_60548_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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

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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