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- EMDB-72036: Cryo-EM structure of the isethionate TRAP transporter IseQM from ... -

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Basic information

Entry
Database: EMDB / ID: EMD-72036
TitleCryo-EM structure of the isethionate TRAP transporter IseQM from Oleidesulfovibrio alaskensis with bound isethionate
Map dataCryoSPARC unsharpened
Sample
  • Complex: IseQM complexed with Megabody C7HopQ
    • Protein or peptide: Isethionate TRAP transporter permease protein DctMQ
    • Protein or peptide: Megabody C7HopQ
  • Ligand: SODIUM ION
  • Ligand: 2-hydroxyethylsulfonic acid
  • Ligand: PHOSPHATIDYLETHANOLAMINE
KeywordsTRAP Transporter / Megabody / Isethionate / TRANSPORT PROTEIN
Function / homologyTRAP transporter large membrane protein DctM / TRAP C4-dicarboxylate transport system permease DctM subunit / : / Tripartite ATP-independent periplasmic transporters, DctQ component / Tripartite ATP-independent periplasmic transporter, DctM component / alkanesulfonate catabolic process / transmembrane transporter activity / plasma membrane / Isethionate TRAP transporter permease protein DctMQ
Function and homology information
Biological speciesOleidesulfovibrio alaskensis G20 (bacteria) / Helicobacter pylori (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.98 Å
AuthorsNewton-Vesty MC / Davies JS / Dobson RCJ
Funding support New Zealand, 1 items
OrganizationGrant numberCountry
Marsden Fund New Zealand
CitationJournal: Structure / Year: 2025
Title: Structural basis of isethionate transport by a TRAP transporter from a sulfate-reducing bacterium
Authors: Newton-Vesty MC / Scalise M / Jamieson SA / Currie MJ / Brown HG / Valimehr S / Tillett ZD / Hall KR / Quan S / Allison JR / Whitten AE / Panjikar S / Indiveri C / Hanssen E / Mace PD / ...Authors: Newton-Vesty MC / Scalise M / Jamieson SA / Currie MJ / Brown HG / Valimehr S / Tillett ZD / Hall KR / Quan S / Allison JR / Whitten AE / Panjikar S / Indiveri C / Hanssen E / Mace PD / North RA / Dobson RC / Davies JS
History
DepositionAug 7, 2025-
Header (metadata) releaseNov 12, 2025-
Map releaseNov 12, 2025-
UpdateNov 12, 2025-
Current statusNov 12, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72036.png

Downloads & links

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Map

FileDownload / File: emd_72036.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoSPARC unsharpened
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.64 Å/pix.
x 400 pix.
= 255.6 Å		0.64 Å/pix.
x 400 pix.
= 255.6 Å		0.64 Å/pix.
x 400 pix.
= 255.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.639 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.075
Minimum - Maximum-0.17036955 - 0.34780687
Average (Standard dev.)-0.0006374799 (±0.008470986)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 255.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A

Fileemd_72036_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 B

Fileemd_72036_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : IseQM complexed with Megabody C7HopQ

EntireName: IseQM complexed with Megabody C7HopQ
Components
  • Complex: IseQM complexed with Megabody C7HopQ
    • Protein or peptide: Isethionate TRAP transporter permease protein DctMQ
    • Protein or peptide: Megabody C7HopQ
  • Ligand: SODIUM ION
  • Ligand: 2-hydroxyethylsulfonic acid
  • Ligand: PHOSPHATIDYLETHANOLAMINE

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Supramolecule #1: IseQM complexed with Megabody C7HopQ

SupramoleculeName: IseQM complexed with Megabody C7HopQ / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Oleidesulfovibrio alaskensis G20 (bacteria)

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Macromolecule #1: Isethionate TRAP transporter permease protein DctMQ

MacromoleculeName: Isethionate TRAP transporter permease protein DctMQ / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oleidesulfovibrio alaskensis G20 (bacteria)
Molecular weightTheoretical: 67.592578 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSDPNVTATI MNAQGECSSG SLESRPGILG WLDANFEKPF LVAGMLAIIF IITFQTLYRY IGVYLHEGAA AAVWTEEMAR FIFIWISYL AVPVAIKNRS SIRVDIIFDR LPVRFQNISW IIVDVCFLTL AATVLWQSLD LIKMQLTYPQ TSPALQLPYY I PYLVLPVS ...String:
MSDPNVTATI MNAQGECSSG SLESRPGILG WLDANFEKPF LVAGMLAIIF IITFQTLYRY IGVYLHEGAA AAVWTEEMAR FIFIWISYL AVPVAIKNRS SIRVDIIFDR LPVRFQNISW IIVDVCFLTL AATVLWQSLD LIKMQLTYPQ TSPALQLPYY I PYLVLPVS FGLMAVRLLQ DLAGQVRICG AADTVIGLIL CAVLAAPLFI ADYIDPLPVL FGYFALFLVV GVPIAIGLGL AA LATIVAA GSLPIDYVAQ IAFTSIDSFP IMAIPFFIAA GVFMGAGGLS RRLLNLADEM LGALPGGMAL ATIGTCMFFA AIS GSGPAT VAAIGSLTIP AMVERGYCKY FSAAIVAAAG AIGVMIPPSN PFVVYGVSAQ ASIGKLFMGG IVPGLLTGLA LMAY SYWYS KKRGWKGEVR DRNLKTFMHA VWEAKWALMV PVIVLGGIYG GIMTPTEAAA LAAFYGLIIG CFVHRELSCG SFYDC VVEA AGTSAMVIVL MSMATIFGNI MTIEEVPTTI AQAMLGLTTD KIAILLMINV LLLIIGTFME ALAAIVILTP ILLPIV LKV GVDPVHFGII MVVNLAIGFV TPPVGVNLFV ASGVANAKIE QLSKVVLPLI ALMLAVLLIT TYVPAIPMFF AG

UniProtKB: Isethionate TRAP transporter permease protein DctMQ

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Macromolecule #2: Megabody C7HopQ

MacromoleculeName: Megabody C7HopQ / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Helicobacter pylori (bacteria)
Molecular weightTheoretical: 55.463898 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: QVSLQESGGG LVQTKTTTSV IDTTNDAQNL LTQAQTIVNT LKDYCPILIA KSSSSNGGTN NANTPSWQTA GGGKNSCATF GAEFSAASD MINNAQKIVQ ETQQLSANQP KNITQPHNLN LNSPSSLTAL AQKMLKNAQS QAEILKLANQ VESDFNKLSS G HLKDYIGK ...String:
QVSLQESGGG LVQTKTTTSV IDTTNDAQNL LTQAQTIVNT LKDYCPILIA KSSSSNGGTN NANTPSWQTA GGGKNSCATF GAEFSAASD MINNAQKIVQ ETQQLSANQP KNITQPHNLN LNSPSSLTAL AQKMLKNAQS QAEILKLANQ VESDFNKLSS G HLKDYIGK CDASAISSAN MTMQNQKNNW GNGCAGVEET QSLLKTSAAD FNNQTPQINQ AQNLANTLIQ ELGNNTYEQL SR LLTNDNG TNSKTSAQAI NQAVNNLNER AKTLAGGTTN SPAYQATLLA LRSVLGLWNS MGYAVICGGY TKSPGENNQK DFH YTDENG NGTTINCGGS TNSNGTHSYN GTNTLKADKN VSLSIEQYEK IHEAYQILSK ALKQAGLAPL NSKGEKLEAH VTTS KYAGG SLRLSCAASG NIFLWANMGW YRQAPGKERE FVASISLGAN TNYADSVKGR FTISRDNAKN TVYLQMNSLK QEDTA VYYC AVWARYPSTY YLGRGYDYLY WGQGTQVTVS S

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Macromolecule #3: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 3 / Number of copies: 1
Molecular weightTheoretical: 22.99 Da

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Macromolecule #4: 2-hydroxyethylsulfonic acid

MacromoleculeName: 2-hydroxyethylsulfonic acid / type: ligand / ID: 4 / Number of copies: 1 / Formula: 8X3
Molecular weightTheoretical: 126.132 Da
Chemical component information

ChemComp-8X3:
2-hydroxyethylsulfonic acid

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Macromolecule #5: PHOSPHATIDYLETHANOLAMINE

MacromoleculeName: PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 5 / Number of copies: 3 / Formula: PTY
Molecular weightTheoretical: 734.039 Da
Chemical component information

ChemComp-PTY:
PHOSPHATIDYLETHANOLAMINE / phospholipid*YM

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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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 66.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 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: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 83854
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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