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- EMDB-67094: CryoEM structure of LacY with Trimbody -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-67094
TitleCryoEM structure of LacY with Trimbody
Map data
Sample
  • Complex: CryoEM structure of LacY with Trimbody
    • Protein or peptide: H3-PrAC-5350A,2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase
    • Protein or peptide: LacY-nanobody-TAIL
    • Protein or peptide: Lactose permease
KeywordsSTRUCTURAL PROTEIN
Function / homology
Function and homology information


lactose:proton symporter activity / lactose transport / D-galactonate catabolic process / carbohydrate:proton symporter activity / 2-dehydro-3-deoxy-6-phosphogalactonate aldolase activity / lactose binding / carbohydrate transport / membrane / plasma membrane
Similarity search - Function
LacY/RafB permease family / LacY/RafB permease family, conserved site / LacY proton/sugar symporter / LacY family proton/sugar symporters signature 1. / LacY family proton/sugar symporters signature 2. / KDPG/KHG aldolase / KDPG and KHG aldolase / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily / Aldolase-type TIM barrel
Similarity search - Domain/homology
Lactose permease / 2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria) / Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8) (bacteria) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsSong JY / Wang W
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: CryoEM structure of LacY with Trimbody
Authors: Song JY / Wang W
History
DepositionNov 15, 2025-
Header (metadata) releaseFeb 11, 2026-
Map releaseFeb 11, 2026-
UpdateFeb 11, 2026-
Current statusFeb 11, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_67094.png

Downloads & links

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Map

FileDownload / File: emd_67094.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 450 pix.
= 418.5 Å		0.93 Å/pix.
x 450 pix.
= 418.5 Å		0.93 Å/pix.
x 450 pix.
= 418.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.001938713 - 2.185758
Average (Standard dev.)-0.0013514216 (±0.017909387)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 418.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : CryoEM structure of LacY with Trimbody

EntireName: CryoEM structure of LacY with Trimbody
Components
  • Complex: CryoEM structure of LacY with Trimbody
    • Protein or peptide: H3-PrAC-5350A,2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase
    • Protein or peptide: LacY-nanobody-TAIL
    • Protein or peptide: Lactose permease

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Supramolecule #1: CryoEM structure of LacY with Trimbody

SupramoleculeName: CryoEM structure of LacY with Trimbody / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli K-12 (bacteria)

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Macromolecule #1: H3-PrAC-5350A,2-dehydro-3-deoxyphosphogluconate aldolase/4-hydrox...

MacromoleculeName: H3-PrAC-5350A,2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase
type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8) (bacteria)
Strain: ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8
Molecular weightTheoretical: 36.12793 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKEIAKIVAE LLRGIARIID DIKGRDREEE VEILAKAVEK TGKPEDVRLA LEAAERGVTL DQAKAIAQIL SMPNLTDEQK RGFVQSLLD DPSVSKEILA EAKKLNEHQA AKAEEAARKM EELFKKHKIV AVLRANSVEE AIEKAVAVFA GGVHLIEITF T VPDADTVI ...String:
MKEIAKIVAE LLRGIARIID DIKGRDREEE VEILAKAVEK TGKPEDVRLA LEAAERGVTL DQAKAIAQIL SMPNLTDEQK RGFVQSLLD DPSVSKEILA EAKKLNEHQA AKAEEAARKM EELFKKHKIV AVLRANSVEE AIEKAVAVFA GGVHLIEITF T VPDADTVI KALSVLKEKG AIIGAGTVTS VEQCRKAVES GAEFIVSPHL DEEISQFCKE KGVFYMPGVM TPTELVKAMK LG HTILKLF PGEVVGPQFV KAMKGPFPNV KFVPTGGVNL DNVCEWFKAG VLAVGVGSAL VKGTPDEVRE KAKAFVEKIR GCT EAAALE HHHHHH

UniProtKB: 2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase

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Macromolecule #2: LacY-nanobody-TAIL

MacromoleculeName: LacY-nanobody-TAIL / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 28.210102 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MQVQLVESGG RLVQAGDSLR LSCAASGRTF TTYLMGWFRQ APGKEREFVA AIRWSGGSTY YADSVKGRFT ISRDNAKNTV YLQMNSLKL EDTAVYYCAA AARPSYSGDY GYTEALRYDY WGQGTLVAVV KTVEDAFLAL LALEQHLGVQ PADLAALAEK L NLSQLLEL ...String:
MQVQLVESGG RLVQAGDSLR LSCAASGRTF TTYLMGWFRQ APGKEREFVA AIRWSGGSTY YADSVKGRFT ISRDNAKNTV YLQMNSLKL EDTAVYYCAA AARPSYSGDY GYTEALRYDY WGQGTLVAVV KTVEDAFLAL LALEQHLGVQ PADLAALAEK L NLSQLLEL GELLKAAGHP LAPQVEALLK EKLKAASAAE AAGVIFQALV KDEELGKKIL EWAKEFGTEE AKKAIEIAEK AY ELYKKYG SWSHPQFEK

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Macromolecule #3: Lactose permease

MacromoleculeName: Lactose permease / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 49.23659 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MYYLKNTNFW MFGLFFFFYF FIMGAYFPFF PIWLHDINHI SKSDTWIIFA AISLFSLLFQ PLFGLLSDKL GLRKYLLWII TGMLVMFAP FFIFIFGPLL QYNILVGSIV GGIYLGFSFN AGAPAVEAFI EKVSRRSNFE FGRARMFGAV GWALVASIVG I MFTINNQF ...String:
MYYLKNTNFW MFGLFFFFYF FIMGAYFPFF PIWLHDINHI SKSDTWIIFA AISLFSLLFQ PLFGLLSDKL GLRKYLLWII TGMLVMFAP FFIFIFGPLL QYNILVGSIV GGIYLGFSFN AGAPAVEAFI EKVSRRSNFE FGRARMFGAV GWALVASIVG I MFTINNQF VFWLGSGMAL ILAVLLFFAK TDAPSSATVA NAVGANHSAF SLKLALELFR QPKLWFLSLY VIGVSSTYDV FD QQFANFF TSFFATGEQG TRVFWYVTTM GELLNASIMF FAPLIINRIG GKNALLLAGT IMSVRIIGSS FATSALEVVI LKT LHMFEV PFLLVGSFKY ITSQFEVRFS ATIYLVAFAF FKQLAMIFMS VLAGNMYESI GFQGAYLVLG LVALGFTLIS VFTL SGPGP LSLLRRQVNE VAWSHPQFEK GSHHHHHHHH HH

UniProtKB: Lactose permease

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 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: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 371100
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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