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- PDB-9xou: CryoEM structure of LacY with Trimbody -

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Basic information

Entry
Database: PDB / ID: 9xou
TitleCryoEM structure of LacY with Trimbody
Components
  • H3-PrAC-5350A,2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase
  • LacY-nanobody-TAIL
  • 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 speciessynthetic construct (others)
Thermotoga maritima (bacteria)
Escherichia coli K-12 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsSong, J.Y. / Wang, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: CryoEM structure of LacY with Trimbody
Authors: Song, J.Y. / Wang, W.
History
DepositionNov 15, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 11, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: H3-PrAC-5350A,2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase
B: H3-PrAC-5350A,2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase
C: H3-PrAC-5350A,2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase
D: LacY-nanobody-TAIL
E: LacY-nanobody-TAIL
F: LacY-nanobody-TAIL
G: Lactose permease
H: Lactose permease
I: Lactose permease


Theoretical massNumber of molelcules
Total (without water)340,7249
Polymers340,7249
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein H3-PrAC-5350A,2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase


Mass: 36127.930 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others), (gene. exp.) Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8) (bacteria)
Strain: ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8
Gene: TM_0066 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WXS1
#2: Antibody LacY-nanobody-TAIL


Mass: 28210.102 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#3: Protein Lactose permease / Lactose-proton symport


Mass: 49236.590 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: lacY, b0343, JW0334 / Production host: Escherichia coli (E. coli) / References: UniProt: P02920
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: CryoEM structure of LacY with Trimbody / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
21Escherichia coli K-12 (bacteria)83333
31Thermotoga maritima (bacteria)243274strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 371100 / Symmetry type: POINT

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