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- EMDB-64015: CryoEM structure of human Galectin-10 with iTrimbody -

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Basic information

Entry
Database: EMDB / ID: EMD-64015
TitleCryoEM structure of human Galectin-10 with iTrimbody
Map data
Sample
  • Complex: CryoEM structure of human Galectin-10 with iTrimbody
    • Complex: PrAC-5350A
      • Protein or peptide: PrAC-5350A,2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase
    • Complex: hGal10-nanobody
      • Protein or peptide: hGal10-nanobody
    • Complex: hGalectin-10
      • Protein or peptide: Galectin-10
KeywordsSTRUCTURAL PROTEIN
Function / homology
Function and homology information


D-galactonate catabolic process / 2-dehydro-3-deoxy-6-phosphogalactonate aldolase activity / regulation of activated T cell proliferation / regulation of T cell cytokine production / T cell apoptotic process / regulation of T cell anergy / : / carbohydrate binding / identical protein binding / cytosol
Similarity search - Function
KDPG/KHG aldolase / KDPG and KHG aldolase / Galectin-like / Galactoside-binding lectin / Galectin / Galectin, carbohydrate recognition domain / Galactoside-binding lectin / Galactoside-binding lectin (galectin) domain profile. / Concanavalin A-like lectin/glucanase domain superfamily / Aldolase-type TIM barrel
Similarity search - Domain/homology
Galectin-10 / 2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase
Similarity search - Component
Biological speciesThermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8) (bacteria) / Thermotoga maritima MSB8 (bacteria) / synthetic construct (others) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.62 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 human Galectin-10 with iTrimbody
Authors: Song JY / Wang W
History
DepositionApr 3, 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_64015.png

Downloads & links

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Map

FileDownload / File: emd_64015.map.gz / Format: CCP4 / Size: 137.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 330 pix.
= 303.6 Å		0.92 Å/pix.
x 330 pix.
= 303.6 Å		0.92 Å/pix.
x 330 pix.
= 303.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.92 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.0018115761 - 2.0167792
Average (Standard dev.)0.000041363845 (±0.03292293)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions330330330
Spacing330330330
CellA=B=C: 303.6 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 human Galectin-10 with iTrimbody

EntireName: CryoEM structure of human Galectin-10 with iTrimbody
Components
  • Complex: CryoEM structure of human Galectin-10 with iTrimbody
    • Complex: PrAC-5350A
      • Protein or peptide: PrAC-5350A,2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase
    • Complex: hGal10-nanobody
      • Protein or peptide: hGal10-nanobody
    • Complex: hGalectin-10
      • Protein or peptide: Galectin-10

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Supramolecule #1: CryoEM structure of human Galectin-10 with iTrimbody

SupramoleculeName: CryoEM structure of human Galectin-10 with iTrimbody / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8) (bacteria)

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Supramolecule #2: PrAC-5350A

SupramoleculeName: PrAC-5350A / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1

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Supramolecule #3: hGal10-nanobody

SupramoleculeName: hGal10-nanobody / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2

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Supramolecule #4: hGalectin-10

SupramoleculeName: hGalectin-10 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3

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

MacromoleculeName: PrAC-5350A,2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase
type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Thermotoga maritima MSB8 (bacteria)
Strain: ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8
Molecular weightTheoretical: 28.13968 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: QANAFAQILN MPNLTEEQRN GFIQSLKDDP SVSKEILAEA KKLNEHQAAK AEEAARKMEE LFKKHKIVAV LRANSVEEAI EKAVAVFAG GVHLIEITFT VPDADTVIKA LSVLKEKGAI IGAGTVTSVE QCRKAVESGA EFIVSPHLDE EISQFCKEKG V FYMPGVMT ...String:
QANAFAQILN MPNLTEEQRN GFIQSLKDDP SVSKEILAEA KKLNEHQAAK AEEAARKMEE LFKKHKIVAV LRANSVEEAI EKAVAVFAG GVHLIEITFT VPDADTVIKA LSVLKEKGAI IGAGTVTSVE QCRKAVESGA EFIVSPHLDE EISQFCKEKG V FYMPGVMT PTELVKAMKL GHTILKLFPG EVVGPQFVKA MKGPFPNVKF VPTGGVNLDN VCEWFKAGVL AVGVGSALVK GT PDEVREK AKAFVEKIRG CTE

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

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Macromolecule #2: hGal10-nanobody

MacromoleculeName: hGal10-nanobody / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 12.480675 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
EVQLLESGGG SVQAGGSLRL SCTASGYTYS VAWFRQAPGN EREGVAVISN YGATTYSDSV KGRFTISRDN AKNAVSLQMN SLKSEDTAM YYCAAGSAFS LSPGRFPYWG QGTQVTVSS

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Macromolecule #3: Galectin-10

MacromoleculeName: Galectin-10 / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.183442 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SLLPVPYTEA ASLSTGSTVT IKGRPLACFL NEPYLQVDFH TEMKEESDIV FHFQVCFGRR VVMNSREYGA WKQQVESKNM PFQDGQEFE LSISVLPDKY QVMVNGQSSY TFDHRIKPEA VKMVQVWRDI SLTKFNVSYL K

UniProtKB: Galectin-10

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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 correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.62 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 700092
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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