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- EMDB-64936: Lectin FRIL from Lablab purpureus with self glycan -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-64936
TitleLectin FRIL from Lablab purpureus with self glycan
Map data
Sample
  • Complex: Tetrameric structure of rFRIL-wt apo form with self-glycan
    • Protein or peptide: Flt3 receptor-interacting lectin
  • Ligand: CALCIUM ION
  • Ligand: MANGANESE (II) ION
  • Ligand: water
KeywordsFlt3 receptor-interacting lectin / carbohydrate binding protein / lectin / glycoprotein / self glycan / FRIL / PLANT PROTEIN
Function / homology
Function and homology information


protein storage vacuole lumen / carbohydrate binding
Similarity search - Function
Legume lectin / Legume lectin, alpha chain, conserved site / Legume lectins alpha-chain signature. / Legume lectins beta-chain signature. / Legume lectin domain / Legume lectin domain / : / Legume lectin, beta chain, Mn/Ca-binding site / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Flt3 receptor-interacting lectin
Similarity search - Component
Biological speciesLablab purpureus (hyacinth bean)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.67 Å
AuthorsNguyen VHT / Liu YM / Chen X / Ma C
Funding support Taiwan, 2 items
OrganizationGrant numberCountry
Academia Sinica (Taiwan)AS-IA-113-L02 Taiwan
Ministry of Science and Technology (MoST, Taiwan)110-2113-M-001-034-MY3 Taiwan
CitationJournal: Nat Commun / Year: 2026
Title: Altering the carbohydrate-binding specificity of the legume lectin FRIL through structure-guided engineering
Authors: Liu YM / Nguyen HTV / Chen X / Shahed-Al-Mahmud M / Chen TH / Liao KS / Lo JM / Kan TC / Ren CT / Ma C
History
DepositionJun 5, 2025-
Header (metadata) releaseMar 18, 2026-
Map releaseMar 18, 2026-
UpdateMar 18, 2026-
Current statusMar 18, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_64936.png

Downloads & links

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Map

FileDownload / File: emd_64936.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.)
0.83 Å/pix.
x 256 pix.
= 212.48 Å		0.83 Å/pix.
x 256 pix.
= 212.48 Å		0.83 Å/pix.
x 256 pix.
= 212.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0179
Minimum - Maximum-0.1172259 - 0.14988132
Average (Standard dev.)-0.00000054547684 (±0.0042893034)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 212.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_64936_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_64936_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 : Tetrameric structure of rFRIL-wt apo form with self-glycan

EntireName: Tetrameric structure of rFRIL-wt apo form with self-glycan
Components
  • Complex: Tetrameric structure of rFRIL-wt apo form with self-glycan
    • Protein or peptide: Flt3 receptor-interacting lectin
  • Ligand: CALCIUM ION
  • Ligand: MANGANESE (II) ION
  • Ligand: water

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Supramolecule #1: Tetrameric structure of rFRIL-wt apo form with self-glycan

SupramoleculeName: Tetrameric structure of rFRIL-wt apo form with self-glycan
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Lablab purpureus (hyacinth bean)
Molecular weightTheoretical: 110 KDa

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Macromolecule #1: Flt3 receptor-interacting lectin

MacromoleculeName: Flt3 receptor-interacting lectin / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Lablab purpureus (hyacinth bean)
Molecular weightTheoretical: 28.610438 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AQSLSFSFTK FDPNQEDLIF QGHATSTNNV LQLTKLDSAG NPVSSSAGRV LYSAPLRLWE DSAVLTSFDT IINFEISTPY TSRIADGLA FFIAPPDSVI SYHGGFLGLF PNANTLNNSS TSENQTTTKA ASSNVVAVEF DTYLNPDYGD PNYIHIGIDV N SIRSKVTA ...String:
AQSLSFSFTK FDPNQEDLIF QGHATSTNNV LQLTKLDSAG NPVSSSAGRV LYSAPLRLWE DSAVLTSFDT IINFEISTPY TSRIADGLA FFIAPPDSVI SYHGGFLGLF PNANTLNNSS TSENQTTTKA ASSNVVAVEF DTYLNPDYGD PNYIHIGIDV N SIRSKVTA KWDWQNGKIA TAHISYNSVS KRLSVTTYYP GSKPATLSYD IELHTVLPEW VRVGLSASTG QDKERNTVHS WS FTSSLWT NVAVDLGHHH HHH

UniProtKB: Flt3 receptor-interacting lectin

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Macromolecule #3: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 3 / Number of copies: 4 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #4: MANGANESE (II) ION

MacromoleculeName: MANGANESE (II) ION / type: ligand / ID: 4 / Number of copies: 4 / Formula: MN
Molecular weightTheoretical: 54.938 Da

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 5 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration0.04 mg/mL
BufferpH: 7.4 / Details: 10%PBS
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: GRAPHENE OXIDE / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
SoftwareName: EPU
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 2500 / Average exposure time: 1.34 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3039399
CTF correctionSoftware - Name: RELION (ver. 3.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1qmo

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.67 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 443332
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classificationNumber classes: 3 / Avg.num./class: 300000 / Software - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

9vbx


Chain - Source name: PDB / Chain - Initial model type: experimental model
SoftwareName: UCSF ChimeraX (ver. 0.91)
RefinementProtocol: OTHER
Output model

PDB-9vby:
Lectin FRIL from Lablab purpureus with self glycan

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