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

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Basic information

Entry
Database: PDB / ID: 9vby
TitleLectin FRIL from Lablab purpureus with self glycan
ComponentsFlt3 receptor-interacting lectin
KeywordsPLANT PROTEIN / Flt3 receptor-interacting lectin / carbohydrate binding protein / lectin / glycoprotein / self glycan / FRIL
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.67 Å
AuthorsNguyen, V.H.T. / Liu, Y.M. / Chen, X. / Ma, C.
Funding support Taiwan, 2items
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, Y.M. / Nguyen, H.T.V. / Chen, X. / Shahed-Al-Mahmud, M. / Chen, T.H. / Liao, K.S. / Lo, J.M. / Kan, T.C. / Ren, C.T. / Ma, C.
History
DepositionJun 5, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 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: Flt3 receptor-interacting lectin
B: Flt3 receptor-interacting lectin
C: Flt3 receptor-interacting lectin
D: Flt3 receptor-interacting lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,00416
Polymers114,4424
Non-polymers2,56212
Water905
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
Flt3 receptor-interacting lectin


Mass: 28610.438 Da / Num. of mol.: 4 / Mutation: V33L/S195T/A198P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lablab purpureus (hyacinth bean) / Gene: FRIL / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q9ZTA9
#2: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose


Type: oligosaccharide / Mass: 545.490 Da / Num. of mol.: 4 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-6DManpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a1122h-1b_1-5][a1122h-1a_1-5][a2122h-1b_1-5_2*NCC/3=O]/1-2-3/a6-b1_b2-c1WURCSPDB2Glycan 1.1.0
[][b-D-Manp]{[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: Tetrameric structure of rFRIL-wt apo form with self-glycan
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.11 MDa / Experimental value: YES
Source (natural)Organism: Lablab purpureus (hyacinth bean)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK-293 / Plasmid: pTT
Buffer solutionpH: 7.4 / Details: 10%PBS
SpecimenConc.: 0.04 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 278 K

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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 magnification: 105000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm
Image recordingAverage exposure time: 1.34 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2500

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Processing

EM software
IDNameVersionCategory
1cisTEMparticle selection
2EPUimage acquisition
4RELION3CTF correction
7UCSF ChimeraX0.91model fitting
9RELION3initial Euler assignment
10RELION3final Euler assignment
11RELION3classification
12RELION33D reconstruction
13PHENIX1.14_3260:model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3039399
SymmetryPoint symmetry: D2 (2x2 fold dihedral)
3D reconstructionResolution: 2.67 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 443332 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER
Atomic model buildingPDB-ID: 9VBX

9vbx


Accession code: 9VBX / Source name: PDB / Type: experimental model

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