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- PDB-9ucl: CryoEM structure of IgV domain of human Nectin-4 with Trimbody -

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Basic information

Entry
Database: PDB / ID: 9ucl
TitleCryoEM structure of IgV domain of human Nectin-4 with Trimbody
Components
  • H3-PrAC-5350A,2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase
  • N4-nanobody-TAIL
  • Nectin-4
KeywordsSTRUCTURAL PROTEIN
Function / homology
Function and homology information


Nectin/Necl trans heterodimerization / D-galactonate catabolic process / 2-dehydro-3-deoxy-6-phosphogalactonate aldolase activity / cell adhesion mediator activity / negative regulation of natural killer cell mediated cytotoxicity / Adherens junctions interactions / heterophilic cell-cell adhesion / homophilic cell-cell adhesion / adherens junction / virus receptor activity ...Nectin/Necl trans heterodimerization / D-galactonate catabolic process / 2-dehydro-3-deoxy-6-phosphogalactonate aldolase activity / cell adhesion mediator activity / negative regulation of natural killer cell mediated cytotoxicity / Adherens junctions interactions / heterophilic cell-cell adhesion / homophilic cell-cell adhesion / adherens junction / virus receptor activity / receptor ligand activity / extracellular exosome / identical protein binding / plasma membrane
Similarity search - Function
Nectin-4 / : / KDPG/KHG aldolase / KDPG and KHG aldolase / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-set domain ...Nectin-4 / : / KDPG/KHG aldolase / KDPG and KHG aldolase / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Aldolase-type TIM barrel / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Nectin-4 / 2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase
Similarity search - Component
Biological speciessynthetic construct (others)
Thermotoga maritima MSB8 (bacteria)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.43 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 IgV domain of human Nectin-4 with Trimbody
Authors: Song, J.Y. / Wang, W.
History
DepositionApr 4, 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

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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: N4-nanobody-TAIL
E: N4-nanobody-TAIL
F: N4-nanobody-TAIL
G: Nectin-4
H: Nectin-4
I: Nectin-4


Theoretical massNumber of molelcules
Total (without water)232,0969
Polymers232,0969
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 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 N4-nanobody-TAIL


Mass: 27671.258 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 Nectin-4 / Ig superfamily receptor LNIR / Nectin cell adhesion molecule 4 / Poliovirus receptor-related protein 4


Mass: 13566.088 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NECTIN4, LNIR, PRR4, PVRL4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96NY8
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

Component
IDNameTypeEntity IDParent-IDSource
1CryoEM structure of IgV domain of human Nectin-4 with TrimbodyCOMPLEXall0RECOMBINANT
2H3-PrAC-5350ACOMPLEX#11RECOMBINANT
3N4-nanobody-TAILCOMPLEX#21RECOMBINANT
4IgV domain of human Nectin-4COMPLEX#31RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8) (bacteria)243274
51Homo sapiens (human)9606
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
4cryoSPARCCTF correction
9PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.43 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 567049 / Symmetry type: POINT
RefinementHighest resolution: 2.43 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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