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- PDB-9kkj: Structure of Nectin-4 D1 domain in complex with the Fab fragment ... -

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Basic information

Entry
Database: PDB / ID: 9kkj
TitleStructure of Nectin-4 D1 domain in complex with the Fab fragment of 9MW2821 mAb
Components
  • 9MW2821 mAb Fab Heavy Chain
  • 9MW2821 mAb Fab Light chain
  • Nectin-4
KeywordsIMMUNE SYSTEM / antibody-antigen complex
Function / homology
Function and homology information


Nectin/Necl trans heterodimerization / 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 / : / 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 ...Nectin-4 / : / 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 / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.26 Å
AuthorsWen, H.Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J Biol Chem / Year: 2025
Title: Structural basis of nectin-4 recognition by the antibody-drug conjugate 9MW2821.
Authors: Peng Fang / Meng You / Haiying Wen / Yuxia Cao / Wei Zhou / Xiaohong Zhu / Lei Shi / Xiaowei Sun / Kaiying Li / Wendi Li / Jin Wang / Hai Wu / Xiaoding Tan /
Abstract: Nectin-4, a membrane protein highly expressed in multiple solid tumors, has become an attractive target for antibody-drug conjugate development. We designed and developed 9MW2821, an anti-nectin-4 ...Nectin-4, a membrane protein highly expressed in multiple solid tumors, has become an attractive target for antibody-drug conjugate development. We designed and developed 9MW2821, an anti-nectin-4 antibody-drug conjugate with an enzymatically cleavable valine-citrulline linker and monomethyl auristatin E as the payload. Although 9MW2821 has shown good efficacy and safety in multiple solid tumors in clinical trials, the interaction between 9MW2821 and nectin-4 at the molecular level remains unclear. In this study, we solved the structure of the antigen-binding fragment of 9MW2821 in complex with nectin-4 at a resolution of 3.26 Å using single-particle cryo-EM. The structure shows that 9MW2821 binds the front β-sheet of nectin-4 D1 through three complementarity-determining region loops from the heavy chain and two complementarity-determining region loops from the light chain. The binding involves extensive hydrogen bonds and hydrophobic interactions. The buried surface area is more than 1600 Å. Mutagenesis studies revealed that four residues (Q77, E78, H83, and E95) of nectin-4 contributed significantly to the binding of 9MW2821 monoclonal antibody (mAb). The structure also shows that 9MW2821 mAb blocks nectin-4 homodimer formation by competing with the nectin-4 partner D1 domain for part of the nectin-4 surface area. Furthermore, 9MW2821 mAb prevents nectin-4 from interacting with nectin-1 and T-cell immunoglobulin and immunoreceptor tyrosine-based inhibitory motif domain, enhancing the activation of NK cells. Based on the structure of the nectin-4 D1-9MW2821 antigen-binding fragment complex resolved in this study, we have elucidated the molecular mechanism of 9MW2821 in cancer therapy. The findings provide a basis for optimizing future mAbs targeting nectin-4.
History
DepositionNov 13, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: 9MW2821 mAb Fab Light chain
H: 9MW2821 mAb Fab Heavy Chain
A: Nectin-4


Theoretical massNumber of molelcules
Total (without water)59,5653
Polymers59,5653
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: Antibody 9MW2821 mAb Fab Light chain


Mass: 23965.576 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#2: Antibody 9MW2821 mAb Fab Heavy Chain


Mass: 23235.301 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#3: Protein Nectin-4 / Ig superfamily receptor LNIR / Nectin cell adhesion molecule 4 / Poliovirus receptor-related protein 4


Mass: 12363.739 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NECTIN4, LNIR, PRR4, PVRL4 / Production host: Homo sapiens (human) / 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

ComponentName: Nectin-4 D1 domain in complex with the Fab fragment of 9MW2821 mAb
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mmol/LTris (hydroxymethyl)aminomethane hydrochlorideTris-HCl1
2200 mmol/Lsodium chlorideNaCl1
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: 2200 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 700 nm / Calibrated defocus max: 2500 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 152403 / Symmetry type: POINT

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