[English] 日本語
Yorodumi
- EMDB-62389: Structure of Nectin-4 D1 domain in complex with the Fab fragment ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-62389
TitleStructure of Nectin-4 D1 domain in complex with the Fab fragment of 9MW2821 mAb
Map data
Sample
  • Complex: Nectin-4 D1 domain in complex with the Fab fragment of 9MW2821 mAb
    • Protein or peptide: 9MW2821 mAb Fab Light chain
    • Protein or peptide: 9MW2821 mAb Fab Heavy Chain
    • Protein or peptide: Nectin-4
Keywordsantibody-antigen complex / IMMUNE SYSTEM
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.26 Å
AuthorsWen HY
Funding support1 items
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, 2024-
Header (metadata) releaseNov 19, 2025-
Map releaseNov 19, 2025-
UpdateNov 26, 2025-
Current statusNov 26, 2025Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_62389.png

Downloads & links

-
Map

FileDownload / File: emd_62389.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 320 pix.
= 262.08 Å		0.82 Å/pix.
x 320 pix.
= 262.08 Å		0.82 Å/pix.
x 320 pix.
= 262.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.819 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.9203972 - 1.3751497
Average (Standard dev.)0.00019281397 (±0.019427625)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 262.08002 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_62389_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_62389_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_62389_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Nectin-4 D1 domain in complex with the Fab fragment of 9MW2821 mAb

EntireName: Nectin-4 D1 domain in complex with the Fab fragment of 9MW2821 mAb
Components
  • Complex: Nectin-4 D1 domain in complex with the Fab fragment of 9MW2821 mAb
    • Protein or peptide: 9MW2821 mAb Fab Light chain
    • Protein or peptide: 9MW2821 mAb Fab Heavy Chain
    • Protein or peptide: Nectin-4

-
Supramolecule #1: Nectin-4 D1 domain in complex with the Fab fragment of 9MW2821 mAb

SupramoleculeName: Nectin-4 D1 domain in complex with the Fab fragment of 9MW2821 mAb
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse)

-
Macromolecule #1: 9MW2821 mAb Fab Light chain

MacromoleculeName: 9MW2821 mAb Fab Light chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.965576 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString: DIVMTQSPDS LAVSLGERAT INCKSSQSLL NTYSQKNYLA WYQQKPGQPP KLLIYFASTR ESGVPDRFSG SGSGTDFTLT ISSLQAEDV AVYYCQQHYN TPFTFGGGTK VEIKRTVAAP SVFIFPPSDE QLKSGTASVV CLLNNFYPRE AKVQWKVDNA L QSGNSQES ...String:
DIVMTQSPDS LAVSLGERAT INCKSSQSLL NTYSQKNYLA WYQQKPGQPP KLLIYFASTR ESGVPDRFSG SGSGTDFTLT ISSLQAEDV AVYYCQQHYN TPFTFGGGTK VEIKRTVAAP SVFIFPPSDE QLKSGTASVV CLLNNFYPRE AKVQWKVDNA L QSGNSQES VTEQDSKDST YSLSSTLTLS KADYEKHKVY ACEVTHQGLS SPVTKSFNRG

-
Macromolecule #2: 9MW2821 mAb Fab Heavy Chain

MacromoleculeName: 9MW2821 mAb Fab Heavy Chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.235301 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString: EVQLQESGPG LVKPSETLSL TCTVSGFSLI DYGVSWIRQP PGKGLEWIGV IWGGGKIYYN SVLKSRVTIS KDNSKSQVSL KLSSVTAAD TAVYYCAKQG GLLFYAMDYW GQGTLVTVSS ASTKGPSVFP LAPSSKSTSG GTAALGCLVK DYFPEPVTVS W NSGALTSG ...String:
EVQLQESGPG LVKPSETLSL TCTVSGFSLI DYGVSWIRQP PGKGLEWIGV IWGGGKIYYN SVLKSRVTIS KDNSKSQVSL KLSSVTAAD TAVYYCAKQG GLLFYAMDYW GQGTLVTVSS ASTKGPSVFP LAPSSKSTSG GTAALGCLVK DYFPEPVTVS W NSGALTSG VHTFPAVLQS SGLYSLSSVV TVPSSSLGTQ TYICNVNHKP SNTKVDKRVE PK

-
Macromolecule #3: Nectin-4

MacromoleculeName: Nectin-4 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.363739 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
GELETSDVVT VVLGQDAKLP CFYRGDSGEQ VGQVAWARVD AGEGAQELAL LHSKYGLHVS PAYEGRVEQP PPPRNPLDGS VLLRNAVQA DEGEYECRVS TFPAGSFQAR LRLRV

UniProtKB: Nectin-4

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mmol/LTris-HClTris (hydroxymethyl)aminomethane hydrochloride
200.0 mmol/LNaClsodium chloride
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 2.5 µm / Calibrated defocus min: 0.7000000000000001 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 152403
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more