9UCL | pdb_00009ucl

CryoEM structure of IgV domain of human Nectin-4 with Trimbody

• PDB DOI: https://doi.org/10.2210/pdb9UCL/pdb
• EM Map EMD-64047: EMDB EMDataResource

• Classification: STRUCTURAL PROTEIN
• Organism(s): synthetic construct, Thermotoga maritima MSB8, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-04-04 Released: 2026-02-11 
• Deposition Author(s): Song, J.Y., Wang, W.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.43 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

CryoEM structure of IgV domain of human Nectin-4 with Trimbody

Song, J.Y., Wang, W.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 9-mer - A3B3C3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 232.1 kDa 
• Atom Count: 15,549 
• Modeled Residue Count: 2,031 
• Deposited Residue Count: 2,118 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
H3-PrAC-5350A,2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase	A, B, C	332	synthetic construct, Thermotoga maritima MSB8 This entity is chimeric	Mutation(s): 0
UniProt
Find proteins for Q9WXS1 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WXS1  Go to UniProtKB:  Q9WXS1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
N4-nanobody-TAIL	D, E, F	251	synthetic construct	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Nectin-4	G, H, I	123	Homo sapiens	Mutation(s): 0  Gene Names: NECTIN4, LNIR, PRR4, PVRL4
UniProt & NIH Common Fund Data Resources
Find proteins for Q96NY8 (Homo sapiens) Explore Q96NY8  Go to UniProtKB:  Q96NY8
PHAROS:  Q96NY8 GTEx:  ENSG00000143217

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.43 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2026-02-11 
Deposition Author(s): Song, J.Y., Wang, W.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2026-02-11
  Type: Initial release