9EZH | pdb_00009ezh

Structure of single-domain antibody VHH_h4 in complex with human Vsig4

• PDB DOI: https://doi.org/10.2210/pdb9EZH/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Camelidae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-04-12 Released: 2025-10-29 
• Deposition Author(s): Vizarraga, D., Cianferoni, D., Delgado, J., van der Kant, R., Garcia, T., Maragkou, K., Zhang, Z., Dewilde, M., Schymkowitz, J., Rousseau, F., Serrano, L.
• Funding Organization(s): Agencia Estatal de Investigacion (AEI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 
  0.239 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

In silico design of stable single-domain antibodies against multiple targets.

van der Kant, R., Zhang, Z., Markovic, I., Vizarraga, D., Garcia, T., Maragkou, K., Delgado, J., Cianferoni, D., Orlando, G., Carolis, C., Savvides, S., N.Volkov, A., Dewilde, M., Schymkowitz, J., Serrano, L., Rousseau, F.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 26.92 kDa 
• Atom Count: 2,060 
• Modeled Residue Count: 239 
• Deposited Residue Count: 239 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
V-set and immunoglobulin domain-containing protein 4	A	118	Homo sapiens	Mutation(s): 0  Gene Names: VSIG4, CRIg, Z39IG, UNQ317/PRO362
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y279 (Homo sapiens) Explore Q9Y279  Go to UniProtKB:  Q9Y279
PHAROS:  Q9Y279 GTEx:  ENSG00000155659

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
VHH_h4	B	121	Camelidae	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL (Subject of Investigation/LOI)	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free:  0.239 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 25.764	α = 90
b = 50.961	β = 90
c = 175.238	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-29 
Deposition Author(s): Vizarraga, D., Cianferoni, D., Delgado, J., van der Kant, R., Garcia, T., Maragkou, K., Zhang, Z., Dewilde, M., Schymkowitz, J., Rousseau, F., Serrano, L.

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Funding Organization	Location	Grant Number
Agencia Estatal de Investigacion (AEI)	Spain	JDC2022-048697-I

Revision History  

• Version 1.0: 2025-10-29
  Type: Initial release