8EE2 | pdb_00008ee2

Crystal Structure of Nanobody VHH219 Bound to Its Antigen PA14 Cif

• PDB DOI: https://doi.org/10.2210/pdb8EE2/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Pseudomonas aeruginosa PA14, Vicugna pacos
• Expression System: Escherichia coli, Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2022-09-06 Released: 2023-09-13 
• Deposition Author(s): Simard, A.R., Madden, D.R.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Cystic Fibrosis Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.227 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Models: experimental

Literature

Convergent strategies for nanobody-mediated inhibition of an epoxide hydrolase

Simard, A.R., Taher, N.M., Beauchemin, K.S., Mishra, A.K., Hederman, A.P., Hampton, T.H., Vasylieva, N., Morisseau, C., Ackerman, M.E., Madden, D.R.

(2026) J Struct Biol X : 100166

• DOI: https://doi.org/10.1016/j.yjsbx.2026.100166

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B1C1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Hetero 4-mer - A2B2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 286.76 kDa 
• Atom Count: 19,194 
• Modeled Residue Count: 2,414 
• Deposited Residue Count: 2,568 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CFTR inhibitory factor	A, B, E, F, I, J	301	Pseudomonas aeruginosa PA14	Mutation(s): 0  Gene Names: PA2394 EC: 3.3.2.10
UniProt
Find proteins for A0A0H2ZD27 (Pseudomonas aeruginosa (strain UCBPP-PA14)) Explore A0A0H2ZD27  Go to UniProtKB:  A0A0H2ZD27

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody VHH219	C, D, G, H, K, L	127	Vicugna pacos	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.227 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.204	α = 90
b = 162.599	β = 95.36
c = 106.255	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
Coot	model building
PHENIX	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-09-13 
Deposition Author(s): Simard, A.R., Madden, D.R.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01-AI091699
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	P30-DK117469
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P20-GM113132
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	T32AI007519
Cystic Fibrosis Foundation	United States	STANTO19R0

Revision History  

• Version 1.0: 2023-09-13
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Structure summary
• Version 1.2: 2026-03-04
  Changes: Refinement description
• Version 1.3: 2026-10-21
  Changes: Database references