8GJR | pdb_00008gjr

Crystal Structure of Nanobody VHH114 Bound to Its Antigen PA14 Cif

• PDB DOI: https://doi.org/10.2210/pdb8GJR/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Pseudomonas aeruginosa PA14, Vicugna pacos
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-03-16 Released: 2024-06-26 
• 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: 1.85 Å
• R-Value Free: 
  0.192 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Starting Models: experimental

Literature

Crystal Structure of Nanobody VHH114 Bound to Its Antigen PA14 Cif

Simard, A.R., Madden, D.R.

To be published.

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

Macromolecule Content 

• Total Structure Weight: 47.24 kDa 
• Atom Count: 3,602 
• Modeled Residue Count: 410 
• Deposited Residue Count: 421 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CFTR inhibitory factor	A [auth C]	295	Pseudomonas aeruginosa PA14	Mutation(s): 0  Gene Names: PA14_26090
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 VHH114	B [auth A]	126	Vicugna pacos	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FLC	C, D [auth C]	CITRATE ANION C6 H5 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.192 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 163.487	α = 90
b = 163.487	β = 90
c = 74.959	γ = 120

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: 2024-06-26 
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: 2024-06-26
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Structure summary