6DYX

Structure of VHH R419 isolated from a pre-immune phage display library

• PDB DOI: https://doi.org/10.2210/pdb6DYX/pdb

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


• Deposited: 2018-07-02 Released: 2019-04-03 
• Deposition Author(s): Brooks, C.L.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.190 
• R-Value Work: 0.176 
• R-Value Observed: 0.177 

Literature

Structure of a VHH isolated from a naive phage display library.

White, B., Huh, I., Brooks, C.L.

(2019) BMC Res Notes 12: 154-154

• PubMed: 30890176 
• DOI: https://doi.org/10.1186/s13104-019-4197-0
• Primary Citation of Related Structures:  
  6DYX


• PubMed Abstract: 
  

  To determine the X-ray structure and biophysical properties of a Camelid V _H H isolated from a naïve phage display library. Single domain antibodies (V _H H) derived from the unique immune system of the Camelidae family have gained traction as useful tools for biotechnology as well as a source of potentially novel therapeutics. Here we report the structure and biophysical characterization of a V _H H originally isolated from a naïve camelid phage display library. V _H H R419 has a melting temperate of 66 °C and was found to be a monomer in solution. The protein crystallized in space group P6 ₅ 22 and the structure was solved by molecular replacement to a resolution of 1.5 Å. The structure revealed a flat paratope with CDR loops that could be classified into existing canonical loop structures. A combination of high expression yield, stability and rapid crystallization might make R419 into a candidate scaffold for CDR grafting and homology modeling.

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Organizational Affiliation: 

Department of Chemistry, California State University Fresno, 2555 E San Ramon Ave, Fresno, CA, 93740, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 13.79 kDa 
• Atom Count: 1,016 
• Modelled Residue Count: 117 
• Deposited Residue Count: 124 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VHH R419	A [auth D]	124	Vicugna pacos	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth D], D	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ACT	C [auth D]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.190 
• R-Value Work: 0.176 
• R-Value Observed: 0.177 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.281	α = 90
b = 58.281	β = 90
c = 155.358	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
xia2	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-04-03 
Deposition Author(s): Brooks, C.L.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	SC3GM112532

Revision History  

• Version 1.0: 2019-04-03
  Type: Initial release
  
• Version 1.1: 2020-01-01
  Changes: Author supporting evidence
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description