Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 27.68 kDa 
• Atom Count: 2177 
• Modelled Residue Count: 246 
• Deposited Residue Count: 249 
• Unique protein chains: 1

5UEI

Crystal Structure of Variable Lymphocyte Receptor (VLR) O13 (Apo)

• PDB DOI: 10.2210/pdb5UEI/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Petromyzon marinus
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2017-01-02 Released: 2017-10-18 
• Deposition Author(s): Gunn, R.J., Collins, B.C., McKitrick, T.R., Cummings, R.D., Herrin, B.R., Cooper, M.D., Wilson, I.A.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.185 
• R-Value Work: 0.159 
• R-Value Observed: 0.160 

Literature

Structural Insights into VLR Fine Specificity for Blood Group Carbohydrates.

Collins, B.C., Gunn, R.J., McKitrick, T.R., Cummings, R.D., Cooper, M.D., Herrin, B.R., Wilson, I.A.

(2017) Structure 25: 1667-1678.e4

• PubMed: 28988747 
• DOI: 10.1016/j.str.2017.09.003
• Primary Citation of Related Structures:  
  5UEI, 5UF1, 5UF4, 5UFB, 5UFC, 5UFD, 5UFF


• PubMed Abstract: 
  

High-quality reagents to study and detect glycans with high specificity for research and clinical applications are severely lacking. Here, we structurally and functionally characterize several variable lymphocyte receptor (VLR)-based antibodies from lampreys immunized with O erythrocytes that specifically recognize the blood group H-trisaccharide type II antigen. Glycan microarray analysis and biophysical data reveal that these VLRs exhibit greater specificity for H-trisaccharide compared with the plant lectin UEA-1, which is widely used in blood typing. Among these antibodies, O13 exhibits superior specificity for H-trisaccharide, the basis for which is revealed by comparative analysis of high-resolution VLR:glycan crystal structures. Using a structure-guided approach, we designed an O13 mutant with further enhanced specificity for H-trisaccharide. These insights into glycan recognition by VLRs suggest that lampreys can produce highly specific glycan antibodies, and are a valuable resource for the production of next-generation glycan reagents for biological and biomedical research and as diagnostics and therapeutics.

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Organizational Affiliation: 

Department of Integrative Structural and Computational Biology and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
O13	A	249	Petromyzon marinus	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.185 
• R-Value Work: 0.159 
• R-Value Observed: 0.160 
• Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.663	α = 90
b = 86.663	β = 90
c = 38.108	γ = 90

Software Package:

Software Name	Purpose
DENZO	data collection
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-01-02 
• Released Date: 2017-10-18 
Deposition Author(s): Gunn, R.J., Collins, B.C., McKitrick, T.R., Cummings, R.D., Herrin, B.R., Cooper, M.D., Wilson, I.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History  

• Version 1.0: 2017-10-18
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Database references
• Version 1.2: 2019-12-11
  Changes: Author supporting evidence