5UFC | pdb_00005ufc

Crystal Structure of Variable Lymphocyte Receptor (VLR) Tn4-22 with H-trisaccharide bound

• PDB DOI: https://doi.org/10.2210/pdb5UFC/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Petromyzon marinus
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2017-01-04 Released: 2017-10-18 
• Deposition Author(s): Collins, B.C., Gunn, R.J., McKitrick, T.R., Cummings, R.D., Cooper, M.D., Herrin, B.R., Wilson, I.A.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 
  0.231 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.198 (Depositor) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

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: https://doi.org/10.1016/j.str.2017.09.003
• Primary Citation 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.

---

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.
National Center for Functional Glycomics, Beth Israel Deaconess Medical Center Department of Surgery, Harvard Medical School, 330 Brookline Avenue, Boston, MA 02215, USA.
Emory Vaccine Center and Department of Pathology and Laboratory Medicine, Emory University, 1462 Clifton Road North-East, Atlanta, GA 30322, USA.
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].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 84.74 kDa 
• Atom Count: 5,934 
• Modeled Residue Count: 720 
• Deposited Residue Count: 744 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tn4-22	A, B, C	248	Petromyzon marinus	Mutation(s): 0

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, E, F	3		N/A
Glycosylation Resources
GlyTouCan: G61459JW GlyCosmos: G61459JW GlyGen: G61459JW

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900036	D, E, F	H type 2 antigen, beta anomer	Oligosaccharide / Antigen

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free:  0.231 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.198 (Depositor) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.916	α = 90
b = 98.916	β = 90
c = 162.875	γ = 120

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

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

---

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
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-10-04
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-10-23
  Changes: Structure summary