9CJ0

The High-Resolution Structure of a Variable Lymphocyte Receptor from Petromyzon marinus Capable of Binding to the Brain Extracellular Matrix

• PDB DOI: https://doi.org/10.2210/pdb9CJ0/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Petromyzon marinus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-07-05 Released: 2024-07-31 
• Deposition Author(s): Appelt, E.A., Thoden, J.B., Shusta, E.V., Holden, H.M.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.222 
• R-Value Work: 0.185 
• R-Value Observed: 0.186 

Starting Model: experimental

Literature

The High-Resolution Structure of a Variable Lymphocyte Receptor from Petromyzon marinus Capable of Binding to the Brain Extracellular Matrix

Appelt, E.A., Thoden, J.B., Gehrke, S.A., Bachmeier, H.D., Rayment, I., Holden, H.M., Shusta, E.V.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 19.19 kDa 
• Atom Count: 1,567 
• Modelled Residue Count: 170 
• Deposited Residue Count: 170 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Variable Lymphocyte Receptor	A	170	Petromyzon marinus	Mutation(s): 0
UniProt
Find proteins for A5H6E1 (Petromyzon marinus) Explore A5H6E1  Go to UniProtKB:  A5H6E1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EP1	B [auth A]	3-[4-(2-HYDROXYETHYL)PIPERAZIN-1-YL]PROPANE-1-SULFONIC ACID C9 H20 N2 O4 S OWXMKDGYPWMGEB-UHFFFAOYSA-N
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.222 
• R-Value Work: 0.185 
• R-Value Observed: 0.186 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.522	α = 90
b = 53.137	β = 90
c = 60.348	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SAINT	data reduction
SADABS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-31 
Deposition Author(s): Appelt, E.A., Thoden, J.B., Shusta, E.V., Holden, H.M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35 GM134643
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	5 T32 GM135066
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	R01 NS099158
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	R01 NS118028

Revision History  

• Version 1.0: 2024-07-31
  Type: Initial release
  
• Version 1.1: 2024-09-04
  Changes: Database references, Structure summary
• Version 1.2: 2024-10-23
  Changes: Structure summary