6FB3

Teneurin 2 Partial Extracellular Domain

• PDB DOI:  https://doi.org/10.2210/pdb6FB3/pdb

• Classification: CELL ADHESION
• Organism(s): Gallus gallus
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2017-12-18 Released: 2018-03-28 
• Deposition Author(s): Jackson, V.A., Carrasquero, M., Lowe, E.D., Seiradake, E.
• Funding Organization(s): Wellcome Trust, Medical Research Council (United Kingdom)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free: 0.242 
• R-Value Work: 0.225 
• R-Value Observed: 0.226 

Literature

Structures of Teneurin adhesion receptors reveal an ancient fold for cell-cell interaction.

Jackson, V.A., Meijer, D.H., Carrasquero, M., van Bezouwen, L.S., Lowe, E.D., Kleanthous, C., Janssen, B.J.C., Seiradake, E.

(2018) Nat Commun 9: 1079-1079

• PubMed: 29540701 
• DOI: https://doi.org/10.1038/s41467-018-03460-0
• Primary Citation of Related Structures:  
  6FAY, 6FB3


• PubMed Abstract: 
  

Teneurins are ancient cell-cell adhesion receptors that are vital for brain development and synapse organisation. They originated in early metazoan evolution through a horizontal gene transfer event when a bacterial YD-repeat toxin fused to a eukaryotic receptor. We present X-ray crystallography and cryo-EM structures of two Teneurins, revealing a ~200 kDa extracellular super-fold in which eight sub-domains form an intricate structure centred on a spiralling YD-repeat shell. An alternatively spliced loop, which is implicated in homophilic Teneurin interaction and specificity, is exposed and thus poised for interaction. The N-terminal side of the shell is 'plugged' via a fibronectin-plug domain combination, which defines a new class of YD proteins. Unexpectedly, we find that these proteins are widespread amongst modern bacteria, suggesting early metazoan receptor evolution from a distinct class of proteins, which today includes both bacterial proteins and eukaryotic Teneurins.

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Organizational Affiliation: 

Department of Biochemistry, Oxford University, OX1 3QU, Oxford, UK. [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.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 853.68 kDa 
• Atom Count: 59,451 
• Modelled Residue Count: 7,344 
• Deposited Residue Count: 7,436 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Teneurin-2	A, B, C, D	1,859	Gallus gallus	Mutation(s): 0  Gene Names: TENM2, ODZ2, TNM2
UniProt
Find proteins for Q9DER5 (Gallus gallus) Explore Q9DER5  Go to UniProtKB:  Q9DER5

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, K, Q, W	8		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G83582BK GlyCosmos:  G83582BK GlyGen:  G83582BK

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AA [auth a], BA [auth b], F, G, H, I, J, L, M, N, O, P, R, S, T, U, V, X, Y, Z	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	CA [auth A], DA [auth A], EA [auth A], FA [auth A], GA [auth A], HA [auth B], IA [auth B], JA [auth B], KA [auth B], LA [auth B], MA [auth C], NA [auth C], OA [auth C], PA [auth C], QA [auth C], RA [auth D], SA [auth D], TA [auth D], UA [auth D], VA [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free: 0.242 
• R-Value Work: 0.225 
• R-Value Observed: 0.226 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.56	α = 90
b = 452.56	β = 95.12
c = 146.36	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-03-28 
Deposition Author(s): Jackson, V.A., Carrasquero, M., Lowe, E.D., Seiradake, E.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	202827/Z/16/Z
Medical Research Council (United Kingdom)	United Kingdom	MR/L018039/1

Revision History  

• Version 1.0: 2018-03-28
  Type: Initial release
  
• Version 1.1: 2019-03-27
  Changes: Data collection, Derived calculations, Other
• Version 1.2: 2019-07-10
  Changes: Data collection
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary