6FAY | pdb_00006fay

Teneurin3 monomer

• PDB DOI: https://doi.org/10.2210/pdb6FAY/pdb
• EM Map EMD-4219: EMDB EMDataResource

• Classification: CELL ADHESION
• Organism(s): Mus musculus
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2017-12-18 Released: 2018-03-28 
• Deposition Author(s): Janssen, B.J.C., Meijer, D.H.M., van Bezouwen, L.S.
• Funding Organization(s): European Molecular Biology Organization, Netherlands Organisation for Scientific Research

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

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.

---

Organizational Affiliation: 
• Department of Biochemistry, Oxford University, OX1 3QU, Oxford, UK. [e-mail].
Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, 3584 CH, Utrecht, The Netherlands.
Department of Biochemistry, Oxford University, OX1 3QU, Oxford, UK.
Cryo-electron Microscopy, Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, 3584 CH, Utrecht, The Netherlands.
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 generated by PISA (software)

Biological Assembly Evidence: microscopy

Macromolecule Content 

• Total Structure Weight: 212.54 kDa 
• Atom Count: 12,130 
• Modeled Residue Count: 1,518 
• Deposited Residue Count: 1,876 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Odz3 protein	A	1,876	Mus musculus	Mutation(s): 0  Gene Names: Tenm3, Odz3
UniProt
Find proteins for Q9WTS6 (Mus musculus) Explore Q9WTS6  Go to UniProtKB:  Q9WTS6
Glycosylation
Glycosylation Sites: 5		Go to GlyGen: Q9WTS6-1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-03-28 
Deposition Author(s): Janssen, B.J.C., Meijer, D.H.M., van Bezouwen, L.S.

---

Funding Organization	Location	Grant Number
European Molecular Biology Organization	Netherlands	125-2015
Netherlands Organisation for Scientific Research	Netherlands	723.012.002

Revision History  

• Version 1.0: 2018-03-28
  Type: Initial release
  
• Version 1.1: 2019-12-11
  Changes: Other
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2024-10-23
  Changes: Data collection, Database references, Refinement description, Structure summary