7PLP | pdb_00007plp

Human Teneurin-4 C-rich domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 
    0.171 (Depositor), 0.172 (DCC) 
  • R-Value Work: 
    0.155 (Depositor), 0.155 (DCC) 
  • R-Value Observed: 
    0.156 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7PLP

This is version 1.5 of the entry. See complete history

Literature

Teneurin4 dimer structures reveal a calcium-stabilized compact conformation supporting homomeric trans-interactions.

Meijer, D.H.Frias, C.P.Beugelink, J.W.Deurloo, Y.N.Janssen, B.J.C.

(2022) EMBO J 41: e107505-e107505

  • DOI: https://doi.org/10.15252/embj.2020107505
  • Primary Citation Related Structures: 
    7BAM, 7BAN, 7BAO, 7PLP

  • PubMed Abstract: 

    Establishment of correct synaptic connections is a crucial step during neural circuitry formation. The Teneurin family of neuronal transmembrane proteins promotes cell-cell adhesion via homophilic and heterophilic interactions, and is required for synaptic partner matching in the visual and hippocampal systems in vertebrates. It remains unclear how individual Teneurins form macromolecular cis- and trans-synaptic protein complexes. Here, we present a 2.7 Å cryo-EM structure of the dimeric ectodomain of human Teneurin4. The structure reveals a compact conformation of the dimer, stabilized by interactions mediated by the C-rich, YD-shell, and ABD domains. A 1.5 Å crystal structure of the C-rich domain shows three conserved calcium binding sites, and thermal unfolding assays and SAXS-based rigid-body modeling demonstrate that the compactness and stability of Teneurin4 dimers are calcium-dependent. Teneurin4 dimers form a more extended conformation in conditions that lack calcium. Cellular assays reveal that the compact cis-dimer is compatible with homomeric trans-interactions. Together, these findings support a role for teneurins as a scaffold for macromolecular complex assembly and the establishment of cis- and trans-synaptic interactions to construct functional neuronal circuits.


  • Organizational Affiliation
    • Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands.

Macromolecule Content 

  • Total Structure Weight: 10.85 kDa 
  • Atom Count: 710 
  • Modeled Residue Count: 83 
  • Deposited Residue Count: 98 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Teneurin-4
A, B
49Homo sapiensMutation(s): 0 
Gene Names: TENM4KIAA1302ODZ4TNM4
UniProt & NIH Common Fund Data Resources
Find proteins for Q6N022 (Homo sapiens)
Explore Q6N022 
Go to UniProtKB:  Q6N022
PHAROS:  Q6N022
GTEx:  ENSG00000149256 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6N022
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
J [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
NI

Query on NI



Download:Ideal Coordinates CCD File
K [auth B]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
FE

Query on FE



Download:Ideal Coordinates CCD File
F [auth A]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
CA
(Subject of Investigation/LOI)

Query on CA



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
G [auth B]
H [auth B]
C [auth A],
D [auth A],
E [auth A],
G [auth B],
H [auth B],
I [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free:  0.171 (Depositor), 0.172 (DCC) 
  • R-Value Work:  0.155 (Depositor), 0.155 (DCC) 
  • R-Value Observed: 0.156 (Depositor) 
Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.343α = 90
b = 66.343β = 90
c = 66.343γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Netherlands Organisation for Scientific Research (NWO)NetherlandsOCENW.KLEIN.026

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-02
    Type: Initial release
  • Version 1.1: 2022-02-09
    Changes: Database references
  • Version 1.2: 2022-02-16
    Changes: Database references
  • Version 1.3: 2022-05-11
    Changes: Database references
  • Version 1.4: 2024-05-01
    Changes: Data collection, Refinement description
  • Version 1.5: 2024-11-13
    Changes: Structure summary