[English] 日本語
Yorodumi
- PDB-7plp: Human Teneurin-4 C-rich domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7plp
TitleHuman Teneurin-4 C-rich domain
ComponentsTeneurin-4
KeywordsCELL ADHESION / cysteine-rich / calcium binding
Function / homology
Function and homology information


cardiac cell fate specification / positive regulation of myelination / central nervous system myelin formation / positive regulation of gastrulation / gastrulation with mouth forming second / cardiac muscle cell proliferation / regulation of myelination / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / positive regulation of oligodendrocyte differentiation / neuron development ...cardiac cell fate specification / positive regulation of myelination / central nervous system myelin formation / positive regulation of gastrulation / gastrulation with mouth forming second / cardiac muscle cell proliferation / regulation of myelination / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / positive regulation of oligodendrocyte differentiation / neuron development / cell adhesion molecule binding / neuron projection / protein heterodimerization activity / signal transduction / protein homodimerization activity / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Teneurin intracellular, N-terminal / Teneurin Intracellular Region / Teneurin N-terminal domain profile. / Tox-GHH domain / GHH signature containing HNH/Endo VII superfamily nuclease toxin / RHS repeat / RHS Repeat / YD repeat / Rhs repeat-associated core / Carboxypeptidase-like, regulatory domain superfamily ...Teneurin intracellular, N-terminal / Teneurin Intracellular Region / Teneurin N-terminal domain profile. / Tox-GHH domain / GHH signature containing HNH/Endo VII superfamily nuclease toxin / RHS repeat / RHS Repeat / YD repeat / Rhs repeat-associated core / Carboxypeptidase-like, regulatory domain superfamily / EGF-like domain, extracellular / EGF-like domain / Six-bladed beta-propeller, TolB-like / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain
Similarity search - Domain/homology
: / NICKEL (II) ION / Teneurin-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsBeugelink, J.W. / Meijer, D.H. / Janssen, B.J.C.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)OCENW.KLEIN.026 Netherlands
CitationJournal: EMBO J / Year: 2022
Title: Teneurin4 dimer structures reveal a calcium-stabilized compact conformation supporting homomeric trans-interactions.
Authors: Dimphna H Meijer / Cátia P Frias / J Wouter Beugelink / Yanthi N Deurloo / Bert J C Janssen /
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 ...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.
History
DepositionSep 1, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 9, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3May 11, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.4May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Teneurin-4
B: Teneurin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,85311
Polymers10,4022
Non-polymers4519
Water1,04558
1
A: Teneurin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,3775
Polymers5,2011
Non-polymers1764
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Teneurin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,4766
Polymers5,2011
Non-polymers2755
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.343, 66.343, 66.343
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-104-

FE

21B-104-

SO4

31B-105-

NI

-
Components

-
Protein/peptide , 1 types, 2 molecules AB

#1: Protein/peptide Teneurin-4 / / Ten-4 / Protein Odd Oz/ten-m homolog 4 / Tenascin-M4 / Ten-m4 / Teneurin transmembrane protein 4


Mass: 5200.784 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TENM4, KIAA1302, ODZ4, TNM4 / Cell line (production host): HEK cells / Production host: Homo sapiens (human) / References: UniProt: Q6N022

-
Non-polymers , 5 types, 67 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.42 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 7.5
Details: 0.085 M HEPES pH 7.5, 1.7 v/v % PEG-400, 1.7 M (NH4)2SO4, 15 w/v % glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.7749 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7749 Å / Relative weight: 1
ReflectionResolution: 1.4→46.91 Å / Num. obs: 19462 / % possible obs: 100 % / Redundancy: 41.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.184 / Rpim(I) all: 0.029 / Rrim(I) all: 0.186 / Net I/σ(I): 14 / Num. measured all: 802023 / Scaling rejects: 715
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allRrim(I) all% possible allRmerge(I) obs
1.4-1.4239.99290.7182.08213.184100
7.67-46.9129.71460.9990.0180.09499.50.092

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimless0.7.7data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: From unpublished anomalous experiment

Resolution: 1.4→33.19 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.976 / SU B: 1.96 / SU ML: 0.032 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.054 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1705 927 4.8 %RANDOM
Rwork0.1548 ---
obs0.1556 18241 98.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 129.83 Å2 / Biso mean: 23.684 Å2 / Biso min: 12 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.4→33.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms598 0 13 58 669
Biso mean--25.32 38.42 -
Num. residues----83
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.013664
X-RAY DIFFRACTIONr_bond_other_d0.0010.017559
X-RAY DIFFRACTIONr_angle_refined_deg1.7031.627909
X-RAY DIFFRACTIONr_angle_other_deg1.5551.6041323
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.966591
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.11727.93129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.72315110
X-RAY DIFFRACTIONr_chiral_restr0.1090.283
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02786
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02110
X-RAY DIFFRACTIONr_rigid_bond_restr2.64831219
LS refinement shellResolution: 1.4→1.437 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree2.483 57 -
Rwork2.21 1085 -
all-1142 -
obs--82.04 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more