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TitleFamily-wide Structural and Biophysical Analysis of Binding Interactions among Non-clustered δ-Protocadherins.
Journal, issue, pagesCell Rep, Vol. 30, Issue 8, Page 2655-22671.e7, Year 2020
Publish dateFeb 25, 2020
AuthorsOliver J Harrison / Julia Brasch / Phinikoula S Katsamba / Goran Ahlsen / Alex J Noble / Hanbin Dan / Rosemary V Sampogna / Clinton S Potter / Bridget Carragher / Barry Honig / Lawrence Shapiro /
PubMed AbstractNon-clustered δ1- and δ2-protocadherins, close relatives of clustered protocadherins, function in cell adhesion and motility and play essential roles in neural patterning. To understand the ...Non-clustered δ1- and δ2-protocadherins, close relatives of clustered protocadherins, function in cell adhesion and motility and play essential roles in neural patterning. To understand the molecular interactions underlying these functions, we used solution biophysics to characterize binding of δ1- and δ2-protocadherins, determined crystal structures of ectodomain complexes from each family, and assessed ectodomain assembly in reconstituted intermembrane junctions by cryoelectron tomography (cryo-ET). Homophilic trans (cell-cell) interactions were preferred for all δ-protocadherins, with additional weaker heterophilic interactions observed exclusively within each subfamily. As expected, δ1- and δ2-protocadherin trans dimers formed through antiparallel EC1-EC4 interfaces, like clustered protocadherins. However, no ectodomain-mediated cis (same-cell) interactions were detectable in solution; consistent with this, cryo-ET of reconstituted junctions revealed dense assemblies lacking the characteristic order observed for clustered protocadherins. Our results define non-clustered protocadherin binding properties and their structural basis, providing a foundation for interpreting their functional roles in neural patterning.
External linksCell Rep / PubMed:32101743 / PubMed Central
MethodsEM (tomography) / X-ray diffraction
Resolution2 - 3.71 Å
Structure data

EMDB-21188:
human delta protocadherin 1 full ectodomains on membranes of liposomes tomogram 1
Method: EM (tomography)

EMDB-21189:
human delta protocadherin 1 full ectodomains on membranes tomogram 2
Method: EM (tomography)

EMDB-21190:
human delta protocadherin 1 full ectodomains on membranes tomogram 3
Method: EM (tomography)

EMDB-21191:
human non-clustered delta protocadherin 10 on membranes tomogram 1
Method: EM (tomography)

EMDB-21192:
human non-clustered delta protocadherin 10 on membranes tomogram 2
Method: EM (tomography)

EMDB-21193:
human non-clustered delta protocadherin 10 full ectodomains on membranes tomogram 3
Method: EM (tomography)

PDB-6vfp:
Crystal structure of human protocadherin 1 EC1-EC4
Method: X-RAY DIFFRACTION / Resolution: 3.2 Å

PDB-6vfq:
Crystal structure of monomeric human protocadherin 10 EC1-EC4
Method: X-RAY DIFFRACTION / Resolution: 2.3 Å

PDB-6vfr:
Crystal structure of human protocadherin 18 EC1-EC4
Method: X-RAY DIFFRACTION / Resolution: 2.79 Å

PDB-6vft:
Crystal structure of human delta protocadherin 17 EC1-EC4
Method: X-RAY DIFFRACTION / Resolution: 3.71 Å

PDB-6vfu:
Crystal structure of human protocadherin 19 EC1-EC4
Method: X-RAY DIFFRACTION / Resolution: 3.5 Å

PDB-6vfv:
Crystal structure of human protocadherin 8 EC5-EC6
Method: X-RAY DIFFRACTION / Resolution: 2.9 Å

PDB-6vfw:
Crystal structure of human delta protocadherin 10 EC1-EC4
Method: X-RAY DIFFRACTION / Resolution: 3.6 Å

PDB-6vg1:
xenopus protocadherin 8.1 EC1-6
Method: X-RAY DIFFRACTION / Resolution: 2.0 Å

PDB-6vg4:
Human protocadherin 10 ectodomain
Method: X-RAY DIFFRACTION / Resolution: 3.298 Å

Chemicals

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

ChemComp-CA:
Unknown entry

ChemComp-HOH:
WATER

ChemComp-MAN:
alpha-D-mannopyranose

ChemComp-ACT:
ACETATE ION

ChemComp-EDO:
1,2-ETHANEDIOL

ChemComp-NA:
Unknown entry

ChemComp-NI:
NICKEL (II) ION

ChemComp-CL:
Unknown entry

ChemComp-TAM:
TRIS(HYDROXYETHYL)AMINOMETHANE / pH buffer*YM

Source
  • homo sapiens (human)
  • xenopus laevis (African clawed frog)
KeywordsCELL ADHESION / cadherin extracellular region / non-clustered delta1 family protocadherin / homophilic adhesion/recognition calcium-dependent adhesion molecule / non-clustered delta2 family protocadherin / non-clustered delta2 family / protocadherin homophilic adhesion/recognition calcium-dependent / adhesion molecule / protocadherin / homophilic / adhesion/recognition calcium-dependent adhesion molecule / non-clustered delta2 protocadherin / homophilic adhesion/recognition calcium-dependent / cadherin / hemophilic / non-clustered / calcium binding

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