γ-Protocadherin structural diversity and functional implications

Abstract
Data availability
Article and author information
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Abstract

Stochastic cell-surface expression of α-, β-, and γ-clustered protocadherins (Pcdhs) provides vertebrate neurons with single-cell identities that underlie neuronal self-recognition. Here we report crystal structures of ectodomain fragments comprising cell-cell recognition regions of mouse γ-Pcdhs γA1, γA8, γB2, and γB7 revealing trans-homodimers, and of C-terminal ectodomain fragments from γ-Pcdhs γA4 and γB2, which depict cis-interacting regions in monomeric form. Together these structures span the entire Pcdhγ ectodomain. The trans-dimer structures reveal determinants of Pcdh-γ isoform-specific homophilic recognition. We identified and structurally mapped cis-dimerization mutations to the C-terminal ectodomain structures. Biophysical studies showed that Pcdh ectodomains from γB-subfamily isoforms formed cis dimers, whereas γA isoforms did not, but both γA and γB isoforms could interact in cis with α-Pcdhs. Together, these data show how interaction specificity is distributed over all domains of the γ-Pcdh trans interface, and suggest that subfamily- or isoform-specific cis-interactions may play a role in the Pcdh-mediated neuronal self-recognition code.

Data availability

The following data sets were generated

1. Goodman KM
2. Bahna F
3. Mannepalli S
4. Honig B
5. Shapiro L
(2016) Protocadherin gamma A1 extracellular cadherin domains 1-4
Publicly available at the RCSB Protein Data Bank (accession no. 5SZL).

http://www.rcsb.org/pdb/explore/explore.do?structureId=5SZL
1. Goodman KM
2. Mannepalli S
3. Bahna F
4. Honig B
5. Shapiro L
(2016) Protocadherin gamma A8 extracellular cadherin domains 1-4
Publicly available at the RCSB Protein Data Bank (accession no. 5SZM).

http://www.rcsb.org/pdb/explore/explore.do?structureId=5SZM
1. Goodman KM
2. Mannepalli S
3. Bahna F
4. Honig B
5. Shapiro L
(2016) Protocadherin gamma A9 extracellular cadherin domains 1-5
Publicly available at the RCSB Protein Data Bank (accession no. 5SZN).

http://www.rcsb.org/pdb/explore/explore.do?structureId=5SZN
1. Goodman KM
2. Mannepalli S
3. Bahna F
4. Honig B
5. Shapiro L
(2016) Protocadherin Gamma B7 extracellular cadherin domains 1-4 P41212 crystal form
Publicly available at the RCSB Protein Data Bank (accession no. 5SZO).

http://www.rcsb.org/pdb/explore/explore.do?structureId=5SZO
1. Goodman KM
2. Mannepalli S
3. Bahna F
4. Honig B
5. Shapiro L
(2016) Protocadherin Gamma B7 extracellular cadherin domains 1-4 P21 crystal form
Publicly available at the RCSB Protein Data Bank (accession no. 5SZP).

http://www.rcsb.org/pdb/explore/explore.do?structureId=5SZP
1. Goodman KM
2. Mannepalli S
3. Bahna F
4. Honig B
5. Shapiro L
(2016) Protocadherin gamma A4 extracellular cadherin domains 3-6
Publicly available at the RCSB Protein Data Bank (accession no. 5SZQ).

http://www.rcsb.org/pdb/search/structidSearch.do?structureId=5SZQ
1. Goodman KM
2. Mannepalli S
3. Bahna F
4. Honig B
5. Shapiro L
(2016) Protocadherin Gamma B2 extracellular cadherin domains 3-6
Publicly available at the RCSB Protein Data Bank (accession no. 5SZR).

http://www.rcsb.org/pdb/explore/explore.do?structureId=5SZR
1. Goodman KM
2. Mannepalli S
3. Bahna F
4. Honig B
5. Shapiro L
(2016) Protocadherin Gamma B2 extracellular cadherin domains 1-5
Publicly available at the RCSB Protein Data Bank (accession no. 5T9T).

http://www.rcsb.org/pdb/explore/explore.do?structureId=5T9T

The following previously published data sets were used

(2015) Structure of mouse clustered PcdhgA1 EC1-3
Publicly available at the RCSB Protein Data Bank (accession no. 4ZI9).

http://www.rcsb.org/pdb/explore/explore.do?structureId=4ZI9
(2015) Crystal Structure of Protocadherin Gamma A8 EC1-3
Publicly available at the RCSB Protein Data Bank (accession no. 4ZPS).

http://www.rcsb.org/pdb/explore/explore.do?structureId=4ZPS
1. Goodman KM
2. Bahna F
3. Honig B
4. Shapiro L
(2016) Protocadherin alpha 7 extracellular cadherin domains 1-5
Publicly available at the RCSB Protein Data Bank (accession no. 5DZV).

http://www.rcsb.org/pdb/explore/explore.do?structureId=5DZV

Article and author information

Author details

Kerry Marie Goodman

Department of Biochemistry and Molecular Biophysics, Columbia University, New York, United States

Competing interests
The authors declare that no competing interests exist.
Rotem Rubinstein

Department of Biochemistry and Molecular Biophysics, Columbia University, New York, United States

Competing interests
The authors declare that no competing interests exist.
Chan Aye Thu

Department of Biochemistry and Molecular Biophysics, Columbia University, New York, United States

Competing interests
The authors declare that no competing interests exist.
Seetha Mannepalli

Department of Biochemistry and Molecular Biophysics, Columbia University, New York, United States

Competing interests
The authors declare that no competing interests exist.
Fabiana Bahna

Department of Biochemistry and Molecular Biophysics, Columbia University, New York, United States

Competing interests
The authors declare that no competing interests exist.
Göran Ahlsén

Department of Systems Biology, Columbia University, New York, United States

Competing interests
The authors declare that no competing interests exist.
Chelsea Rittenhouse

Department of Biochemistry and Molecular Biophysics, Columbia University, New York, United States

Competing interests
The authors declare that no competing interests exist.
Tom Maniatis

Department of Biochemistry and Molecular Biophysics, Columbia University, New York, United States

Competing interests
The authors declare that no competing interests exist.
Barry Honig

Center for Computational Biology and Bioinformatics, Department of Systems Biology, Columbia University, New York, United States

For correspondence
bh6@cumc.columbia.edu

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-2480-6696
Lawrence Shapiro

Department of Biochemistry and Molecular Biophysics, Columbia University, New York, United States

For correspondence
shapiro@convex.hhmi.columbia.edu

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0001-9943-8819

Funding

National Institutes of Health (R01GM107571)

Tom Maniatis
Lawrence Shapiro

Howard Hughes Medical Institute (R01GM062270)

Fabiana Bahna
Barry Honig

National Science Foundation (MCB-1412472)

Barry Honig

Howard Hughes Medical Institute

Fabiana Bahna
Göran Ahlsén
Barry Honig

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.