Protocadherin Gamma B7 extracellular cadherin domains 1-4 P21 crystal form

Experimental Data Snapshot

  • Resolution: 3.10 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.256 
  • R-Value Observed: 0.259 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.5 of the entry. See complete history


gamma-Protocadherin structural diversity and functional implications.

Goodman, K.M.Rubinstein, R.Thu, C.A.Mannepalli, S.Bahna, F.Ahlsen, G.Rittenhouse, C.Maniatis, T.Honig, B.Shapiro, L.

(2016) Elife 5

  • DOI: https://doi.org/10.7554/eLife.20930
  • Primary Citation of Related Structures:  
    5SZL, 5SZM, 5SZN, 5SZO, 5SZP, 5SZQ, 5SZR, 5T9T

  • PubMed 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 γ-Pcdh ectodomain. The trans -dimer structures reveal determinants of γ-Pcdh 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.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protocadherin Gamma B7
A, B
423Mus musculusMutation(s): 0 
Gene Names: Pcdhgb7mCG_133388
Find proteins for Q91XX3 (Mus musculus)
Explore Q91XX3 
Go to UniProtKB:  Q91XX3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ91XX3
Glycosylation Sites: 5Go to GlyGen: Q91XX3-1
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NAG

Download Ideal Coordinates CCD File 
P [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
Query on MAN

Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth B]
CA [auth B]
L [auth A]
M [auth A]
AA [auth B],
BA [auth B],
CA [auth B],
L [auth A],
M [auth A],
N [auth A],
O [auth A]
C6 H12 O6
Query on TMO

Download Ideal Coordinates CCD File 
Q [auth A]trimethylamine oxide
C3 H9 N O
Query on CA

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
V [auth B],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.813α = 90
b = 45.549β = 96.91
c = 127.072γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM103403
National Institutes of Health/Office of the DirectorUnited StatesOD012351
National Institutes of Health/Office of the DirectorUnited StatesOD021764

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-19
    Type: Initial release
  • Version 1.1: 2016-11-09
    Changes: Database references
  • Version 1.2: 2017-09-20
    Changes: Author supporting evidence, Derived calculations
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.4: 2022-03-23
    Changes: Author supporting evidence, Database references, Structure summary
  • Version 1.5: 2023-10-04
    Changes: Data collection, Refinement description