Protocadherin Gamma B2 extracellular cadherin domains 3-6

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.251 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 2.2 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
Protein Pcdhgb2
A, B, C
441Mus musculusMutation(s): 0 
Gene Names: Pcdhgb2
UniProt & NIH Common Fund Data Resources
Find proteins for Q91XX7 (Mus musculus)
Explore Q91XX7 
Go to UniProtKB:  Q91XX7
IMPC:  MGI:1935170
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ91XX7
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
D, F
Glycosylation Resources
GlyTouCan:  G32152BH
GlyCosmos:  G32152BH
GlyGen:  G32152BH
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
E, G, I
Glycosylation Resources
GlyTouCan:  G86851RC
GlyCosmos:  G86851RC
GlyGen:  G86851RC
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
Glycosylation Resources
GlyTouCan:  G21290RB
GlyCosmos:  G21290RB
GlyGen:  G21290RB
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on MAN

Download Ideal Coordinates CCD File 
CB [auth C]
DB [auth C]
EB [auth C]
FB [auth C]
GB [auth C]
CB [auth C],
DB [auth C],
EB [auth C],
FB [auth C],
GB [auth C],
HB [auth C],
IB [auth C],
MA [auth B],
NA [auth B],
OA [auth B],
PA [auth B],
QA [auth B],
RA [auth B],
S [auth A],
SA [auth B],
T [auth A],
U [auth A],
V [auth A],
W [auth A],
X [auth A],
Y [auth A]
C6 H12 O6
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth A],
BA [auth A],
CA [auth A],
JB [auth C],
Z [auth A]
C2 H6 O2
Query on CA

Download Ideal Coordinates CCD File 
AB [auth C]
BB [auth C]
DA [auth B]
EA [auth B]
FA [auth B]
AB [auth C],
BB [auth C],
DA [auth B],
EA [auth B],
FA [auth B],
GA [auth B],
HA [auth B],
IA [auth B],
J [auth A],
JA [auth B],
K [auth A],
KA [auth B],
L [auth A],
LA [auth B],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
TA [auth C],
UA [auth C],
VA [auth C],
WA [auth C],
XA [auth C],
YA [auth C],
ZA [auth C]
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.755α = 90
b = 104.755β = 90
c = 352.136γ = 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: 2017-11-01
    Changes: Author supporting evidence
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2022-03-23
    Changes: Author supporting evidence, Database references, Derived calculations, Structure summary
  • Version 2.2: 2023-10-04
    Changes: Data collection, Refinement description