5SZR | pdb_00005szr

Protocadherin Gamma B2 extracellular cadherin domains 3-6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.278 (Depositor), 0.292 (DCC) 
  • R-Value Work: 
    0.250 (Depositor), 0.256 (DCC) 
  • R-Value Observed: 
    0.251 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 5SZR

Ligand Structure Quality Assessment 


This is version 2.3 of the entry. See complete history

Literature

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 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.

Macromolecule Content 

  • Total Structure Weight: 152.85 kDa 
  • Atom Count: 10,333 
  • Modeled Residue Count: 1,261 
  • Deposited Residue Count: 1,323 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
Glycosylation
Glycosylation Sites: 9Go to GlyGen: Q91XX7-1
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
D, F
4N-Glycosylation
Glycosylation Resources
GlyTouCan: G32152BH
GlyCosmos: G32152BH
GlyGen: G32152BH
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose
E, G, I
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G86851RC
GlyCosmos: G86851RC
GlyGen: G86851RC
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
H
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G21290RB
GlyCosmos: G21290RB
GlyGen: G21290RB

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MAN

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]
alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
AA [auth A],
BA [auth A],
CA [auth A],
JB [auth C],
Z [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA

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]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.278 (Depositor), 0.292 (DCC) 
  • R-Value Work:  0.250 (Depositor), 0.256 (DCC) 
  • R-Value Observed: 0.251 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.755α = 90
b = 104.755β = 90
c = 352.136γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



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
  • Version 2.3: 2024-10-23
    Changes: Structure summary