5SZN | pdb_00005szn

Protocadherin gamma A9 extracellular cadherin domains 1-5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.94 Å
  • R-Value Free: 
    0.295 (Depositor), 0.310 (DCC) 
  • R-Value Work: 
    0.241 (Depositor), 0.244 (DCC) 
  • R-Value Observed: 
    0.244 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5SZN

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: 61.77 kDa 
  • Atom Count: 4,052 
  • Modeled Residue Count: 523 
  • Deposited Residue Count: 537 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Protocadherin gamma A9537Mus musculusMutation(s): 0 
Gene Names: Pcdhga9
UniProt
Find proteins for Q91XX9 (Mus musculus)
Explore Q91XX9 
Go to UniProtKB:  Q91XX9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ91XX9
Glycosylation
Glycosylation Sites: 5Go to GlyGen: Q91XX9-1
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)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
F [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
MAN

Query on MAN



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
E [auth A]
alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
V [auth A],
W [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
G [auth A]
H [auth A]
I [auth A]
J [auth A]
K [auth A]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.94 Å
  • R-Value Free:  0.295 (Depositor), 0.310 (DCC) 
  • R-Value Work:  0.241 (Depositor), 0.244 (DCC) 
  • R-Value Observed: 0.244 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 191.68α = 90
b = 107.61β = 97.14
c = 49.87γ = 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 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, Structure summary
  • Version 2.2: 2024-04-03
    Changes: Data collection, Refinement description
  • Version 2.3: 2024-10-30
    Changes: Structure summary