4ZPS | pdb_00004zps

Crystal Structure of Protocadherin Gamma A8 EC1-3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 
    0.286 (Depositor), 0.292 (DCC) 
  • R-Value Work: 
    0.264 (Depositor), 0.269 (DCC) 
  • R-Value Observed: 
    0.266 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Molecular Logic of Neuronal Self-Recognition through Protocadherin Domain Interactions.

Rubinstein, R.Thu, C.A.Goodman, K.M.Wolcott, H.N.Bahna, F.Mannepalli, S.Ahlsen, G.Chevee, M.Halim, A.Clausen, H.Maniatis, T.Shapiro, L.Honig, B.

(2015) Cell 163: 629-642

  • DOI: https://doi.org/10.1016/j.cell.2015.09.026
  • Primary Citation Related Structures: 
    4ZPL, 4ZPM, 4ZPN, 4ZPO, 4ZPP, 4ZPQ, 4ZPS

  • PubMed Abstract: 

    Self-avoidance, a process preventing interactions of axons and dendrites from the same neuron during development, is mediated in vertebrates through the stochastic single-neuron expression of clustered protocadherin protein isoforms. Extracellular cadherin (EC) domains mediate isoform-specific homophilic binding between cells, conferring cell recognition through a poorly understood mechanism. Here, we report crystal structures for the EC1-EC3 domain regions from four protocadherin isoforms representing the α, β, and γ subfamilies. All are rod shaped and monomeric in solution. Biophysical measurements, cell aggregation assays, and computational docking reveal that trans binding between cells depends on the EC1-EC4 domains, which interact in an antiparallel orientation. We also show that the EC6 domains are required for the formation of cis-dimers. Overall, our results are consistent with a model in which protocadherin cis-dimers engage in a head-to-tail interaction between EC1-EC4 domains from apposed cell surfaces, possibly forming a zipper-like protein assembly, and thus providing a size-dependent self-recognition mechanism.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Department of Systems Biology, Columbia University, New York, NY 10032, USA.

Macromolecule Content 

  • Total Structure Weight: 36.43 kDa 
  • Atom Count: 2,416 
  • Modeled Residue Count: 313 
  • Deposited Residue Count: 321 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
MCG133388, isoform CRA_m321Mus musculusMutation(s): 0 
Gene Names: Pcdhga8mCG_133388
UniProt
Find proteins for Q91XY0 (Mus musculus)
Explore Q91XY0 
Go to UniProtKB:  Q91XY0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ91XY0
Glycosylation
Glycosylation Sites: 2Go to GlyGen: Q91XY0-1
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MAN

Query on MAN



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

Query on CA



Download:Ideal Coordinates CCD File
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free:  0.286 (Depositor), 0.292 (DCC) 
  • R-Value Work:  0.264 (Depositor), 0.269 (DCC) 
  • R-Value Observed: 0.266 (Depositor) 
Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.06α = 90
b = 78.12β = 90
c = 167.73γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-10-28
    Type: Initial release
  • Version 1.1: 2015-11-04
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.3: 2024-11-06
    Changes: Data collection, Database references, Structure summary