7ZC9

Human Pikachurin/EGFLAM C-terminal Laminin-G domain (LG3)

  • Classification: SIGNALING PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): No 

  • Deposited: 2022-03-26 Released: 2023-07-19 
  • Deposition Author(s): Pantalone, S., Forneris, F.
  • Funding Organization(s): Velux Stiftung, The Giovanni Armenise-Harvard Foundation, Ministero dell Universita e della Ricerca

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structure of the photoreceptor synaptic assembly of the extracellular matrix protein pikachurin with the orphan receptor GPR179.

Patil, D.N.Pantalone, S.Cao, Y.Laboute, T.Novick, S.J.Singh, S.Savino, S.Faravelli, S.Magnani, F.Griffin, P.R.Singh, A.K.Forneris, F.Martemyanov, K.A.

(2023) Sci Signal 16: eadd9539-eadd9539

  • DOI: https://doi.org/10.1126/scisignal.add9539
  • Primary Citation of Related Structures:  
    7ZC9, 7ZCB, 8D1B

  • PubMed Abstract: 

    Precise synapse formation is essential for normal functioning of the nervous system. Retinal photoreceptors establish selective contacts with bipolar cells, aligning the neurotransmitter release apparatus with postsynaptic signaling cascades. This involves transsynaptic assembly between the dystroglycan-dystrophin complex on the photoreceptor and the orphan receptor GPR179 on the bipolar cell, which is mediated by the extracellular matrix protein pikachurin (also known as EGFLAM). This complex plays a critical role in the synaptic organization of photoreceptors and signal transmission, and mutations affecting its components cause blinding disorders in humans. Here, we investigated the structural organization and molecular mechanisms by which pikachurin orchestrates transsynaptic assembly and solved structures of the human pikachurin domains by x-ray crystallography and of the GPR179-pikachurin complex by single-particle, cryo-electron microscopy. The structures reveal molecular recognition principles of pikachurin by the Cache domains of GPR179 and show how the interaction is involved in the transsynaptic alignment of the signaling machinery. Together, these data provide a structural basis for understanding the synaptic organization of photoreceptors and ocular pathology.


  • Organizational Affiliation

    Department of Neuroscience, Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, University of Florida, Jupiter, FL 33458, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PikachurinA [auth B],
B [auth A]
201Homo sapiensMutation(s): 0 
Gene Names: EGFLAMAGRINLAGRNLPIKA
UniProt & NIH Common Fund Data Resources
Find proteins for Q63HQ2 (Homo sapiens)
Explore Q63HQ2 
Go to UniProtKB:  Q63HQ2
PHAROS:  Q63HQ2
GTEx:  ENSG00000164318 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ63HQ2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
C [auth B]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth B]
E [auth B]
F [auth B]
G [auth B]
H [auth B]
D [auth B],
E [auth B],
F [auth B],
G [auth B],
H [auth B],
I [auth B],
J [auth B],
K [auth B],
L [auth B],
M [auth B],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.208 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.805α = 90
b = 103.818β = 90
c = 133.534γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
ARP/wARPmodel building

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Velux StiftungSwitzerland1375
The Giovanni Armenise-Harvard FoundationUnited StatesCDA 2013
Ministero dell Universita e della RicercaItalyDipartimenti di Eccellenza 2018-2022

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-19
    Type: Initial release
  • Version 1.1: 2023-08-02
    Changes: Database references
  • Version 1.2: 2024-02-07
    Changes: Data collection, Refinement description