6IRE | pdb_00006ire

Complex structure of INAD PDZ45 and NORPA CC-PBM

• PDB DOI: https://doi.org/10.2210/pdb6IRE/pdb

• Classification: HYDROLASE/PROTEIN BINDING
• Organism(s): Drosophila melanogaster
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2018-11-12 Released: 2019-01-23 
• Deposition Author(s): Ye, F., Li, J., Deng, X., Liu, W., Zhang, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.25 Å
• R-Value Free: 
  0.275 (Depositor), 0.273 (DCC) 
• R-Value Work: 
  0.225 (Depositor), 0.227 (DCC) 
• R-Value Observed: 
  0.228 (Depositor) 

Literature

An unexpected INAD PDZ tandem-mediated plc beta binding in Drosophila photo receptors.

Ye, F., Huang, Y., Li, J., Ma, Y., Xie, C., Liu, Z., Deng, X., Wan, J., Xue, T., Liu, W., Zhang, M.

(2018) Elife 7

• PubMed: 30526850 
• DOI: https://doi.org/10.7554/eLife.41848
• Primary Citation Related Structures: 
  6IRB, 6IRC, 6IRD, 6IRE


• PubMed Abstract: 
  

  INAD assembles key enzymes of the Drosophila compound eye photo-transduction pathway into a supramolecular complex, supporting efficient and fast light signaling. However, the molecular mechanism that governs the interaction between INAD and NORPA (phospholipase Cβ, PLCβ), a key step for the fast kinetics of the light signaling, is not known. Here, we show that the NORPA C-terminal coiled-coil domain and PDZ-binding motif (CC-PBM) synergistically bind to INAD PDZ45 tandem with an unexpected mode and unprecedented high affinity. Guided by the structure of the INAD-NORPA complex, we discover that INADL is probably a mammalian counterpart of INAD. The INADL PDZ89 tandem specifically binds to PLCβ4 with a mode that is strikingly similar to that of the INAD-NORPA complex, as revealed by the structure of the INADL PDZ89-PLCβ4 CC-PBM complex. Therefore, our study suggests that the highly specific PDZ tandem - PLCβ interactions are an evolutionarily conserved mechanism in PLCβ signaling in the animal kingdom.

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Organizational Affiliation: 
• Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China.
Institute for Advanced Study, Hong Kong University of Science and Technology, Hong Kong, China.
Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, China.
Hefei National Laboratory for Physical Sciences at Microscale,CAS Key Laboratory of Brain Function and Disease, Neurodegenerative Disorder Research Center, School of Life Sciences, University of Science and Technology of China, Hefei, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 48.39 kDa 
• Atom Count: 2,982 
• Modeled Residue Count: 416 
• Deposited Residue Count: 428 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase	A	234	Drosophila melanogaster	Mutation(s): 8  Gene Names: norpA, PLC-beta, CG3620 EC: 3.1.4.11
UniProt
Find proteins for P13217 (Drosophila melanogaster) Explore P13217  Go to UniProtKB:  P13217

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Inactivation-no-after-potential D protein	B	194	Drosophila melanogaster	Mutation(s): 0  Gene Names: inaD, CG3504
UniProt
Find proteins for Q24008 (Drosophila melanogaster) Explore Q24008  Go to UniProtKB:  Q24008

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.25 Å
• R-Value Free:  0.275 (Depositor), 0.273 (DCC) 
• R-Value Work:  0.225 (Depositor), 0.227 (DCC) 
• R-Value Observed: 0.228 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.946	α = 90
b = 157.213	β = 90
c = 60.986	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-01-23 
Deposition Author(s): Ye, F., Li, J., Deng, X., Liu, W., Zhang, M.

Revision History  

• Version 1.0: 2019-01-23
  Type: Initial release
  
• Version 1.1: 2020-10-28
  Changes: Database references
• Version 1.2: 2024-03-27
  Changes: Data collection, Database references