5LO8 | pdb_00005lo8

The C2B domain of Rabphilin 3A in complex with PI(4,5)P2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.265 (Depositor), 0.246 (DCC) 
  • R-Value Work: 
    0.252 (Depositor) 
  • R-Value Observed: 
    0.271 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Structural characterization of the Rabphilin-3A-SNAP25 interaction.

Ferrer-Orta, C.Perez-Sanchez, M.D.Coronado-Parra, T.Silva, C.Lopez-Martinez, D.Baltanas-Copado, J.Gomez-Fernandez, J.C.Corbalan-Garcia, S.Verdaguer, N.

(2017) Proc Natl Acad Sci U S A 114: E5343-E5351

  • DOI: https://doi.org/10.1073/pnas.1702542114
  • Primary Citation Related Structures: 
    5LO8, 5LOB, 5LOW

  • PubMed Abstract: 

    Membrane fusion is essential in a myriad of eukaryotic cell biological processes, including the synaptic transmission. Rabphilin-3A is a membrane trafficking protein involved in the calcium-dependent regulation of secretory vesicle exocytosis in neurons and neuroendocrine cells, but the underlying mechanism remains poorly understood. Here, we report the crystal structures and biochemical analyses of Rabphilin-3A C2B-SNAP25 and C2B-phosphatidylinositol 4,5-bisphosphate (PIP 2 ) complexes, revealing how Rabphilin-3A C2 domains operate in cooperation with PIP 2 /Ca 2+ and SNAP25 to bind the plasma membrane, adopting a conformation compatible to interact with the complete SNARE complex. Comparisons with the synaptotagmin1-SNARE show that both proteins contact the same SNAP25 surface, but Rabphilin-3A uses a unique structural element. Data obtained here suggest a model to explain the Ca 2+ -dependent fusion process by membrane bending with a myriad of variations depending on the properties of the C2 domain-bearing protein, shedding light to understand the fine-tuning control of the different vesicle fusion events.


  • Organizational Affiliation
    • Structural Biology Unit, Institut de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Cientificas, 08028 Barcelona, Spain; cfocri@ibmb.csic.es senena@um.es nvmcri@ibmb.csic.es.

Macromolecule Content 

  • Total Structure Weight: 39.55 kDa 
  • Atom Count: 2,465 
  • Modeled Residue Count: 282 
  • Deposited Residue Count: 324 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Rabphilin-3A
A, B
162Rattus norvegicusMutation(s): 0 
Gene Names: Rph3a
UniProt
Find proteins for P47709 (Rattus norvegicus)
Explore P47709 
Go to UniProtKB:  P47709
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP47709
Sequence Annotations
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Reference Sequence

Small Molecules

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

Query on PIO



Download:Ideal Coordinates CCD File
J [auth A],
P [auth B]
[(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate
C25 H49 O19 P3
XLNCEHRXXWQMPK-MJUMVPIBSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
I [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
G [auth A]
H [auth A]
M [auth B]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
M [auth B],
N [auth B],
O [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
K [auth B],
L [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.265 (Depositor), 0.246 (DCC) 
  • R-Value Work:  0.252 (Depositor) 
  • R-Value Observed: 0.271 (Depositor) 
Space Group: P 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.52α = 90
b = 92.52β = 90
c = 40.02γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
SCALAdata 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: 2017-06-21
    Type: Initial release
  • Version 1.1: 2017-12-06
    Changes: Database references
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description