5LOB | pdb_00005lob

Structure of the Ca2+-bound Rabphilin3A C2B- SNAP25 complex (C2 space group)

• PDB DOI: https://doi.org/10.2210/pdb5LOB/pdb

• Classification: EXOCYTOSIS
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2016-08-09 Released: 2017-06-21 
• Deposition Author(s): Ferrer-Orta, C., Verdaguer, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 
  0.286 (Depositor), 0.289 (DCC) 
• R-Value Work: 
  0.240 (Depositor), 0.241 (DCC) 
• R-Value Observed: 
  0.242 (Depositor) 

Starting Model: experimental

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

• PubMed: 28634303 
• 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.

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Organizational Affiliation: 
• Structural Biology Unit, Institut de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Cientificas, 08028 Barcelona, Spain; [e-mail] [e-mail] [e-mail].
Departamento de Bioquímica y Biología Molecular-A, Facultad de Veterinaria, Regional Campus of International Excellence "Campus Mare Nostrum," Universidad de Murcia, Instituto Murciano de Investigación Biosanitaria Virgen de la Arrixaca, 30100 Murcia, Spain.
Structural Biology Unit, Institut de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Cientificas, 08028 Barcelona, Spain.
Departamento de Bioquímica y Biología Molecular-A, Facultad de Veterinaria, Regional Campus of International Excellence "Campus Mare Nostrum," Universidad de Murcia, Instituto Murciano de Investigación Biosanitaria Virgen de la Arrixaca, 30100 Murcia, Spain [e-mail] [e-mail] [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 7-mer - A3B2C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 7-mer - A3B2C2 

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

Macromolecule Content 

• Total Structure Weight: 101.13 kDa 
• Atom Count: 5,922 
• Modeled Residue Count: 725 
• Deposited Residue Count: 878 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rabphilin-3A	A, B, C	162	Rattus norvegicus	Mutation(s): 0  Gene Names: Rph3a
UniProt
Find proteins for P47709 (Rattus norvegicus) Explore P47709  Go to UniProtKB:  P47709

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Synaptosomal-associated protein 25	D, F	100	Rattus norvegicus	Mutation(s): 0  Gene Names: Snap25, Snap
UniProt
Find proteins for P60881 (Rattus norvegicus) Explore P60881  Go to UniProtKB:  P60881

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Synaptosomal-associated protein 25	E, G	96	Rattus norvegicus	Mutation(s): 0  Gene Names: Snap25, Snap
UniProt
Find proteins for P60881 (Rattus norvegicus) Explore P60881  Go to UniProtKB:  P60881

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	AA [auth F], DA [auth G], J [auth A], K [auth A], L [auth A], M [auth A], S [auth B], T [auth B], X [auth C], Z [auth E]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	BA [auth F], CA [auth F], EA [auth G], FA [auth G], N [auth A], O [auth A], P [auth A], U [auth B], Y [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	H [auth A], I [auth A], Q [auth B], R [auth B], V [auth C], W [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free:  0.286 (Depositor), 0.289 (DCC) 
• R-Value Work:  0.240 (Depositor), 0.241 (DCC) 
• R-Value Observed: 0.242 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 153.97	α = 90
b = 58.754	β = 103.24
c = 125.311	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALA	data scaling
MOLREP	phasing
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-06-21 
Deposition Author(s): Ferrer-Orta, C., Verdaguer, N.

Revision History  

• 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