Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 24.03 kDa 
• Atom Count: 1653 
• Residue Count: 204 
• Unique protein chains: 1

2C08

Rat endophilin A1 BAR domain

• DOI: 10.2210/pdb2C08/pdb

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


• Deposited: 2005-08-26 Released: 2006-06-14 
• Deposition Author(s): Gallop, J.L., Kent, H.M., Mcmahon, H.T., Evans, P.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.295 
• R-Value Work: 0.279 
• R-Value Observed: 0.280 

Literature

Mechanism of Endophilin N-Bar Domain-Mediated Membrane Curvature.

Gallop, J.L., Jao, C.C., Kent, H.M., Butler, P.J., Evans, P.R., Langen, R., Mcmahon, H.T.

(2006) EMBO J 25: 2898

• PubMed: 16763559 
• DOI: 10.1038/sj.emboj.7601174
• Primary Citation of Related Structures:  
  2C08


• PubMed Abstract: 
  

Endophilin-A1 is a BAR domain-containing protein enriched at synapses and is implicated in synaptic vesicle endocytosis. It binds to dynamin and synaptojanin via a C-terminal SH3 domain. We examine the mechanism by which the BAR domain and an N-terminal amphipathic helix, which folds upon membrane binding, work as a functional unit (the N-BAR domain) to promote dimerisation and membrane curvature generation. By electron paramagnetic resonance spectroscopy, we show that this amphipathic helix is peripherally bound in the plane of the membrane, with the midpoint of insertion aligned with the phosphate level of headgroups. This places the helix in an optimal position to effect membrane curvature generation. We solved the crystal structure of rat endophilin-A1 BAR domain and examined a distinctive insert protruding from the membrane interaction face. This insert is predicted to form an additional amphipathic helix and is important for curvature generation. Its presence defines an endophilin/nadrin subclass of BAR domains. We propose that N-BAR domains function as low-affinity dimers regulating binding partner recruitment to areas of high membrane curvature.

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Organizational Affiliation: 

MRC Laboratory of Molecular Biology, Cambridge, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SH3-CONTAINING GRB2-LIKE PROTEIN 2	A	204	Rattus norvegicus	Mutation(s): 0  Gene Names: Sh3gl2, Sh3d2a, Sh3p4 EC: 2.3.1
Find proteins for O35179 (Rattus norvegicus) Explore O35179  Go to UniProtKB:  O35179

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.295 
• R-Value Work: 0.279 
• R-Value Observed: 0.280 
• Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.578	α = 90
b = 126.578	β = 90
c = 101.226	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-08-26 
• Released Date: 2006-06-14 
Deposition Author(s): Gallop, J.L., Kent, H.M., Mcmahon, H.T., Evans, P.R.

Revision History 

• Version 1.0: 2006-06-14
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-05-29
  Changes: Data collection, Derived calculations, Experimental preparation, Other