Database accession: MF7000126
Name: Endophilin BAR domain (human)
PDB ID: 1x03
Experimental method: X-ray (3.10 Å)
Assembly: Homodimer
Source organism: Homo sapiens
Primary publication of the structure:
Masuda M, Takeda S, Sone M, Ohki T, Mori H, Kamioka Y, Mochizuki N
Endophilin BAR domain drives membrane curvature by two newly identified structure-based mechanisms.
(2006) EMBO J. 25: 2889-97
PMID: 16763557
Abstract:
The crescent-shaped BAR (Bin/Amphiphysin/Rvs-homology) domain dimer is a versatile protein module that senses and generates positive membrane curvature. The BAR domain dimer of human endophilin-A1, solved at 3.1 A, has a unique structure consisting of a pair of helix-loop appendages sprouting out from the crescent. The appendage's short helices form a hydrophobic ridge, which runs across the concave surface at its center. Examining liposome binding and tubulation in vitro using purified BAR domain and its mutants indicated that the ridge penetrates into the membrane bilayer and enhances liposome tubulation. BAR domain-expressing cells exhibited marked plasma membrane tubulation in vivo. Furthermore, a swinging-arm mutant lost liposome tubulation activity yet retaining liposome binding. These data suggested that the rigid crescent dimer shape is crucial for the tubulation. We here propose that the BAR domain drives membrane curvature by coordinate action of the crescent's scaffold mechanism and the ridge's membrane insertion in addition to membrane binding via amino-terminal amphipathic helix.
Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown. Molecular function:
identical protein binding identical protein binding
lipid binding lipid binding
Biological process:
cellular response to brain-derived neurotrophic factor stimulus cellular response to brain-derived neurotrophic factor stimulus
central nervous system development central nervous system development
dendrite extension dendrite extension
negative regulation of blood-brain barrier permeability negative regulation of blood-brain barrier permeability
negative regulation of gene expression negative regulation of gene expression
negative regulation of protein phosphorylation negative regulation of protein phosphorylation
neuron projection development neuron projection development
signal transduction signal transduction
synaptic vesicle uncoating synaptic vesicle uncoating
Cellular component:
cell projection cell projection
clathrin-coated endocytic vesicle membrane clathrin-coated endocytic vesicle membrane
cytoplasm cytoplasm
cytosol cytosol
early endosome early endosome
glutamatergic synapse glutamatergic synapse
Golgi membrane Golgi membrane
perinuclear region of cytoplasm perinuclear region of cytoplasm
plasma membrane plasma membrane
presynapse presynapse
Structural annotations of the participating protein chains.Entry contents: 2 distinct polypeptide molecules
Chains: A, A-2
Notes: All chains according to the most probable oligomerization state stored in PDBe were considered.
Number of unique protein segments: 1
Name: Endophilin-A1
Source organism: Homo sapiens
Length: 352 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMSVAGLKKQFHKATQKVSEKVGGAEGTKLDDDFKEMERKVDVTSRAVMEIMTKTIEYLQPNPASRAKLSMINTMSKIRGQEKGPGYPQAEALLAEAMLKFGRELGDDCNFGPALGEVGEAMRELSEVKDSLDIEVKQNFIDPLQNLHDKDLREIQHHLKKLEGRRLDFDYKKKRQGKIPDEELRQALEKFDESKEIAESSMFNLLEMDIEQVSQLSALVQAQLEYHKQAVQILQQVTVRLEERIRQASSQPRREYQPKPRMSLEFPTGDSTQPNGGLSHTGTPKPSGVQMDQPCCRALYDFEPENEGELGFKEGDIITLTNQIDENWYEGMLHGHSGFFPINYVEILVALPH
UniProtKB AC: Q99962 (positions: 26-247)
Coverage: 63%
Name: Endophilin-A1
Source organism: Homo sapiens
Length: 352 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMSVAGLKKQFHKATQKVSEKVGGAEGTKLDDDFKEMERKVDVTSRAVMEIMTKTIEYLQPNPASRAKLSMINTMSKIRGQEKGPGYPQAEALLAEAMLKFGRELGDDCNFGPALGEVGEAMRELSEVKDSLDIEVKQNFIDPLQNLHDKDLREIQHHLKKLEGRRLDFDYKKKRQGKIPDEELRQALEKFDESKEIAESSMFNLLEMDIEQVSQLSALVQAQLEYHKQAVQILQQVTVRLEERIRQASSQPRREYQPKPRMSLEFPTGDSTQPNGGLSHTGTPKPSGVQMDQPCCRALYDFEPENEGELGFKEGDIITLTNQIDENWYEGMLHGHSGFFPINYVEILVALPH
UniProtKB AC: Q99962 (positions: 26-247)
Coverage: 63%
Evidence demonstrating that the participating proteins are unstructured prior to the interaction and their folding is coupled to binding. Representative domain in related structures: N-BAR domain
Evidence level: Direct evidence
Evidence coverage: The full structure participates in mutual synergistic folding.
Complex Evidence:
The human AmphyphisinII/Bin1 and Endophilin BAR domains (N-BARs) display two-state equilibrium unfolding from the dimeric to unfolded monomeric forms (PMID:26368922, PMID:34423187).
Chain A:
N/A
Chain A-2:
N/A
Surface and contacts features:
Structures from the PDB that contain the same number of proteins, and the proteins from the two structures show a sufficient degree of pairwise similarity, i.e. they belong to the same UniRef90 cluster (the full proteins exhibit at least 90% sequence identity) and convey roughly the same region to their respective interactions (the two regions from the two proteins share a minimum of 70% overlap). Download the CIF file (.cif)
Download this entry's XML file (.xml)
Download this entry's JSON file (.json)
