Database accession: MF7000691
Name: EFC/F-BAR domain (Drosophila Syndapin/PACSIN)
PDB ID: 3i2w
Experimental method: X-ray (2.67 Å)
Assembly: Homodimer
Source organism: Drosophila melanogaster
Primary publication of the structure:
Edeling MA, Sanker S, Shima T, Umasankar PK, Höning S, Kim HY, Davidson LA, Watkins SC, Tsang M, Owen DJ, Traub LM
Structural requirements for PACSIN/Syndapin operation during zebrafish embryonic notochord development.
(2009) PLoS ONE 4: e8150
PMID: 19997509
Abstract:
PACSIN/Syndapin proteins are membrane-active scaffolds that participate in endocytosis. The structure of the Drosophila Syndapin N-terminal EFC domain reveals a crescent shaped antiparallel dimer with a high affinity for phosphoinositides and a unique membrane-inserting prong upon the concave surface. Combined structural, biochemical and reverse genetic approaches in zebrafish define an important role for Syndapin orthologue, Pacsin3, in the early formation of the notochord during embryonic development. In pacsin3-morphant embryos, midline convergence of notochord precursors is defective as axial mesodermal cells fail to polarize, migrate and differentiate properly. The pacsin3 morphant phenotype of a stunted body axis and contorted trunk is rescued by ectopic expression of Drosophila Syndapin, and depends critically on both the prong that protrudes from the surface of the bowed Syndapin EFC domain and the ability of the antiparallel dimer to bind tightly to phosphoinositides. Our data confirm linkage between directional migration, endocytosis and cell specification during embryonic morphogenesis and highlight a key role for Pacsin3 in this coupling in the notochord.
Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown. Molecular function:
lipid binding lipid binding
phospholipid binding phospholipid binding
Biological process:
cleavage furrow ingression cleavage furrow ingression
cytoskeleton organization cytoskeleton organization
male meiosis cytokinesis male meiosis cytokinesis
membrane organization membrane organization
mitotic cytokinesis mitotic cytokinesis
plasma membrane tubulation plasma membrane tubulation
positive regulation of synaptic assembly at neuromuscular junction positive regulation of synaptic assembly at neuromuscular junction
regulation of endocytosis regulation of endocytosis
spindle assembly involved in male meiosis spindle assembly involved in male meiosis
Cellular component:
cleavage furrow cleavage furrow
cytoplasm cytoplasm
endosome endosome
midbody midbody
plasma membrane plasma membrane
postsynaptic membrane postsynaptic membrane
subsynaptic reticulum subsynaptic reticulum
Structural annotations of the participating protein chains.Entry contents: 2 distinct polypeptide molecules
Chains: A, B
Notes: All chains according to the most probable oligomerization state stored in PDBe were considered.
Number of unique protein segments: 1
Name: LD46328p
Source organism: Drosophila melanogaster
Length: 494 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMSHHSDDQLLQAGSDSFWEPGNYKRTTKRIEDGYKLCNDLQQLIQERADIEKGYAKSLRTWSKKWGELIEKGPEYGTTEAAWKGVLTESERISDVHMKIKDNLCNDVNSQIKTWQKENYHHTLMQIKERKDLEDLFKKAQKPWAKLLAKVEKAKADYHSACKTERSATNQERNANADSSLSPDQVKKMHDRVQKTKDQVQKCREKYEQAIAEITKYNSVYIEDMTSVFEKCQTFEKTRLQFFKEILFNVHSCLDLTKVQSLPQIYEEFSHTINNADQQKDLKWWSNNHGINMAMNWPSFVEYTEEFRDIAKGNKSKEALPAAPITLINQRPVAEDVHEYPQTNSLKKNTSTLSSVSSRASVKSEIATTQSSVTTSEAKTSAAVAGAATATAAATAASAASNRNSSVTNGNGKVDANPFDEEEEWDESDNVLVDNGEPGVPVKALYDYEGAESDELTFKQGDVFEKLEDEDEQGWCKGRMNGRVGLYPANYVETA
UniProtKB AC: Q9VDI1 (positions: 14-303)
Coverage: 58%
Name: LD46328p
Source organism: Drosophila melanogaster
Length: 494 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMSHHSDDQLLQAGSDSFWEPGNYKRTTKRIEDGYKLCNDLQQLIQERADIEKGYAKSLRTWSKKWGELIEKGPEYGTTEAAWKGVLTESERISDVHMKIKDNLCNDVNSQIKTWQKENYHHTLMQIKERKDLEDLFKKAQKPWAKLLAKVEKAKADYHSACKTERSATNQERNANADSSLSPDQVKKMHDRVQKTKDQVQKCREKYEQAIAEITKYNSVYIEDMTSVFEKCQTFEKTRLQFFKEILFNVHSCLDLTKVQSLPQIYEEFSHTINNADQQKDLKWWSNNHGINMAMNWPSFVEYTEEFRDIAKGNKSKEALPAAPITLINQRPVAEDVHEYPQTNSLKKNTSTLSSVSSRASVKSEIATTQSSVTTSEAKTSAAVAGAATATAAATAASAASNRNSSVTNGNGKVDANPFDEEEEWDESDNVLVDNGEPGVPVKALYDYEGAESDELTFKQGDVFEKLEDEDEQGWCKGRMNGRVGLYPANYVETA
UniProtKB AC: Q9VDI1 (positions: 14-298)
Coverage: 57%
Evidence demonstrating that the participating proteins are unstructured prior to the interaction and their folding is coupled to binding. Representative domain in related structures: F-BAR domain
Evidence level: Direct evidence
Evidence coverage: The full structure participates in mutual synergistic folding.
Complex Evidence:
F-BAR domains form an intimately packed six-helix bundle and bury a large, hydrophobic dimerization interface. They exist as dimers in solution, with no evidence for monomeric forms (PMID:17512409). Other BAR domains (N-BAR) displayed a two-state equilibrium unfolding (PMID:26368922, PMID:34423187).
Chain A:
N/A
Chain B:
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)
