Database accession: MF7000692
Name: EFC/F-BAR domain of human PACSIN2/Syndapin II
PDB ID: 3abh
Experimental method: X-ray (2.00 Å)
Assembly: Homodimer
Source organism: Homo sapiens
Primary publication of the structure:
Shimada A, Takano K, Shirouzu M, Hanawa-Suetsugu K, Terada T, Toyooka K, Umehara T, Yamamoto M, Yokoyama S, Suetsugu S
Mapping of the basic amino-acid residues responsible for tubulation and cellular protrusion by the EFC/F-BAR domain of pacsin2/Syndapin II.
(2010) FEBS Lett. 584: 1111-8
PMID: 20188097
Abstract:
The extended Fes-CIP4 homology (EFC)/FCH-BAR (F-BAR) domain tubulates membranes. Overexpression of the pacsin2 EFC/F-BAR domain resulted in tubular localization inside cells and deformed liposomes into tubules in vitro. We found that overexpression of the pacsin2 EFC/F-BAR domain induced cellular microspikes, with the pacsin2 EFC/F-BAR domain concentrated at the neck. The hydrophobic loops and the basic amino-acid residues on the concave surface of the pacsin2 EFC/F-BAR domain are essential for both the microspike formation and tubulation. Since the curvature of the neck of the microspike and that of the tubulation share similar geometry, the pacsin2 EFC/F-BAR domain is considered to facilitate both microspike formation and tubulation.
Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown. Molecular function:
cadherin binding cadherin binding
cytoskeletal protein binding cytoskeletal protein binding
identical protein binding identical protein binding
phosphatidic acid binding phosphatidic acid binding
phospholipid binding phospholipid binding
Biological process:
actin cytoskeleton organization actin cytoskeleton organization
caveola assembly caveola assembly
caveolin-mediated endocytosis caveolin-mediated endocytosis
cell projection morphogenesis cell projection morphogenesis
cytoskeleton organization cytoskeleton organization
modulation of chemical synaptic transmission modulation of chemical synaptic transmission
negative regulation of endocytosis negative regulation of endocytosis
plasma membrane tubulation plasma membrane tubulation
protein localization to endosome protein localization to endosome
regulation of endocytosis regulation of endocytosis
Cellular component:
caveola caveola
cell-cell junction cell-cell junction
centriolar satellite centriolar satellite
cytoplasm cytoplasm
cytosol cytosol
early endosome early endosome
endosome endosome
extracellular exosome extracellular exosome
focal adhesion focal adhesion
glutamatergic synapse glutamatergic synapse
intracellular membrane-bounded organelle intracellular membrane-bounded organelle
nuclear speck nuclear speck
plasma membrane plasma membrane
recycling endosome membrane recycling endosome membrane
ruffle membrane ruffle membrane
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: Protein kinase C and casein kinase substrate in neurons protein 2
Source organism: Homo sapiens
Length: 486 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMSVTYDDSVGVEVSSDSFWEVGNYKRTVKRIDDGHRLCSDLMNCLHERARIEKAYAQQLTEWARRWRQLVEKGPQYGTVEKAWMAFMSEAERVSELHLEVKASLMNDDFEKIKNWQKEAFHKQMMGGFKETKEAEDGFRKAQKPWAKKLKEVEAAKKAHHAACKEEKLAISREANSKADPSLNPEQLKKLQDKIEKCKQDVLKTKEKYEKSLKELDQGTPQYMENMEQVFEQCQQFEEKRLRFFREVLLEVQKHLDLSNVAGYKAIYHDLEQSIRAADAVEDLRWFRANHGPGMAMNWPQFEEWSADLNRTLSRREKKKATDGVTLTGINQTGDQSLPSKPSSTLNVPSNPAQSAQSQSSYNPFEDEDDTGSTVSEKDDTKAKNVSSYEKTQSYPTDWSDDESNNPFSSTDANGDSNPFDDDATSGTEVRVRALYDYEGQEHDELSFKAGDELTKMEDEDEQGWCKGRLDNGQVGLYPANYVEAIQ
UniProtKB AC: Q9UNF0 (positions: 16-303)
Coverage: 59%
Name: Protein kinase C and casein kinase substrate in neurons protein 2
Source organism: Homo sapiens
Length: 486 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMSVTYDDSVGVEVSSDSFWEVGNYKRTVKRIDDGHRLCSDLMNCLHERARIEKAYAQQLTEWARRWRQLVEKGPQYGTVEKAWMAFMSEAERVSELHLEVKASLMNDDFEKIKNWQKEAFHKQMMGGFKETKEAEDGFRKAQKPWAKKLKEVEAAKKAHHAACKEEKLAISREANSKADPSLNPEQLKKLQDKIEKCKQDVLKTKEKYEKSLKELDQGTPQYMENMEQVFEQCQQFEEKRLRFFREVLLEVQKHLDLSNVAGYKAIYHDLEQSIRAADAVEDLRWFRANHGPGMAMNWPQFEEWSADLNRTLSRREKKKATDGVTLTGINQTGDQSLPSKPSSTLNVPSNPAQSAQSQSSYNPFEDEDDTGSTVSEKDDTKAKNVSSYEKTQSYPTDWSDDESNNPFSSTDANGDSNPFDDDATSGTEVRVRALYDYEGQEHDELSFKAGDELTKMEDEDEQGWCKGRLDNGQVGLYPANYVEAIQ
UniProtKB AC: Q9UNF0 (positions: 16-303)
Coverage: 59%
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)
