Database accession: MF7000690
Name: Human PACSIN2 F-BAR domain (p212121 lattice)
PDB ID: 3haj
Experimental method: X-ray (2.78 Å)
Assembly: Homodimer
Source organism: Homo sapiens
Primary publication of the structure:
Wang Q, Navarro MV, Peng G, Molinelli E, Goh SL, Judson BL, Rajashankar KR, Sondermann H
Molecular mechanism of membrane constriction and tubulation mediated by the F-BAR protein Pacsin/Syndapin.
(2009) Proc. Natl. Acad. Sci. U.S.A. 106: 12700-5
PMID: 19549836
Abstract:
Peripheral membrane proteins of the Bin/amphiphysin/Rvs (BAR) and Fer-CIP4 homology-BAR (F-BAR) family participate in cellular membrane trafficking and have been shown to generate membrane tubules. The degree of membrane bending appears to be encoded in the structure and immanent curvature of the particular protein domains, with BAR and F-BAR domains inducing high- and low-curvature tubules, respectively. In addition, oligomerization and the formation of ordered arrays influences tubule stabilization. Here, the F-BAR domain-containing protein Pacsin was found to possess a unique activity, creating small tubules and tubule constrictions, in addition to the wide tubules characteristic for this subfamily. Based on crystal structures of the F-BAR domain of Pacsin and mutagenesis studies, vesiculation could be linked to the presence of unique structural features distinguishing it from other F-BAR proteins. Tubulation was suppressed in the context of the full-length protein, suggesting that Pacsin is autoinhibited in solution. The regulated deformation of membranes and promotion of tubule constrictions by Pacsin suggests a more versatile function of these proteins in vesiculation and endocytosis beyond their role as scaffold proteins.
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: 16-301)
Coverage: 58%
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: 16-299)
Coverage: 58%
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)
