Database accession: MF7000689
Name: Human PACSIN1 F-BAR domain (C2 lattice)
PDB ID: 3hah
Experimental method: X-ray (2.77 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:
cytoskeletal protein binding cytoskeletal protein binding
identical protein binding identical protein binding
phospholipid binding phospholipid binding
Biological process:
actin filament organization actin filament organization
cytoskeleton organization cytoskeleton organization
negative regulation of endocytosis negative regulation of endocytosis
neuron projection morphogenesis neuron projection morphogenesis
plasma membrane tubulation plasma membrane tubulation
positive regulation of dendrite development positive regulation of dendrite development
protein localization to membrane protein localization to membrane
protein localization to plasma membrane protein localization to plasma membrane
regulation of endocytosis regulation of endocytosis
synaptic vesicle endocytosis synaptic vesicle endocytosis
Cellular component:
axon terminus axon terminus
COPI-coated vesicle COPI-coated vesicle
cytoplasm cytoplasm
cytoplasmic vesicle membrane cytoplasmic vesicle membrane
cytosol cytosol
endosome endosome
perinuclear region of cytoplasm perinuclear region of cytoplasm
photoreceptor ribbon synapse photoreceptor ribbon synapse
plasma membrane plasma membrane
presynaptic endocytic zone presynaptic endocytic zone
ruffle membrane ruffle membrane
synapse synapse
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 1
Source organism: Homo sapiens
Length: 444 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMSSSYDEASLAPEETTDSFWEVGNYKRTVKRIDDGHRLCNDLMNCVQERAKIEKAYGQQLTDWAKRWRQLIEKGPQYGSLERAWGAIMTEADKVSELHQEVKNNLLNEDLEKVKNWQKDAYHKQIMGGFKETKEAEDGFRKAQKPWAKKMKELEAAKKAYHLACKEEKLAMTREMNSKTEQSVTPEQQKKLQDKVDKCKQDVQKTQEKYEKVLEDVGKTTPQYMENMEQVFEQCQQFEEKRLVFLKEVLLDIKRHLNLAENSSYIHVYRELEQAIRGADAQEDLRWFRSTSGPGMPMNWPQFEEWNPDLPHTTTKKEKQPKKAEGVALTNATGAVESTSQAGDRGSVSSYDRGQPYATEWSDDESGNPFGGSETNGGANPFEDDSKGVRVRALYDYDGQEQDELSFKAGDELTKLGEEDEQGWCRGRLDSGQLGLYPANYVEAI
UniProtKB AC: Q9BY11 (positions: 16-304)
Coverage: 65%
Name: Protein kinase C and casein kinase substrate in neurons protein 1
Source organism: Homo sapiens
Length: 444 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMSSSYDEASLAPEETTDSFWEVGNYKRTVKRIDDGHRLCNDLMNCVQERAKIEKAYGQQLTDWAKRWRQLIEKGPQYGSLERAWGAIMTEADKVSELHQEVKNNLLNEDLEKVKNWQKDAYHKQIMGGFKETKEAEDGFRKAQKPWAKKMKELEAAKKAYHLACKEEKLAMTREMNSKTEQSVTPEQQKKLQDKVDKCKQDVQKTQEKYEKVLEDVGKTTPQYMENMEQVFEQCQQFEEKRLVFLKEVLLDIKRHLNLAENSSYIHVYRELEQAIRGADAQEDLRWFRSTSGPGMPMNWPQFEEWNPDLPHTTTKKEKQPKKAEGVALTNATGAVESTSQAGDRGSVSSYDRGQPYATEWSDDESGNPFGGSETNGGANPFEDDSKGVRVRALYDYDGQEQDELSFKAGDELTKLGEEDEQGWCRGRLDSGQLGLYPANYVEAI
UniProtKB AC: Q9BY11 (positions: 16-305)
Coverage: 65%
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)
