Database accession: MF7000698
Name: Rgd1p F-BAR domain
PDB ID: 4wpc
Experimental method: X-ray (3.34 Å)
Assembly: Homodimer
Source organism: Saccharomyces cerevisiae
Primary publication of the structure:
Moravcevic K, Alvarado D, Schmitz KR, Kenniston JA, Mendrola JM, Ferguson KM, Lemmon MA
Comparison of Saccharomyces cerevisiae F-BAR domain structures reveals a conserved inositol phosphate binding site.
(2015) Structure 23: 352-63
PMID: 25620000
Abstract:
F-BAR domains control membrane interactions in endocytosis, cytokinesis, and cell signaling. Although they are generally thought to bind curved membranes containing negatively charged phospholipids, numerous functional studies argue that differences in lipid-binding selectivities of F-BAR domains are functionally important. Here, we compare membrane-binding properties of the Saccharomyces cerevisiae F-BAR domains in vitro and in vivo. Whereas some F-BAR domains (such as Bzz1p and Hof1p F-BARs) bind equally well to all phospholipids, the F-BAR domain from the RhoGAP Rgd1p preferentially binds phosphoinositides. We determined X-ray crystal structures of F-BAR domains from Hof1p and Rgd1p, the latter bound to an inositol phosphate. The structures explain phospholipid-binding selectivity differences and reveal an F-BAR phosphoinositide binding site that is fully conserved in a mammalian RhoGAP called Gmip and is partly retained in certain other F-BAR domains. Our findings reveal previously unappreciated determinants of F-BAR domain lipid-binding specificity and provide a basis for its prediction from sequence.
Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown. Molecular function:
GTPase activator activity GTPase activator activity
identical protein binding identical protein binding
phosphatidylinositol-3,5-bisphosphate binding phosphatidylinositol-3,5-bisphosphate binding
phosphatidylinositol-3-phosphate binding phosphatidylinositol-3-phosphate binding
phosphatidylinositol-4,5-bisphosphate binding phosphatidylinositol-4,5-bisphosphate binding
phosphatidylinositol-4-phosphate binding phosphatidylinositol-4-phosphate binding
phosphatidylinositol-5-phosphate binding phosphatidylinositol-5-phosphate binding
Biological process:
actin cytoskeleton organization actin cytoskeleton organization
response to acidic pH response to acidic pH
response to osmotic stress response to osmotic stress
signal transduction signal transduction
Cellular component:
actin cortical patch actin cortical patch
cellular bud cellular bud
cytoplasm cytoplasm
mating projection tip mating projection tip
prospore membrane prospore 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: RHO GTPase-activating protein RGD1
Source organism: Saccharomyces cerevisiae
Length: 666 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMEETAKKPASATVSAKSSHDGGTDDLAHLFSTPEIKKVLNSDVAINALLSRLKQSLLTCEEFMKFIRKKYAFEEEHVQELSKQYKHFFNIQGSTNSSLKKMIHEVLGFDGKMAQVKQSYITALQKMYSEISSLLLTMTKLRKSVKENSKRLEKDVSDAIHSAEKAQSRYNSLCQDWDKLRMTDPTKTKLTLRGSKTTKEQEEELLRKIDNADLEYKQKVDHSNSLRNTFITKERPRIVQELKDLILEIDTAMTIQLQKYTIWTENLVLNTGVTISPLDSTKSMKSFAGSVSNERDLYSFLNKYNQTGKHSLLINKNLIPVSYKKHPSMNHGQKNKSPPKFAVDPSRNSIPKRMISTHNESPFLSSSSNTAAVPNANLNSATPSLNTNKQLPPTMASSISSTSNAAGAMSPSSSIVTSDTTSSITKTLDPGNNSPQIPEELINSLDSDRPISHIQTNNNMPPGVQKNFKTFGVPLESLIEFEQDMVPAIVRQCIYVIDKFGLDQEGIYRKSANVLDVSKLKEEIDKDPANISMILPSKPHSDSDIYLVGSLLKTFFASLPDSVLPKALSSEIKVCLQIEDPTTRKNFMHGLIYNLPDAQYWTLRALVFHLKRVLAHEAQNRMNLRALCIIWGPTIAPANPDDANDVNFQIMAMEVLLEVSDQAFEPE
UniProtKB AC: P38339 (positions: 30-326)
Coverage: 44%
Name: RHO GTPase-activating protein RGD1
Source organism: Saccharomyces cerevisiae
Length: 666 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMEETAKKPASATVSAKSSHDGGTDDLAHLFSTPEIKKVLNSDVAINALLSRLKQSLLTCEEFMKFIRKKYAFEEEHVQELSKQYKHFFNIQGSTNSSLKKMIHEVLGFDGKMAQVKQSYITALQKMYSEISSLLLTMTKLRKSVKENSKRLEKDVSDAIHSAEKAQSRYNSLCQDWDKLRMTDPTKTKLTLRGSKTTKEQEEELLRKIDNADLEYKQKVDHSNSLRNTFITKERPRIVQELKDLILEIDTAMTIQLQKYTIWTENLVLNTGVTISPLDSTKSMKSFAGSVSNERDLYSFLNKYNQTGKHSLLINKNLIPVSYKKHPSMNHGQKNKSPPKFAVDPSRNSIPKRMISTHNESPFLSSSSNTAAVPNANLNSATPSLNTNKQLPPTMASSISSTSNAAGAMSPSSSIVTSDTTSSITKTLDPGNNSPQIPEELINSLDSDRPISHIQTNNNMPPGVQKNFKTFGVPLESLIEFEQDMVPAIVRQCIYVIDKFGLDQEGIYRKSANVLDVSKLKEEIDKDPANISMILPSKPHSDSDIYLVGSLLKTFFASLPDSVLPKALSSEIKVCLQIEDPTTRKNFMHGLIYNLPDAQYWTLRALVFHLKRVLAHEAQNRMNLRALCIIWGPTIAPANPDDANDVNFQIMAMEVLLEVSDQAFEPE
UniProtKB AC: P38339 (positions: 25-326)
Coverage: 45%
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)
