Database accession: MF7000945
Name: Rubella virus capsid protein
PDB ID: 5khf
Experimental method: Electron Microscopy
Assembly: Homodimer
Source organism: Rubella virus
Primary publication of the structure:
Mangala Prasad V, Klose T, Rossmann MG
Assembly, maturation and three-dimensional helical structure of the teratogenic rubella virus.
(2017) PLoS Pathog. 13: e1006377
PMID: 28575072
Abstract:
Viral infections during pregnancy are a significant cause of infant morbidity and mortality. Of these, rubella virus infection is a well-substantiated example that leads to miscarriages or severe fetal defects. However, structural information about the rubella virus has been lacking due to the pleomorphic nature of the virions. Here we report a helical structure of rubella virions using cryo-electron tomography. Sub-tomogram averaging of the surface spikes established the relative positions of the viral glycoproteins, which differed from the earlier icosahedral models of the virus. Tomographic analyses of in vitro assembled nucleocapsids and virions provide a template for viral assembly. Comparisons of immature and mature virions show large rearrangements in the glycoproteins that may be essential for forming the infectious virions. These results present the first known example of a helical membrane-enveloped virus, while also providing a structural basis for its assembly and maturation pathway.
Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown. Molecular function:
metal ion binding metal ion binding
RNA binding RNA binding
Biological process:
clathrin-dependent endocytosis of virus by host cell clathrin-dependent endocytosis of virus by host cell
fusion of virus membrane with host endosome membrane fusion of virus membrane with host endosome membrane
virion attachment to host cell virion attachment to host cell
Cellular component:
host cell Golgi membrane host cell Golgi membrane
host cell mitochondrion host cell mitochondrion
membrane membrane
T=4 icosahedral viral capsid T=4 icosahedral viral capsid
viral envelope viral envelope
viral nucleocapsid viral nucleocapsid
virion membrane virion 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: Structural polyprotein
Source organism: Rubella virus
Length: 1063 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMASTTPITMEDLQKALEAQSRALRAELAAGASQSRRPRPPRQRDSSTSGDDSGRDSGGPRRRRGNRGRGQRRDWSRAPPPPEERQETRSQTPAPKPSRAPPQQPQPPRMQTGRGGSAPRPELGPPTNPFQAAVARGLRPPLHDPDTEAPTEACVTSWLWSEGEGAVFYRVDLHFTNLGTPPLDEDGRWDPALMYNPCGPEPPAHVVRAYNQPAGDVRGVWGKGERTYAEQDFRVGGTRWHRLLRMPVRGLDGDSAPLPPHTTERIETRSARHPWRIRFGAPQAFLAGLLLATVAVGTARAGLQPRADMAAPPTLPQPPCAHGQHYGHHHHQLPFLGHDGHHGGTLRVGQHYRNASDVLPGHWLQGGWGCYNLSDWHQGTHVCHTKHMDFWCVEHDRPPPATPTPLTTAANSTTAATPATAPAPCHAGLNDSCGGFLSGCGPMRLRHGADTRCGRLICGLSTTAQYPPTRFGCAMRWGLPPWELVVLTARPEDGWTCRGVPAHPGARCPELVSPMGRATCSPASALWLATANALSLDHALAAFVLLVPWVLIFMVCRRACRRRGAAAALTAVVLQGYNPPAYGEEAFTYLCTAPGCATQAPVPVRLAGVRFESKIVDGGCFAPWDLEATGACICEIPTDVSCEGLGAWVPAAPCARIWNGTQRACTFWAVNAYSSGGYAQLASYFNPGGSYYKQYHPTACEVEPAFGHSDAACWGFPTDTVMSVFALASYVQHPHKTVRVKFHTETRTVWQLSVAGVSCNVTTEHPFCNTPHGQLEVQVPPDPGDLVEYIMNYTGNQQSRWGLGSPNCHGPDWASPVCQRHSPDCSRLVGATPERPRLRLVDADDPLLRTAPGPGEVWVTPVIGSQARKCGLHIRAGPYGHATVEMPEWIHAHTTSDPWHPPGPLGLKFKTVRPVALPRTLAPPRNVRVTGCYQCGTPALVEGLAPGGGNCHLTVNGEDLGAVPPGKFVTAALLNTPPPYQVSCGGESDRATARVIDPAAQSFTGVVYGTHTTAVSETRQTWAEWAAAHWWQLTLGAICALPLAGLLACCAKCLYYLRGAIAPR
UniProtKB AC: P07566 (positions: 150-247)
Coverage: 9%
Name: Structural polyprotein
Source organism: Rubella virus
Length: 1063 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMASTTPITMEDLQKALEAQSRALRAELAAGASQSRRPRPPRQRDSSTSGDDSGRDSGGPRRRRGNRGRGQRRDWSRAPPPPEERQETRSQTPAPKPSRAPPQQPQPPRMQTGRGGSAPRPELGPPTNPFQAAVARGLRPPLHDPDTEAPTEACVTSWLWSEGEGAVFYRVDLHFTNLGTPPLDEDGRWDPALMYNPCGPEPPAHVVRAYNQPAGDVRGVWGKGERTYAEQDFRVGGTRWHRLLRMPVRGLDGDSAPLPPHTTERIETRSARHPWRIRFGAPQAFLAGLLLATVAVGTARAGLQPRADMAAPPTLPQPPCAHGQHYGHHHHQLPFLGHDGHHGGTLRVGQHYRNASDVLPGHWLQGGWGCYNLSDWHQGTHVCHTKHMDFWCVEHDRPPPATPTPLTTAANSTTAATPATAPAPCHAGLNDSCGGFLSGCGPMRLRHGADTRCGRLICGLSTTAQYPPTRFGCAMRWGLPPWELVVLTARPEDGWTCRGVPAHPGARCPELVSPMGRATCSPASALWLATANALSLDHALAAFVLLVPWVLIFMVCRRACRRRGAAAALTAVVLQGYNPPAYGEEAFTYLCTAPGCATQAPVPVRLAGVRFESKIVDGGCFAPWDLEATGACICEIPTDVSCEGLGAWVPAAPCARIWNGTQRACTFWAVNAYSSGGYAQLASYFNPGGSYYKQYHPTACEVEPAFGHSDAACWGFPTDTVMSVFALASYVQHPHKTVRVKFHTETRTVWQLSVAGVSCNVTTEHPFCNTPHGQLEVQVPPDPGDLVEYIMNYTGNQQSRWGLGSPNCHGPDWASPVCQRHSPDCSRLVGATPERPRLRLVDADDPLLRTAPGPGEVWVTPVIGSQARKCGLHIRAGPYGHATVEMPEWIHAHTTSDPWHPPGPLGLKFKTVRPVALPRTLAPPRNVRVTGCYQCGTPALVEGLAPGGGNCHLTVNGEDLGAVPPGKFVTAALLNTPPPYQVSCGGESDRATARVIDPAAQSFTGVVYGTHTTAVSETRQTWAEWAAAHWWQLTLGAICALPLAGLLACCAKCLYYLRGAIAPR
UniProtKB AC: P07566 (positions: 150-247)
Coverage: 9%
Evidence demonstrating that the participating proteins are unstructured prior to the interaction and their folding is coupled to binding. Representative domain in related structures: Rubella capsid protein
Evidence level: Indirect evidence
Evidence coverage: The full structure participates in mutual synergistic folding.
Complex Evidence:
RV capsid proteins form a tight, disulfide-linked dimer. There is beta sheet augmentation between the monomers. The resultant 10-stranded, left-handed twisted sheet forms a partially open β-barrel with the two helices lying in the center of the barrel. The β-strands A and B from one monomer are inserted into the BH loop of the other monomer, forming a tightly bound dimeric structure consistent with the previous observation that the RV capsid protein forms dimers when isolated from the virion (PMID:24282305).
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)
