SUPERFAMILY 1.75 HMM library and genome assignments server

ENV polyprotein, receptor-binding domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   ENV polyprotein, receptor-binding domain [ 49829]
Superfamily:   ENV polyprotein, receptor-binding domain [ 49830]
Families:   ENV polyprotein, receptor-binding domain [ 49831] (2)


Superfamily statistics
Genomes (15) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 159 1,033 2
Proteins 159 1,033 2


Functional annotation
General category Other
Detailed category Viral proteins

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details) Document: GO annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processHost-virus interaction0Moderately InformativeDirect
Biological processVirus entry into host cell0InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentHost membrane0InformativeDirect
Cellular componentViral envelope protein0Highly InformativeDirect
DomainSignal0Least InformativeDirect
DomainTransmembrane0.00000000002114Least InformativeDirect
DomainCoiled coil0Moderately InformativeDirect
Molecular functionZinc0.00002542Least InformativeDirect
Post-translational modificationGlycoprotein0Least InformativeDirect
Post-translational modificationDisulfide bond0.0000000000004341Least InformativeDirect
Post-translational modificationCleavage on pair of basic residues0Moderately InformativeDirect
Post-translational modificationPalmitate0Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR008981 SSF49830 Protein matches
Abstract

The F-MuLV receptor-binding domain forms part of the retroviral envelope glycoprotein in the murine leukaemia virus. Envelope glycoproteins are synthesized as single chain precursors, which are subsequently cleaved into the surface subunit (SU) and the transmembrane subunit TM. The N-terminal half of SU forms the receptor-binding domain (RBD), which is responsible for binding to the cell surface receptor, the cationic amino acid transporter mCAT-1. The RBD is structurally partitioned into a conserved beta sandwich framework of Greek key topology and a variable helical loop subdomain [PubMed9287219]. The RBD contains three variable regions, VRA, VRB and VRC, which vary in sequence and length between MuLVs that use different receptors. VRA and VRB are closely associated with one another in the helical subdomain. There is a putative receptor-binding pocket in VRA, which may play a role in helping to determine receptor specificity [PubMed12634359].


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

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Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.


Alignments of sequences to 2 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.


Browse and view proteins in genomes which have different domain combinations including a ENV polyprotein, receptor-binding domain domain.


Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.


Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 2 hidden Markov models representing the ENV polyprotein, receptor-binding domain superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.


Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-coverage) · UniProtKB KeyWords (KW) · Internal database links ]