SUPERFAMILY 1.75 HMM library and genome assignments server

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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 (14) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 158 1,292 2
Proteins 158 1,292 2

Functional annotation
General category Other
Detailed category Viral proteins

Function annotation of SCOP domain superfamilies

InterPro annotation
Cross references IPR008981 SSF49830 Protein matches

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

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation ]

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 · Internal database links ]