SUPERFAMILY 1.75 HMM library and genome assignments server

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gp120 core superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   gp120 core [ 56501]
Superfamily:   gp120 core [ 56502]
Families:   gp120 core [ 56503]


Superfamily statistics
Genomes (0) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 0 277,599 14
Proteins 0 217,161 14


Functional annotation
General category Other
Detailed category Viral proteins

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) cellular component organization or biogenesis 0 Least Informative Direct
Biological Process (BP) response to stimulus 0.0000002897 Least Informative Direct
Biological Process (BP) biological regulation 0.00003197 Least Informative Direct
Biological Process (BP) multi-organism process 0 Moderately Informative Direct
Biological Process (BP) single organism signaling 0 Moderately Informative Direct
Biological Process (BP) regulation of response to stimulus 0 Moderately Informative Direct
Biological Process (BP) immune system process 0 Moderately Informative Direct
Biological Process (BP) cell communication 0.0000000001384 Moderately Informative Direct
Biological Process (BP) cell surface receptor signaling pathway 0 Informative Direct
Biological Process (BP) positive regulation of immune system process 0 Informative Direct
Biological Process (BP) interspecies interaction between organisms 0 Informative Direct
Biological Process (BP) vesicle-mediated transport 0 Informative Direct
Biological Process (BP) regulation of defense response 0 Informative Direct
Biological Process (BP) regulation of immune response 0 Informative Direct
Biological Process (BP) activation of innate immune response 0 Highly Informative Direct
Biological Process (BP) biological adhesion 0 Highly Informative Direct
Biological Process (BP) viral process 0 Highly Informative Direct
Biological Process (BP) multi-organism cellular process 0 Highly Informative Direct
Biological Process (BP) immune response-activating signal transduction 0 Highly Informative Direct

Document: GO annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processApoptosis0Moderately InformativeDirect
Biological processHost-virus interaction0Moderately InformativeDirect
Biological processViral immunoevasion0InformativeDirect
Biological processVirus entry into host cell0InformativeDirect
Biological processClathrin-mediated endocytosis of virus by host0Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentVirion0Moderately InformativeDirect
Cellular componentHost membrane0InformativeDirect
Cellular componentViral envelope protein0Highly InformativeDirect
Cellular componentHost endosome0Highly InformativeDirect
DiseaseAIDS0Moderately InformativeDirect
DomainSignal0Least InformativeDirect
DomainTransmembrane0Least InformativeDirect
DomainCoiled coil0Moderately InformativeDirect
Post-translational modificationGlycoprotein0Least InformativeDirect
Post-translational modificationDisulfide bond0Least InformativeDirect
Post-translational modificationCleavage on pair of basic residues0Moderately InformativeDirect
Post-translational modificationPalmitate0Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR000777 SSF56502 Protein matches
Abstract

The entry of HIV requires interaction of viral GP120, an envelope glycoprotein with human T-cell surface glycoprotein CD4 and a chemokine receptor on the cell surface. These envelope glycoproteins are found in HIV types 1 and 2, and Simian Immunodeficiency virus (SIV).


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 · Gene Ontology (high-coverage) · UniProtKB KeyWords (KW) ]

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 3 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 gp120 core 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 3 hidden Markov models representing the gp120 core 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 ]