4FW1

Crystal structure of two-domain RSV INTEGRASE covalently linked with DNA


ChainDomainClassArchitectureTopologyHomology
A3.30.420.10 Alpha Beta 2-Layer Sandwich Nucleotidyltransferase domain 5
A2.30.30.10 Mainly Beta Roll SH3 type barrels. Integrase, C-terminal domain superfamily, retroviral
B3.30.420.10 Alpha Beta 2-Layer Sandwich Nucleotidyltransferase domain 5
B2.30.30.10 Mainly Beta Roll SH3 type barrels. Integrase, C-terminal domain superfamily, retroviral

Protein Family Annotation Pfam Database Homepage

ChainsAccessionIdentifierDescriptionCommentsSource
A, BPF06817Reverse transcriptase thumb domain (RVT_thumb)Reverse transcriptase thumb domainThis domain is known as the thumb domain. It is composed of a four helix bundle [1].Domain
A, BPF02813Retroviral M domain (Retro_M)Retroviral M domain- Family
A, BPF00607gag gene protein p24 (core nucleocapsid protein) (Gag_p24)gag gene protein p24 (core nucleocapsid protein)- Family
A, BPF02022Integrase Zinc binding domain (Integrase_Zn)Integrase Zinc binding domainIntegrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. This domain is the amino-terminal domain zinc binding domain. The central domain is the catalytic domain Pfam:PF00665 ...Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. This domain is the amino-terminal domain zinc binding domain. The central domain is the catalytic domain Pfam:PF00665. The carboxyl terminal domain is a DNA binding domain Pfam:PF00552.
Domain
A, BPF00098Zinc knuckle (zf-CCHC)Zinc knuckleThe zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eu ...The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger.
Domain
A, BPF00077Retroviral aspartyl protease (RVP)Retroviral aspartyl proteaseSingle domain aspartyl proteases from retroviruses, retrotransposons, and badnaviruses (plant dsDNA viruses). These proteases are generally part of a larger polyprotein; usually pol, more rarely gag. Retroviral proteases appear to be homologous to a ...Single domain aspartyl proteases from retroviruses, retrotransposons, and badnaviruses (plant dsDNA viruses). These proteases are generally part of a larger polyprotein; usually pol, more rarely gag. Retroviral proteases appear to be homologous to a single domain of the two-domain eukaryotic aspartyl proteases such as pepsins, cathepsins, and renins (Pfam:PF00026).
Domain
A, BPF00078Reverse transcriptase (RNA-dependent DNA polymerase) (RVT_1)Reverse transcriptase (RNA-dependent DNA polymerase)- Family
A, BPF00552Integrase DNA binding domain (IN_DBD_C)Integrase DNA binding domainIntegrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain. The central domain is the catalytic domain Pfam:PF00665. This do ...Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain. The central domain is the catalytic domain Pfam:PF00665. This domain is the carboxyl terminal domain that is a non-specific DNA binding domain [1].
Domain
A, BPF00665Integrase core domain (rve)Integrase core domainIntegrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain Pfam:PF02022. This domain is the central catalytic domain. The ca ...Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain Pfam:PF02022. This domain is the central catalytic domain. The carboxyl terminal domain that is a non-specific DNA binding domain Pfam:PF00552. The catalytic domain acts as an endonuclease when two nucleotides are removed from the 3' ends of the blunt-ended viral DNA made by reverse transcription. This domain also catalyses the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site [1].
Domain

Gene Product Annotation Gene Product Annotation