EBI Databases InterPro	Search Open in usermanual InterPro:
Jump to: InterProScan Databases Documentation FTP site Help Click on the icon for context sensitive help from the user manual. Advanced search

InterPro: IPR008919 Retrovirus capsid, N-terminal core

Protein matches Help

UniProtKB

Matches:

25991 proteins

Overview:	sorted by AC,	sorted by name,	of known structure,	proteins with splice variants
Detailed:	sorted by AC,	sorted by name,	of known structure	proteins with splice variants
Table:	For all matching proteins,	of known structure
Architectures
Accession List
Matches in BioMart

Accession

IPR008919 Retrov_capsid_N

Type

Domain

Signatures Help

Database	ID	Name	Proteins
Gene3D	G3DSA:1.10.375.10	Retrov_capsid_N	25924
SuperFamily	SSF47943	Retrov_capsid_N	24088
Signatures in BioMart

InterPro Relationships Help

Found in

IPR000721 Retroviral nucleocapsid protein Gag

GO Term annotation Help

Process

GO:0016032 viral reproduction

InterPro annotation

Entry Details in BioMart

Abstract

The Gag polyprotein from retroviruses is processed by viral protease to produce the major structural proteins, including the capsid protein. The newly formed capsid protein rearranges to form the capsid core particle that surrounds the viral genome of the mature virus. The capsid is composed of two domains, the N-terminal domain (NTD), which contributes to viral core formation, and the C-terminal domain (CTD), which is required for capsid dimerisation, Gag oligomerization and viral formation. The NTD is composed of a five-helix bundle [1, 2].

Structural links Help

PDB - click here

SCOP: a.28.3.1 , a.61.1.1 , a.61.1.5 , a.73.1.1

CATH: 1.10.1200.30 , 1.10.150.90 , 1.10.375.10

Taxonomic coverage Help

Overlapping InterPro entries Help

IPR008919

Numbers of overlapping proteins

Average numbers of overlapping amino acids

Example proteins Help

O12158 Gag-Pol polyprotein

P03975 IgE-binding protein

P62683 HERV-K_12q14.1 provirus ancestral Gag polyprotein

More proteins

Example Proteins Key

InterPro entry accession number/name and structure databases		Colour code
IPR003308	Integrase, N-terminal zinc-binding domain
IPR012337	Polynucleotidyl transferase, ribonuclease H fold
IPR008919	Retrovirus capsid, N-terminal core
IPR008916	Retrovirus capsid, C-terminal
IPR002156	Ribonuclease H
IPR018061	Peptidase A2A, retrovirus RVP subgroup
IPR001878	Zinc finger, CCHC-type
IPR017856	Integrase, N-terminal zinc-binding domain-like
IPR009007	Peptidase aspartic, catalytic
IPR001969	Peptidase aspartic, active site
IPR003322	Beta-retroviral matrix, N-terminal
IPR010659	Reverse transcriptase connection
IPR010999	Retroviral matrix, N-terminal
IPR010661	Reverse transcriptase thumb
IPR000477	RNA-directed DNA polymerase (reverse transcriptase)
IPR013084	Zinc finger, CCHC retroviral-type
IPR000721	Retroviral nucleocapsid protein Gag
IPR000071	Immunodeficiency lentiviral matrix, N-terminal
IPR012344	Matrix protein, N-terminal, lentiviral and alpha-retroviral
IPR001584	Integrase, catalytic core
IPR001995	Peptidase A2A, retrovirus, catalytic
IPR001037	Integrase, C-terminal, retroviral
	ModBase
	SWISS-MODEL
	PDB Chain
	CATH Domain

Publications Open in usermanual
1.	Jin Z, Jin L, Peterson DL, Lawson CL. Model for lentivirus capsid core assembly based on crystal dimers of EIAV p26. J. Mol. Biol. 286 83-93 1999 [PubMed: 9931251] http://dx.doi.org/10.1006/jmbi.1998.2443
2.	Campos-Olivas R, Newman JL, Summers MF. Solution structure and dynamics of the Rous sarcoma virus capsid protein and comparison with capsid proteins of other retroviruses. J. Mol. Biol. 296 633-49 2000 [PubMed: 10669613] http://dx.doi.org/10.1006/jmbi.1999.3475

Additional Reading Open in usermanual
	Ternois F, Sticht J, Duquerroy S, Krausslich HG, Rey FA. The HIV-1 capsid protein C-terminal domain in complex with a virus assembly inhibitor. Nat. Struct. Mol. Biol. 12 2005 678-82 [PubMed: 16041386] http://dx.doi.org/10.1038/nsmb967
	Sticht J, Humbert M, Findlow S, Bodem J, Muller B, Dietrich U, Werner J, Krausslich HG. A peptide inhibitor of HIV-1 assembly in vitro. Nat. Struct. Mol. Biol. 12 2005 671-7 [PubMed: 16041387] http://dx.doi.org/10.1038/nsmb964
	Kelly BN, Kyere S, Kinde I, Tang C, Howard BR, Robinson H, Sundquist WI, Summers MF, Hill CP. Structure of the antiviral assembly inhibitor CAP-1 complex with the HIV-1 CA protein. J. Mol. Biol. 373 2007 355-66 [PubMed: 17826792] http://dx.doi.org/10.1016/j.jmb.2007.07.070
	Saad JS, Miller J, Tai J, Kim A, Ghanam RH, Summers MF. Structural basis for targeting HIV-1 Gag proteins to the plasma membrane for virus assembly. Proc. Natl. Acad. Sci. U.S.A. 103 2006 11364-9 [PubMed: 16840558] http://dx.doi.org/10.1073/pnas.0602818103
	Kelly BN, Howard BR, Wang H, Robinson H, Sundquist WI, Hill CP. Implications for viral capsid assembly from crystal structures of HIV-1 Gag(1-278) and CA(N)(133-278). Biochemistry 45 2006 11257-66 [PubMed: 16981686] http://dx.doi.org/10.1021/bi060927x

InterPro 23.1