1F6U

NMR structure of the HIV-1 nucleocapsid protein bound to stem-loop sl2 of the psi-RNA packaging signal. Implications for genome recognition

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B [auth A]	d1f6ua_	Small proteins	Retrovirus zinc finger-like domains	Retrovirus zinc finger-like domains	Retrovirus zinc finger-like domains	HIV nucleocapsid	(Human immunodeficiency virus 1 ) [TaxId: 11676 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B [auth A]	zf-CCHC_2	e1f6uA2	A: few secondary structure elements	X: CCHC-type 1 zinc finger	H: Retrovirus zinc finger-related domains (From Topology)	T: Retrovirus zinc finger-related domains	F: zf-CCHC_2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth A]	4.10.60.10	Few Secondary Structures	Irregular	HIV-1 Nucleocapsid Protein	Zinc finger, CCHC-type	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth A]	PF00098	Zinc knuckle (zf-CCHC)	Zinc knuckle	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 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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth B]	HIV-1 STEM-LOOP SL2 FROM PSI-RNA PACKAGING	-	-	-
B [auth A]	HIV-1 NUCLEOCAPSID PROTEIN	catalytic activity, acting on RNA RNA exonuclease activity, producing 5'-phosphomonoesters catalytic activity, acting on a nucleic acid RNA exonuclease activity RNA nuclease activity hydrolase activity exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters nuclease activity hydrolase activity, acting on ester bonds exoribonuclease H activity exonuclease activity catalytic activity catalytic activity, acting on DNA DNA-directed DNA polymerase activity catalytic activity, acting on RNA RNA exonuclease activity, producing 5'-phosphomonoesters catalytic activity, acting on a nucleic acid RNA exonuclease activity RNA nuclease activity hydrolase activity exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters nuclease activity hydrolase activity, acting on ester bonds exoribonuclease H activity exonuclease activity catalytic activity catalytic activity, acting on DNA DNA-directed DNA polymerase activity DNA polymerase activity transferase activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups DNA binding binding organic cyclic compound binding nucleic acid binding RNA-directed DNA polymerase activity RNA binding aspartic-type peptidase activity peptidase activity catalytic activity, acting on a protein aspartic-type endopeptidase activity endopeptidase activity lipid binding endonuclease activity RNA endonuclease activity, producing 5'-phosphomonoesters RNA-DNA hybrid ribonuclease activity RNA endonuclease activity endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters structural molecule activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	viral genome integration into host DNA viral process viral life cycle viral penetration into host nucleus intracellular transport of virus transport of virus biological process involved in interspecies interaction between organisms symbiont entry into host cell symbiont entry into host biological process involved in interaction with host biological process involved in symbiotic interaction cellular metabolic process cellular nitrogen compound metabolic process primary metabolic process viral genome integration into host DNA viral process viral life cycle viral penetration into host nucleus intracellular transport of virus transport of virus biological process involved in interspecies interaction between organisms symbiont entry into host cell symbiont entry into host biological process involved in interaction with host biological process involved in symbiotic interaction cellular metabolic process cellular nitrogen compound metabolic process primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process heterocycle metabolic process nitrogen compound metabolic process metabolic process cellular process macromolecule metabolic process DNA integration cellular aromatic compound metabolic process establishment of integrated proviral latency viral latency establishment of viral latency DNA recombination symbiont-mediated perturbation of host cellular process symbiont-mediated suppression of host gene expression modulation by symbiont of host process symbiont-mediated perturbation of host gene expression modulation of process of another organism organonitrogen compound metabolic process proteolysis protein metabolic process	membrane cellular anatomical entity host intracellular membrane-bounded organelle host cellular component host intracellular part host multivesicular body host cell cytoplasm part host intracellular organelle host cell cytoplasm host cell part host cell late endosome host cell endosome host intracellular region viral nucleocapsid membrane cellular anatomical entity host intracellular membrane-bounded organelle host cellular component host intracellular part host multivesicular body host cell cytoplasm part host intracellular organelle host cell cytoplasm host cell part host cell late endosome host cell endosome host intracellular region viral nucleocapsid viral capsid virion component host cell plasma membrane host cell membrane virion membrane host cell nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth A]	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
B [auth A]	IPR043128	Reverse transcriptase/Diguanylate cyclase domain	Homologous Superfamily
B [auth A]	IPR001995	Peptidase A2A, retrovirus, catalytic	Domain
B [auth A]	IPR001878	Zinc finger, CCHC-type	Domain
B [auth A]	IPR008919	Retrovirus capsid, N-terminal	Homologous Superfamily
B [auth A]	IPR012344	Matrix protein, lentiviral and alpha-retroviral, N-terminal	Homologous Superfamily
B [auth A]	IPR036862	Integrase, C-terminal domain superfamily, retroviral	Homologous Superfamily
B [auth A]	IPR018061	Retropepsins	Domain
B [auth A]	IPR010661	Reverse transcriptase thumb	Domain
B [auth A]	IPR002156	Ribonuclease H domain	Domain
B [auth A]	IPR036875	Zinc finger, CCHC-type superfamily	Homologous Superfamily
B [auth A]	IPR003308	Integrase, N-terminal zinc-binding domain	Domain
B [auth A]	IPR001584	Integrase, catalytic core	Domain
B [auth A]	IPR045345	Retroviral nucleocapsid Gag protein p24, C-terminal domain	Domain
B [auth A]	IPR010999	Retroviral matrix protein	Homologous Superfamily
B [auth A]	IPR021109	Aspartic peptidase domain superfamily	Homologous Superfamily
B [auth A]	IPR001969	Aspartic peptidase, active site	Active Site
B [auth A]	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
B [auth A]	IPR017856	Integrase-like, N-terminal	Homologous Superfamily
B [auth A]	IPR000071	Immunodeficiency lentiviral matrix, N-terminal	Domain
B [auth A]	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
B [auth A]	IPR001037	Integrase, C-terminal, retroviral	Domain
B [auth A]	IPR034170	Retropepsin-like catalytic domain	Domain
B [auth A]	IPR000477	Reverse transcriptase domain	Domain
B [auth A]	IPR010659	Reverse transcriptase connection	Domain
B [auth A]	IPR008916	Retrovirus capsid, C-terminal	Homologous Superfamily

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A [auth B]	CG1	Parent Component: G
B [auth A]	NH2	RESID: AA0081 , AA0083 , AA0084 , AA0086 , AA0087 , AA0088 , AA0090 , AA0091 , AA0092 , AA0093 , AA0095 , AA0096 , AA0097 , AA0098 , AA0099 , AA0100 PSI-MOD : L-alanine amide MOD:00090 , L-asparagine amide MOD:00092 , L-aspartic acid 1-amide MOD:00093 , L-glutamine amide MOD:00095 , L-glutamic acid 1-amide MOD:00096 , glycine amide MOD:00097 , L-isoleucine amide MOD:00099 , L-leucine amide MOD:00100 , L-lysine amide MOD:00101 , L-methionine amide MOD:00102 , L-proline amide MOD:00104 , L-serine amide MOD:00105 , L-threonine amide MOD:00106 , L-tryptophan amide MOD:00107 , L-tyrosine amide MOD:00108 , L-valine amide MOD:00109