##gff-version 3
P03406	UniProtKB	Initiator methionine	1	1	.	.	.	Note=Removed%3B by host;Ontology_term=ECO:0000255;evidence=ECO:0000255|HAMAP-Rule:MF_04078	
P03406	UniProtKB	Chain	2	206	.	.	.	ID=PRO_0000038335;Note=Protein Nef;Ontology_term=ECO:0000255;evidence=ECO:0000255|HAMAP-Rule:MF_04078	
P03406	UniProtKB	Chain	58	206	.	.	.	ID=PRO_0000038336;Note=C-terminal core protein;Ontology_term=ECO:0000255;evidence=ECO:0000255|HAMAP-Rule:MF_04078	
P03406	UniProtKB	Region	62	65	.	.	.	Note=Acidic%3B interacts with host PACS1 and PACS2%3B stabilizes the interaction of NEF/MHC-I with host AP1M1%3B necessary for MHC-I internalization;Ontology_term=ECO:0000255;evidence=ECO:0000255|HAMAP-Rule:MF_04078	
P03406	UniProtKB	Region	69	78	.	.	.	Note=SH3-binding%3B interaction with Src family tyrosine kinases;Ontology_term=ECO:0000255,ECO:0000269,ECO:0000269;evidence=ECO:0000255|HAMAP-Rule:MF_04078,ECO:0000269|PubMed:7859737,ECO:0000269|PubMed:8681387;Dbxref=PMID:7859737,PMID:8681387	
P03406	UniProtKB	Region	108	124	.	.	.	Note=Mediates dimerization%2C Nef-PTE1 interaction;Ontology_term=ECO:0000255;evidence=ECO:0000255|HAMAP-Rule:MF_04078	
P03406	UniProtKB	Region	108	124	.	.	.	Note=Mediates dimerization%2C Nef-PTE1 interaction%2C Nef-induced CD4 and MHC-I down-regulation and enhancement of infectivity;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:19781555;Dbxref=PMID:19781555	
P03406	UniProtKB	Region	148	180	.	.	.	Note=Binding to ATP6V1H;Ontology_term=ECO:0000255;evidence=ECO:0000255|HAMAP-Rule:MF_04078	
P03406	UniProtKB	Motif	72	75	.	.	.	Note=PxxP%3B stabilizes the interaction of NEF/MHC-I with host AP1M1%3B necessary for MHC-I internalization;Ontology_term=ECO:0000255;evidence=ECO:0000255|HAMAP-Rule:MF_04078	
P03406	UniProtKB	Motif	164	165	.	.	.	Note=Dileucine internalization motif%3B necessary for CD4 internalization;Ontology_term=ECO:0000255;evidence=ECO:0000255|HAMAP-Rule:MF_04078	
P03406	UniProtKB	Motif	174	175	.	.	.	Note=Diacidic%3B necessary for CD4 internalization;Ontology_term=ECO:0000255,ECO:0000269;evidence=ECO:0000255|HAMAP-Rule:MF_04078,ECO:0000269|PubMed:18032517;Dbxref=PMID:18032517	
P03406	UniProtKB	Site	20	20	.	.	.	Note=Might play a role in AP-1 recruitment to the Nef-MHC-I complex;Ontology_term=ECO:0000255;evidence=ECO:0000255|HAMAP-Rule:MF_04078	
P03406	UniProtKB	Site	57	58	.	.	.	Note=Cleavage%3B by viral protease;Ontology_term=ECO:0000255,ECO:0000269;evidence=ECO:0000255|HAMAP-Rule:MF_04078,ECO:0000269|PubMed:7835426;Dbxref=PMID:7835426	
P03406	UniProtKB	Modified residue	6	6	.	.	.	Note=Phosphoserine%3B by host;Ontology_term=ECO:0000255;evidence=ECO:0000255|HAMAP-Rule:MF_04078	
P03406	UniProtKB	Lipidation	2	2	.	.	.	Note=N-myristoyl glycine%3B by host;Ontology_term=ECO:0000255;evidence=ECO:0000255|HAMAP-Rule:MF_04078	
P03406	UniProtKB	Natural variant	11	11	.	.	.	Note=In strain: Clone pNL4-3. V->I	
P03406	UniProtKB	Natural variant	15	15	.	.	.	Note=In strain: Clone pNL4-3. T->A	
P03406	UniProtKB	Natural variant	33	33	.	.	.	Note=In strain: Clone pNL4-3. A->V	
P03406	UniProtKB	Natural variant	51	51	.	.	.	Note=In strain: Clone pNL4-3. T->N	
P03406	UniProtKB	Mutagenesis	2	3	.	.	.	Note=70%25 loss of infectivity. GG->AA;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:8151761;Dbxref=PMID:8151761	
P03406	UniProtKB	Mutagenesis	20	20	.	.	.	Note=Amost complete loss of Nef-induced MHC-I down-regulation. M->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:10684310;Dbxref=PMID:10684310	
P03406	UniProtKB	Mutagenesis	20	20	.	.	.	Note=Amost complete loss of Nef-induced MHC-I down-regulation. M->R;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:10684310;Dbxref=PMID:10684310	
P03406	UniProtKB	Mutagenesis	71	71	.	.	.	Note=Increases infectivity by a factor of three. T->R;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:11525746;Dbxref=PMID:11525746	
P03406	UniProtKB	Mutagenesis	72	72	.	.	.	Note=Complete loss of binding to HCKSH3 domain and altered viral growth%3B when associated with P-76. No effect on Nef-induced CD4 down-regulation. P->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:7859737;Dbxref=PMID:7859737	
P03406	UniProtKB	Mutagenesis	75	75	.	.	.	Note=Complete loss of binding to HCKSH3 domain and altered viral growth%3B when associated with P-73. No effect on Nef-induced CD4 down-regulation. P->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:7859737;Dbxref=PMID:7859737	
P03406	UniProtKB	Mutagenesis	147	147	.	.	.	Note=Complete loss of binding to HCKSH3 domain and altered viral growth. No effect on Nef-induced CD4 down-modulation. P->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:7859737;Dbxref=PMID:7859737	
P03406	UniProtKB	Mutagenesis	150	150	.	.	.	Note=No effect. P->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:7859737;Dbxref=PMID:7859737	
P03406	UniProtKB	Mutagenesis	164	165	.	.	.	Note=Loss of interaction with AP-2 complex. LL->AA;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:18032517;Dbxref=PMID:18032517	
P03406	UniProtKB	Mutagenesis	174	175	.	.	.	Note=Loss of interaction with AP-2 complex. DD->AA;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:18032517;Dbxref=PMID:18032517	
P03406	UniProtKB	Turn	49	51	.	.	.	Ontology_term=ECO:0007829;evidence=ECO:0007829|PDB:6URI	
P03406	UniProtKB	Helix	53	58	.	.	.	Ontology_term=ECO:0007829;evidence=ECO:0007829|PDB:6URI	
P03406	UniProtKB	Helix	63	66	.	.	.	Ontology_term=ECO:0007829;evidence=ECO:0007829|PDB:6URI	
P03406	UniProtKB	Helix	81	93	.	.	.	Ontology_term=ECO:0007829;evidence=ECO:0007829|PDB:1EFN	
P03406	UniProtKB	Turn	97	99	.	.	.	Ontology_term=ECO:0007829;evidence=ECO:0007829|PDB:1AVZ	
P03406	UniProtKB	Helix	104	118	.	.	.	Ontology_term=ECO:0007829;evidence=ECO:0007829|PDB:1EFN	
P03406	UniProtKB	Beta strand	130	132	.	.	.	Ontology_term=ECO:0007829;evidence=ECO:0007829|PDB:1EFN	
P03406	UniProtKB	Beta strand	136	138	.	.	.	Ontology_term=ECO:0007829;evidence=ECO:0007829|PDB:1EFN	
P03406	UniProtKB	Beta strand	143	147	.	.	.	Ontology_term=ECO:0007829;evidence=ECO:0007829|PDB:1EFN	
P03406	UniProtKB	Helix	150	156	.	.	.	Ontology_term=ECO:0007829;evidence=ECO:0007829|PDB:6URI	
P03406	UniProtKB	Helix	167	169	.	.	.	Ontology_term=ECO:0007829;evidence=ECO:0007829|PDB:6URI	
P03406	UniProtKB	Beta strand	170	172	.	.	.	Ontology_term=ECO:0007829;evidence=ECO:0007829|PDB:6URI	
P03406	UniProtKB	Beta strand	181	185	.	.	.	Ontology_term=ECO:0007829;evidence=ECO:0007829|PDB:1EFN	
P03406	UniProtKB	Helix	187	190	.	.	.	Ontology_term=ECO:0007829;evidence=ECO:0007829|PDB:1EFN	
P03406	UniProtKB	Helix	194	198	.	.	.	Ontology_term=ECO:0007829;evidence=ECO:0007829|PDB:1EFN	
P03406	UniProtKB	Helix	200	202	.	.	.	Ontology_term=ECO:0007829;evidence=ECO:0007829|PDB:1EFN