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Title :   STRUCTURE OF THE C-TERMINAL DOMAIN OF A PUTATIVE HIV-1 GP41 FUSION INTERMEDIATE

Authors :   J. Liu

Date :   08 Apr 09 (Deposition) - 15 Dec 09 (Release) - 04 Feb 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,C  (1x)
Biol. Unit 2: B,D  (1x)

Keywords :   Viral Membrane Fusion, Hiv-1, Gp41, Envelope Protein, Neutralizing Antibodies, Aids, Apoptosis, Cell Membrane, Cleavage On Pair Of Basic Residues, Disulfide Bond, Fusion Protein, Glycoprotein, Host- Virus Interaction, Lipoprotein, Membrane, Palmitate, Transmembrane, Viral Immunoevasion, Virion, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Liu, Y. Deng, Q. Li, A. K. Dey, J. P. Moore, M. Lu
Role Of A Putative Gp41 Dimerization Domain In Human Immunodeficiency Virus Type 1 Membrane Fusion.
J. Virol. V. 84 201 2010
PubMed-ID: 19846514 | Reference-DOI: 10.1128/JVI.01558-09

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
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Chain A from PDB  Type:PROTEIN  Length:39
 aligned with ENV_HV1LW | Q70626 from UniProtKB/Swiss-Prot  Length:856

    Alignment length:39
                                   645       655       665         
            ENV_HV1LW   636 NNYTSLIHSLIEESQNQQEKNEQELLELDKWASLWNWFN 674
               SCOP domains --------------------------------------- SCOP domains
               CATH domains --------------------------------------- CATH domains
               Pfam domains --------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------- PROSITE
                 Transcript --------------------------------------- Transcript
                 3h00 A   1 NNYTSLIHSLIEESQNQQEKNEQELLELDKWASLWNWFN  39
                                    10        20        30

Chain B from PDB  Type:PROTEIN  Length:38
 aligned with ENV_HV1LW | Q70626 from UniProtKB/Swiss-Prot  Length:856

    Alignment length:38
                                   645       655       665        
            ENV_HV1LW   636 NNYTSLIHSLIEESQNQQEKNEQELLELDKWASLWNWF 673
               SCOP domains -------------------------------------- SCOP domains
               CATH domains -------------------------------------- CATH domains
               Pfam domains -------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------- PROSITE
                 Transcript -------------------------------------- Transcript
                 3h00 B   1 NNYTSLIHSLIEESQNQQEKNEQELLELDKWASLWNWF  38
                                    10        20        30

Chain C from PDB  Type:PROTEIN  Length:39
 aligned with ENV_HV1LW | Q70626 from UniProtKB/Swiss-Prot  Length:856

    Alignment length:39
                                   645       655       665         
            ENV_HV1LW   636 NNYTSLIHSLIEESQNQQEKNEQELLELDKWASLWNWFN 674
               SCOP domains --------------------------------------- SCOP domains
               CATH domains --------------------------------------- CATH domains
               Pfam domains --------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------- PROSITE
                 Transcript --------------------------------------- Transcript
                 3h00 C   1 NNYTSLIHSLIEESQNQQEKNEQELLELDKWASLWNWFN  39
                                    10        20        30

Chain D from PDB  Type:PROTEIN  Length:36
 aligned with ENV_HV1LW | Q70626 from UniProtKB/Swiss-Prot  Length:856

    Alignment length:36
                                   645       655       665      
            ENV_HV1LW   636 NNYTSLIHSLIEESQNQQEKNEQELLELDKWASLWN 671
               SCOP domains ------------------------------------ SCOP domains
               CATH domains ------------------------------------ CATH domains
               Pfam domains ------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------ PROSITE
                 Transcript ------------------------------------ Transcript
                 3h00 D   1 NNYTSLIHSLIEESQNQQEKNEQELLELDKWASLWN  36
                                    10        20        30

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (21, 21)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (ENV_HV1LW | Q70626)

molecular function
	GO:0005198	structural molecule activity	The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
biological process
	GO:0075512	clathrin-dependent endocytosis of virus by host cell	Any clathrin-mediated endocytosis that is involved in the uptake of a virus into a host cell. Begins by invagination of a specific region of the host cell plasma membrane around the bound virus to form a clathrin-coated pit, which then pinches off to form a clathrin-coated endocytic vesicle containing the virus.
	GO:0075509	endocytosis involved in viral entry into host cell	Any endocytosis that is involved in the uptake of a virus into a host cell.
	GO:0030683	evasion or tolerance by virus of host immune response	Any process, either active or passive, by which a virus avoids the effects of the host organism's immune response. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	GO:0039654	fusion of virus membrane with host endosome membrane	Fusion of a virus membrane with a host endosome membrane. Occurs after internalization of the virus through the endosomal pathway, and results in release of the virus contents into the cell.
	GO:0019064	fusion of virus membrane with host plasma membrane	Fusion of a viral membrane with the host cell membrane during viral entry. Results in release of the virion contents into the cytoplasm.
	GO:0039663	membrane fusion involved in viral entry into host cell	Merging of the virion membrane and a host membrane (host plasma membrane or host organelle membrane) that is involved in the uptake of a virus into a host cell.
	GO:0002223	stimulatory C-type lectin receptor signaling pathway	Any series of molecular signals generated as a consequence of binding to a C-type lectin receptor capable of cellular activation.
	GO:0046718	viral entry into host cell	The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
	GO:0019082	viral protein processing	Any protein maturation process achieved by the cleavage of a peptide bond or bonds within a viral protein.
	GO:0019062	virion attachment to host cell	The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
cellular component
	GO:0044174	host cell endosome	A membrane-bounded organelle that carries materials newly ingested by endocytosis. It passes many of the materials to host cell lysosomes for degradation.
	GO:0044175	host cell endosome membrane	The lipid bilayer surrounding a host cell endosome.
	GO:0033644	host cell membrane	Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	GO:0020002	host cell plasma membrane	The plasma membrane surrounding a host cell.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0019031	viral envelope	The lipid bilayer of a virion that surrounds the protein capsid. May also contain glycoproteins.
	GO:0019012	virion	The complete fully infectious extracellular virus particle.
	GO:0055036	virion membrane	The lipid bilayer surrounding a virion.

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