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(-)Asym./Biol. Unit
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(-) Description

Title :  HIV GP41 SIX-HELIX BUNDLE CONTAINING A MUTANT CHR ALPHA-PEPTIDE SEQUENCE
 
Authors :  W. S. Horne, S. H. Gellman
Date :  03 Nov 08  (Deposition) - 15 Sep 09  (Release) - 20 Oct 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Helix Bundle, Aids, Apoptosis, Cell Membrane, Cleavage On Pair Of Basic Residues, Coiled Coil, Envelope Protein, Fusion Protein, Glycoprotein, Host-Virus Interaction, Lipoprotein, Membrane, Palmitate, Transmembrane, Viral Immunoevasion, Virion, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. S. Horne, L. M. Johnson, T. J. Ketas, P. J. Klasse, M. Lu, J. P. Moore, S. H. Gellman
Structural And Biological Mimicry Of Protein Surface Recognition By Alpha/Beta-Peptide Foldamers
Proc. Natl. Acad. Sci. Usa V. 106 14751 2009
PubMed-ID: 19706443  |  Reference-DOI: 10.1073/PNAS.0902663106
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ENVELOPE GLYCOPROTEIN GP160
    Chains: A, B, C
    Engineered: YES
    Fragment: HIV GP41 NHR DOMAIN
    Other Details: THE PEPTIDE IS CHEMICALLY SYNTHESIZED. IT OCCURS NATURALLY IN HIV.
    Synonym: ENV POLYPROTEIN, SURFACE PROTEIN, SU, GLYCOPROTEIN 120, GP120, TRANSMEMBRANE PROTEIN, TM, GLYCOPROTEIN 41, GP41
    Synthetic: YES
 
Molecule 2 - MUTANT PEPTIDE DERIVED FROM HIV GP41 CHR DOMAIN
    Chains: D, E, F
    Engineered: YES
    Fragment: HIV GP41 CHR DOMAIN MUTANT
    Mutation: YES
    Other Details: THE PEPTIDE IS CHEMICALLY SYNTHESIZED. IT IS A SEQUENCE MUTANT TO A SEQUENCE THAT OCCURS NATURALLY IN HIV.
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric/Biological Unit (2, 12)
No.NameCountTypeFull Name
1ACE6Mod. Amino AcidACETYL GROUP
2NH26Mod. Amino AcidAMINO GROUP

(-) Sites  (0, 0)

(no "Site" information available for 3F4Y)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3F4Y)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3F4Y)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3F4Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3F4Y)

(-) Exons   (0, 0)

(no "Exon" information available for 3F4Y)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:38
 aligned with ENV_HV1Z6 | P04580 from UniProtKB/Swiss-Prot  Length:855

    Alignment length:38
                                   553       563       573        
            ENV_HV1Z6   544 MSGIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARILA 581
               SCOP domains -------------------------------------- SCOP domains
               CATH domains -------------------------------------- CATH domains
               Pfam domains -------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------- PROSITE
                 Transcript -------------------------------------- Transcript
                 3f4y A   0 xSGIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARILx  37
                            |        9        19        29       |
                            |                                   37-NH2
                            0-ACE                                 


Chain B from PDB  Type:PROTEIN  Length:38
 aligned with ENV_HV1Z6 | P04580 from UniProtKB/Swiss-Prot  Length:855

    Alignment length:38
                                   553       563       573        
            ENV_HV1Z6   544 MSGIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARILA 581
               SCOP domains -------------------------------------- SCOP domains
               CATH domains -------------------------------------- CATH domains
               Pfam domains -------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------- PROSITE
                 Transcript -------------------------------------- Transcript
                 3f4y B   0 xSGIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARILx  37
                            |        9        19        29       |
                            |                                   37-NH2
                            0-ACE                                 


Chain C from PDB  Type:PROTEIN  Length:38
 aligned with ENV_HV1Z6 | P04580 from UniProtKB/Swiss-Prot  Length:855

    Alignment length:38
                                   553       563       573        
            ENV_HV1Z6   544 MSGIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARILA 581
               SCOP domains -------------------------------------- SCOP domains
               CATH domains -------------------------------------- CATH domains
               Pfam domains -------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------- PROSITE
                 Transcript -------------------------------------- Transcript
                 3f4y C   0 xSGIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARILx  37
                            |        9        19        29       |
                            |                                   37-NH2
                            0-ACE                                 


Chain D from PDB  Type:PROTEIN  Length:40
                                                                        
               SCOP domains ---------------------------------------- SCOP domains
               CATH domains ---------------------------------------- CATH domains
               Pfam domains ---------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------- PROSITE
                 Transcript ---------------------------------------- Transcript
                 3f4y D   0 xTTWEAWDRAIAEYAARIEALIRAAQEQQEKNEAALRELx  39
                            |        9        19        29        39
                            |                                     39-NH2
                            0-ACE                                   


Chain E from PDB  Type:PROTEIN  Length:40
                                                                        
               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
                 3f4y E   0 xTTWEAWDRAIAEYAARIEALIRAAQEQQEKNEAALRELx  39
                            |        9        19        29        39
                            |                                     39-NH2
                            0-ACE                                   


Chain F from PDB  Type:PROTEIN  Length:40
                                                                        
               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
                 3f4y F   0 xTTWEAWDRAIAEYAARIEALIRAAQEQQEKNEAALRELx  39
                            |        9        19        29        39
                            |                                     39-NH2
                            0-ACE
   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)

(no "SCOP Domain" information available for 3F4Y)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3F4Y)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3F4Y)

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (ENV_HV1Z6 | P04580)
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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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        ENV_HV1Z6 | P04580: 1tjh 1tji 2zzo 3f50 3g7a 3moa 3mob 3mod 4i2l

(-) Related Entries Specified in the PDB File

1aik HIV GP41 SIX-HELIX BUNDLE WITH CHR PEPTIDE DERIVED FROM THE NATIVE GP41 SEQUENCE
3f4z
3f50