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(-) Description

Title :  CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN GP41 FRAGMENTS N36 AND C34 MUTANT N126K/E137Q
 
Authors :  K. Izumi, S. Nakamura, H. Nakano, K. Shimura, Y. Sakagami, S. Oishi, S. U T. Ohkubo, Y. Kobayashi, N. Fujii, M. Matsuoka, E. N. Kodama
Date :  22 Apr 10  (Deposition) - 19 May 10  (Release) - 31 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Coiled-Coil, Viral Protein-Inhibitor Complex, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Izumi, S. Nakamura, H. Nakano, K. Shimura, Y. Sakagami, S. Oishi, S. Uchiyama, T. Ohkubo, Y. Kobayashi, N. Fujii, M. Matsuoka, E. N. Kodama
Characterization Of Hiv-1 Resistance To A Fusion Inhibitor, N36, Derived From The Gp41 Amino Terminal Heptad Repeat.
Antiviral Res. 2010
PubMed-ID: 20438763  |  Reference-DOI: 10.1016/J.ANTIVIRAL.2010.04.011

(-) Compounds

Molecule 1 - TRANSMEMBRANE PROTEIN GP41
    Chains: A, C, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: GP41 FRAGMENT N36
    Gene: ENV
    Organism Common: HIV-1
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
 
Molecule 2 - TRANSMEMBRANE PROTEIN GP41
    Chains: B, D, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: GP41 FRAGMENT C34
    Gene: ENV
    Mutation: YES
    Organism Common: HIV-1
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 15)

Asymmetric/Biological Unit (4, 15)
No.NameCountTypeFull Name
1ACE6Mod. Amino AcidACETYL GROUP
2CL2Ligand/IonCHLORIDE ION
3MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
4NH26Mod. Amino AcidAMINO GROUP

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU B:143 , HOH B:171 , HIS C:53 , GLN C:56 , TYR D:127BINDING SITE FOR RESIDUE MPD B 5001
2AC2SOFTWAREGLN A:41 , GLN C:41 , GLN E:41BINDING SITE FOR RESIDUE CL C 2
3AC3SOFTWARETRP D:117 , HOH D:185BINDING SITE FOR RESIDUE CL D 1

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3AHA)

(-) 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_HV1LW | Q70626 from UniProtKB/Swiss-Prot  Length:856

    Alignment length:38
                                   554       564       574        
            ENV_HV1LW   545 LSGIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARILA 582
               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
                 3aha A  34 xSDIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARILx  71
                            |       43        53        63       |
                            |                                   71-NH2
                           34-ACE                                 


Chain A from PDB  Type:PROTEIN  Length:38
 aligned with Q72502_9HIV1 | Q72502 from UniProtKB/TrEMBL  Length:854

    Alignment length:38
                                   552       562       572        
         Q72502_9HIV1   543 LSDIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARILA 580
               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
                 3aha A  34 xSDIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARILx  71
                            |       43        53        63       |
                            |                                   71-NH2
                           34-ACE                                 


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

    Alignment length:36
                                   636       646       656      
            ENV_HV1LW   627 TWMEWDREINNYTSLIHSLIEESQNQQEKNEQELLE 662
               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
                 3aha B 116 xWMEWDREINKYTSLIHSLIEQSQNQQEKNEQELLx 151
                            |      125       135       145     |
                            |                                151-NH2
                          116-ACE                               


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

    Alignment length:38
                                   554       564       574        
            ENV_HV1LW   545 LSGIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARILA 582
               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
                 3aha C  34 xSDIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARILx  71
                            |       43        53        63       |
                            |                                   71-NH2
                           34-ACE                                 


Chain C from PDB  Type:PROTEIN  Length:38
 aligned with Q72502_9HIV1 | Q72502 from UniProtKB/TrEMBL  Length:854

    Alignment length:38
                                   552       562       572        
         Q72502_9HIV1   543 LSDIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARILA 580
               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
                 3aha C  34 xSDIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARILx  71
                            |       43        53        63       |
                            |                                   71-NH2
                           34-ACE                                 


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

    Alignment length:36
                                   636       646       656      
            ENV_HV1LW   627 TWMEWDREINNYTSLIHSLIEESQNQQEKNEQELLE 662
               SCOP domains ------------------------------------ SCOP domains
               CATH domains ------------------------------------ CATH domains
               Pfam domains ------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------ PROSITE
                 Transcript ------------------------------------ Transcript
                 3aha D 116 xWMEWDREINKYTSLIHSLIEQSQNQQEKNEQELLx 151
                            |      125       135       145     |
                            |                                151-NH2
                          116-ACE                               


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

    Alignment length:38
                                   554       564       574        
            ENV_HV1LW   545 LSGIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARILA 582
               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
                 3aha E  34 xSDIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARILx  71
                            |       43        53        63       |
                            |                                   71-NH2
                           34-ACE                                 


Chain E from PDB  Type:PROTEIN  Length:38
 aligned with Q72502_9HIV1 | Q72502 from UniProtKB/TrEMBL  Length:854

    Alignment length:38
                                   552       562       572        
         Q72502_9HIV1   543 LSDIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARILA 580
               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
                 3aha E  34 xSDIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARILx  71
                            |       43        53        63       |
                            |                                   71-NH2
                           34-ACE                                 


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

    Alignment length:36
                                   636       646       656      
            ENV_HV1LW   627 TWMEWDREINNYTSLIHSLIEESQNQQEKNEQELLE 662
               SCOP domains ------------------------------------ SCOP domains
               CATH domains ------------------------------------ CATH domains
               Pfam domains ------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------ PROSITE
                 Transcript ------------------------------------ Transcript
                 3aha F 116 xWMEWDREINKYTSLIHSLIEQSQNQQEKNEQELLx 151
                            |      125       135       145     |
                            |                                151-NH2
                          116-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 3AHA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (21, 35)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (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.

Chain A,C,E   (Q72502_9HIV1 | Q72502)
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: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: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: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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  3aha
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  ENV_HV1LW | Q70626
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  Q72502_9HIV1 | Q72502
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 Related Entries

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

UniProtKB/Swiss-Prot
        ENV_HV1LW | Q70626: 1if3 2x7r 2z2t 3cp1 3cyo 3gwo 3h00 3h01 4i48 5hfm
UniProtKB/TrEMBL
        Q72502_9HIV1 | Q72502: 2jnr

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3AHA)