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(-) Description

Title :  STRUCTURE OF GP41 T21/CP621-652
 
Authors :  X. Yao, S. Waltersperger, M. Wang, S. Cui
Date :  22 Aug 11  (Deposition) - 25 Apr 12  (Release) - 26 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.74
Chains :  Asym. Unit :  C,D
Biol. Unit 1:  C,D  (3x)
Keywords :  6-Helix Bundle, Membrane Fusion, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Chong, X. Yao, Z. Qiu, B. Qin, R. Han, S. Waltersperger, M. Wang, S. Cui, Y. He
Discovery Of Critical Residues For Viral Entry And Inhibition Through Structural Insight Of Hiv-1 Fusion Inhibitor Cp621-652.
J. Biol. Chem. V. 287 20281 2012
PubMed-ID: 22511760  |  Reference-DOI: 10.1074/JBC.M112.354126

(-) Compounds

Molecule 1 - ENVELOPE GLYCOPROTEIN GP160
    Chains: C
    Engineered: YES
    Fragment: NHR (UNP RESIDIES 553-590)
    Organism Common: HIV-1
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1
    Organism Taxid: 11676
    Other Details: THIS SEQUENCE OCCURS NATURALLY IN HUMANS.
    Synonym: ENV POLYPROTEIN, SURFACE PROTEIN GP120, SU, GLYCOPROTEIN 120, GP120, TRANSMEMBRANE PROTEIN GP41, TM, GLYCOPROTEIN 41, GP41
    Synthetic: YES
 
Molecule 2 - ENVELOPE GLYCOPROTEIN GP160
    Chains: D
    Engineered: YES
    Fragment: CHR (UNP RESIDIES 621-652)
    Organism Common: HIV-1
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1
    Organism Taxid: 11676
    Other Details: THIS SEQUENCE OCCURS NATURALLY IN HUMANS.
    Synonym: ENV POLYPROTEIN, SURFACE PROTEIN GP120, SU, GLYCOPROTEIN 120, GP120, TRANSMEMBRANE PROTEIN GP41, TM, GLYCOPROTEIN 41, GP41
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : CD
Biological Unit 1 (3x): CD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (4, 4)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2ACY1Ligand/IonACETIC ACID
3GOL1Ligand/IonGLYCEROL
4NH21Mod. Amino AcidAMINO GROUP
Biological Unit 1 (4, 12)
No.NameCountTypeFull Name
1ACE3Mod. Amino AcidACETYL GROUP
2ACY3Ligand/IonACETIC ACID
3GOL3Ligand/IonGLYCEROL
4NH23Mod. Amino AcidAMINO GROUP

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG C:585 , LYS C:588BINDING SITE FOR RESIDUE ACY C 601
2AC2SOFTWAREHOH C:701 , HOH C:733BINDING SITE FOR RESIDUE GOL C 602

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3VGX)

(-) Sequences/Alignments

Asymmetric 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 C from PDB  Type:PROTEIN  Length:40
 aligned with ENV_HV1B1 | P03375 from UniProtKB/Swiss-Prot  Length:856

    Alignment length:40
                                   561       571       581       591
            ENV_HV1B1   552 QNNLLRAIEAQQHLLQLTVWGIKQLQARILAVERYLKDQQ 591
               SCOP domains ---------------------------------------- SCOP domains
               CATH domains ---------------------------------------- CATH domains
               Pfam domains ---------------------------------------- Pfam domains
         Sec.struct. author ........................................ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------- PROSITE
                 Transcript ---------------------------------------- Transcript
                 3vgx C 552 xNNLLRAIEAQQHLLQLTVWGIKQLQARILAVERYLKDQx 591
                            |      561       571       581       591
                            |                                    591-NH2
                          552-ACE                                   


Chain C from PDB  Type:PROTEIN  Length:40
 aligned with ENV_HV1BR | P03377 from UniProtKB/Swiss-Prot  Length:861

    Alignment length:40
                                   566       576       586       596
            ENV_HV1BR   557 QNNLLRAIEAQQHLLQLTVWGIKQLQARILAVERYLKDQQ 596
               SCOP domains ---------------------------------------- SCOP domains
               CATH domains ---------------------------------------- CATH domains
               Pfam domains ---------------------------------------- Pfam domains
         Sec.struct. author ........................................ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------- PROSITE
                 Transcript ---------------------------------------- Transcript
                 3vgx C 552 xNNLLRAIEAQQHLLQLTVWGIKQLQARILAVERYLKDQx 591
                            |      561       571       581       591
                          552-ACE                                591-NH2


Chain D from PDB  Type:PROTEIN  Length:28
 aligned with ENV_HV1B1 | P03375 from UniProtKB/Swiss-Prot  Length:856

    Alignment length:28
                                   633       643        
            ENV_HV1B1   624 NNMTWMEWDREINNYTSLIHSLIEESQN 651
               SCOP domains ---------------------------- SCOP domains
               CATH domains ---------------------------- CATH domains
               Pfam domains ---------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------- SAPs(SNPs)
                    PROSITE ---------------------------- PROSITE
                 Transcript ---------------------------- Transcript
                 3vgx D 624 NNMTWMEWDREINNYTSLIHSLIEESQN 651
                                   633       643        


Chain D from PDB  Type:PROTEIN  Length:28
 aligned with ENV_HV1BR | P03377 from UniProtKB/Swiss-Prot  Length:861

    Alignment length:28
                                   638       648        
            ENV_HV1BR   629 NNMTWMEWDREINNYTSLIHSLIEESQN 656
               SCOP domains ---------------------------- SCOP domains
               CATH domains ---------------------------- CATH domains
               Pfam domains ---------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------- SAPs(SNPs)
                    PROSITE ---------------------------- PROSITE
                 Transcript ---------------------------- Transcript
                 3vgx D 624 NNMTWMEWDREINNYTSLIHSLIEESQN 651
                                   633       643
   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 3VGX)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (26, 47)

Asymmetric Unit(hide GO term definitions)
Chain C,D   (ENV_HV1B1 | P03375)
molecular function
    GO:0042609    CD4 receptor binding    Interacting selectively and non-covalently with a CD4, a receptor found on the surface of T cells, monocytes and macrophages.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0032403    protein complex binding    Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    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:0044220    host cell perinuclear region of cytoplasm    The host cell cytoplasm situated near, or occurring around, the host nucleus.
    GO:0044538    host cell periphery    The part of a cell encompassing the cell cortex, the plasma membrane, and any external encapsulating structures of a host cell.
    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 C,D   (ENV_HV1BR | P03377)
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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  3vgx
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  ENV_HV1B1 | P03375
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  ENV_HV1BR | P03377
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 Related Entries

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

UniProtKB/Swiss-Prot
        ENV_HV1B1 | P03375: 2ari 3vgy 3vh7 3vu5 3vu6 3w19
        ENV_HV1BR | P03377: 1env 1erf 1fav 1p5a 1u6u 1u6v 2zzo 3g9r 3mnw 3vtp

(-) Related Entries Specified in the PDB File

3vgy 3vh7