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(-) Description

Title :  STRUCTURE OF THE C-TERMINAL DOMAIN OF A PUTATIVE HIV-1 GP41 FUSION INTERMEDIATE
 
Authors :  J. Liu
Date :  01 Apr 09  (Deposition) - 15 Dec 09  (Release) - 19 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A,B
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

Molecule 1 - ENVELOPE GLYCOPROTEIN GP160
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: C-TERMINAL DOMAIN (UNP RESIDUES 630 TO 683)
    Gene: ENV
    Organism Common: HIV-1
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 LW12.3 ISOLATE
    Organism Taxid: 82834
    Strain: HXB2 ISOLATE
    Synonym: ENV POLYPROTEIN, SURFACE PROTEIN, SU, GLYCOPROTEIN 120, GP120, TRANSMEMBRANE PROTEIN, TM, GLYCOPROTEIN 41, GP41

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1JEF2Ligand/IonO-(O-(2-AMINOPROPYL)-O'-(2-METHOXYETHYL)POLYPROPYLENEGLYCOL 500)
2NA1Ligand/IonSODIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:37 , TRP A:41 , THR A:47 , ASN A:48 , TRP A:51 , TRP B:37 , TRP B:41 , TRP B:51BINDING SITE FOR RESIDUE JEF A 55
2AC2SOFTWAREHOH A:89 , TRP B:37 , LEU B:40 , TRP B:51BINDING SITE FOR RESIDUE JEF A 56
3AC3SOFTWARETRP A:2 , SER A:39 , HOH A:75 , HOH A:78 , HOH B:61BINDING SITE FOR RESIDUE NA A 57

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3GWO)

(-) 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:53
 aligned with ENV_HV1LW | Q70626 from UniProtKB/Swiss-Prot  Length:856

    Alignment length:53
                                   640       650       660       670       680   
            ENV_HV1LW   631 WDREINNYTSLIHSLIEESQNQQEKNEQELLELDKWASLWNWFNITNWLWYIK 683
               SCOP domains ----------------------------------------------------- SCOP domains
               CATH domains 3gwoA00 A:2-54  [code=1.10.287.210, no name defined]  CATH domains
               Pfam domains ----------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------- Transcript
                 3gwo A   2 WDREINNYTSLIHSLIEESQNQQEKNEQELLELDKWASLWNWFNITNWLWYIK  54
                                    11        21        31        41        51   


Chain B from PDB  Type:PROTEIN  Length:41
 aligned with ENV_HV1LW | Q70626 from UniProtKB/Swiss-Prot  Length:856

    Alignment length:41
                                   650       660       670       680 
            ENV_HV1LW   641 LIHSLIEESQNQQEKNEQELLELDKWASLWNWFNITNWLWY 681
               SCOP domains ----------------------------------------- SCOP domains
               CATH domains ----------------------------------------- CATH domains
               Pfam domains ----------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------- PROSITE
                 Transcript ----------------------------------------- Transcript
                 3gwo B  12 LIHSLIEESQNQQEKNEQELLELDKWASLWNWFNITNWLWY  52
                                    21        31        41        51
   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 3GWO)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (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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  3gwo
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 Related Entries

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

UniProtKB/Swiss-Prot
        ENV_HV1LW | Q70626: 1if3 2x7r 2z2t 3aha 3cp1 3cyo 3h00 3h01 4i48 5hfm

(-) Related Entries Specified in the PDB File

3h00 3h01