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(-) Description

Title :  HIV GP41 CORE STRUCTURE
 
Authors :  D. C. Chan, D. Fass, J. M. Berger, P. S. Kim
Date :  20 Apr 97  (Deposition) - 16 Jun 97  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  C,N
Biol. Unit 1:  C,N  (3x)
Keywords :  Hiv, Gp41, Envelope Glycoprotein, Retrovirus, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. C. Chan, D. Fass, J. M. Berger, P. S. Kim
Core Structure Of Gp41 From The Hiv Envelope Glycoprotein.
Cell(Cambridge, Mass. ) V. 89 263 1997
PubMed-ID: 9108481  |  Reference-DOI: 10.1016/S0092-8674(00)80205-6

(-) Compounds

Molecule 1 - HIV-1 GP41 GLYCOPROTEIN
    Cellular Location: VIRAL MEMBRANE
    Chains: N
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Gene: GP41
    Expression System Taxid: 562
    Fragment: PROTEASE-RESISTANT CORE
    Gene: GP41
    Organism Taxid: 11706
    Other Details: N36 AND C34 ARE SYNTHETIC PEPTIDES
    Strain: HXB2
 
Molecule 2 - HIV-1 GP41 GLYCOPROTEIN
    Cellular Location: VIRAL MEMBRANE
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Gene: GP41
    Expression System Taxid: 562
    Fragment: PROTEASE-RESISTANT CORE
    Gene: GP41
    Organism Taxid: 11706
    Other Details: N36 AND C34 ARE SYNTHETIC PEPTIDES
    Strain: HXB2

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1ACE2Mod. Amino AcidACETYL GROUP
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1ACE6Mod. Amino AcidACETYL GROUP

(-) Sites  (0, 0)

(no "Site" information available for 1AIK)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1AIK)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1AIK)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1AIK)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1AIK)

(-) Exons   (0, 0)

(no "Exon" information available for 1AIK)

(-) 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:35
 aligned with ENV_HV1H2 | P04578 from UniProtKB/Swiss-Prot  Length:856

    Alignment length:35
                                   636       646       656     
            ENV_HV1H2   627 TWMEWDREINNYTSLIHSLIEESQNQQEKNEQELL 661
               SCOP domains d1aik.1 N:,C:                       SCOP domains
               CATH domains ----------------------------------- CATH domains
               Pfam domains ----------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------- PROSITE
                 Transcript ----------------------------------- Transcript
                 1aik C 627 xWMEWDREINNYTSLIHSLIEESQNQQEKNEQELL 661
                            |      636       646       656     
                            |                                  
                          627-ACE                              


Chain N from PDB  Type:PROTEIN  Length:37
 aligned with ENV_HV1H2 | P04578 from UniProtKB/Swiss-Prot  Length:856

    Alignment length:37
                                   554       564       574       
            ENV_HV1H2   545 LSGIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARIL 581
               SCOP domains d1aik.1 N:,C:                         SCOP domains
               CATH domains ------------------------------------- CATH domains
               Pfam domains ------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------- PROSITE
                 Transcript ------------------------------------- Transcript
                 1aik N 545 xSGIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARIL 581
                            |      554       564       574       
                          545-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  (1, 1)

Asymmetric Unit
(-)
Class: Coiled coil proteins (689)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1AIK)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1AIK)

(-) Gene Ontology  (32, 32)

Asymmetric Unit(hide GO term definitions)
Chain C,N   (ENV_HV1H2 | P04578)
molecular function
    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: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:0090527    actin filament reorganization    A process that is carried out at the cellular level which results in dynamic structural changes to the arrangement of actin filaments.
    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:0030260    entry into host cell    The invasion by an organism of a cell of its host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    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:1903905    positive regulation of establishment of T cell polarity    Any process that activates or increases the frequency, rate or extent of establishment of T cell polarity.
    GO:1903908    positive regulation of plasma membrane raft polarization    Any process that activates or increases the frequency, rate or extent of plasma membrane raft polarization.
    GO:1903911    positive regulation of receptor clustering    Any process that activates or increases the frequency, rate or extent of receptor clustering.
    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:0019058    viral life cycle    A set of processes which all viruses follow to ensure survival; includes attachment and entry of the virus particle, decoding of genome information, translation of viral mRNA by host ribosomes, genome replication, and assembly and release of viral particles containing the genome.
    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:0019068    virion assembly    A late phase of the viral life cycle during which all the components necessary for the formation of a mature virion collect at a particular site in the cell and the basic structure of the virus particle is formed.
    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:0000139    Golgi membrane    The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    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_HV1H2 | P04578: 1df4 1df5 1dlb 1g9m 1gc1 1gzl 1k33 1k34 1mzi 1opn 1opt 1opw 1rzj 2cmr 2me1 2mg1 2mg2 2mg3 2ny7 2pv6 2x7r 2xra 2zzo 3d0v 3dnl 3dnn 3dno 3dro 3idx 3idy 3j70 3tyg 3vie 4jpj 4jpk 4ydv 4zto 5bn0 5c0r 5c0s 5cil 5cin 5cmu 5cmz 5cn0 5dd0 5ghw 5h0n 5hfl 5hm1 5ivx 5ka5 5ka6 5x08

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