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(-) Description

Title :  NMR STRUCTURE OF THE 0.5B ANTI-HIV ANTIBODY COMPLEX WITH THE GP120 V3 PEPTIDE
 
Authors :  V. Tugarinov, A. Zvi, R. Levy, Y. Hayek, S. Matsushita, J. Anglister
Date :  26 Oct 99  (Deposition) - 03 Jun 00  (Release) - 07 Aug 13  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  H,L,P
NMR Structure *:  H,L,P  (1x)
Keywords :  Antibody, V3 Peptide, Binding Site, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Tugarinov, A. Zvi, R. Levy, Y. Hayek, S. Matsushita, J. Anglister
Nmr Structure Of An Anti-Gp120 Antibody Complex With A V3 Peptide Reveals A Surface Important For Co-Receptor Binding
Structure V. 8 385 2000
PubMed-ID: 10801487  |  Reference-DOI: 10.1016/S0969-2126(00)00119-2

(-) Compounds

Molecule 1 - 0.5B ANTIBODY (LIGHT CHAIN)
    Chains: L
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: FV
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - 0.5B ANTIBODY (HEAVY CHAIN)
    Chains: H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: FV
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 3 - GP120
    Chains: P
    Engineered: YES
    Fragment: V3 PEPTIDE
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
NMR Structure : HLP
NMR Structure * (1x): HLP

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1QNZ)

(-) Sites  (0, 0)

(no "Site" information available for 1QNZ)

(-) SS Bonds  (2, 2)

NMR Structure
No.Residues
1H:134 -H:208
2L:23 -L:92

(-) Cis Peptide Bonds  (2, 2)

NMR Structure
No.Residues
1Asp L:98 -Pro L:99
2Gly P:240 -Pro P:241

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1QNZ)

(-) Sequences/Alignments

NMR Structure
   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 H from PDB  Type:PROTEIN  Length:119
 aligned with HVM06_MOUSE | P01750 from UniProtKB/Swiss-Prot  Length:117

    Alignment length:119
                                                                                                                           117                     
                                    29        39        49        59        69        79        89        99       109       | -         -         
          HVM06_MOUSE    20 HVQLQQPGAELVKPGASVKVSCKASGYTFTSYWMHWVKQRPGQGLEWIGRIHPSDSDTNYNQKFKGKATLTVDKSSSTAYMQLSSLTSEDSAVYYCAI---------------------   -
               SCOP domains d1qnzh_ H: Immunoglobulin heavy chain variable domain, VH                                                               SCOP domains
               CATH domains 1qnzH00 H:113-231 Immunoglobulins                                                                                       CATH domains
               Pfam domains -V-set-1qnzH01 H:114-210                                                                          --------------------- Pfam domains
         Sec.struct. author ..eeeee..........eeeeeeee........eeeeeee.....eeeeeee....eeee.......eeee......eeeeee........eeeeeee..............eee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 1qnz H 113 QVQLQQSGAELVKPGASVKMSCKASGYTFTTYPIEWMKQNHGKSLEWIGNFHPYSDDTNYNEKFKGKAKLTVEKSSSTVYLEFSRLTSDDSAVYYCAIHYGSAYAMDYWGQGTSVTVSS 231
                                   122       132       142       152       162       172       182       192       202       212       222         


Chain L from PDB  Type:PROTEIN  Length:112
 aligned with KV3AD_MOUSE | P01665 from UniProtKB/Swiss-Prot  Length:111

    Alignment length:112
                                                                                                                                        111 
                                    10        20        30        40        50        60        70        80        90       100       110| 
          KV3AD_MOUSE     1 DIVLTQSPASLAVSLGQRATISCKASQSVDYDGDSYMNWYQQKPGQPPKLLIYAASNLESGIPARFSGSGSGTDFTLNIHPVEEEDAATYYCQQSNEDPFTFGSGTKLEIK-   -
               SCOP domains d1qnzl_ L: Immunoglobulin light chain kappa variable domain, VL-kappa                                            SCOP domains
               CATH domains 1qnzL00 L:1-112 Immunoglobulins                                                                                  CATH domains
               Pfam domains V-set-1qnzL01 L:1-110                                                                                         -- Pfam domains
         Sec.struct. author ...eee...eeeee....eeeeeee...........eeeeeee.....eeee.............eee.....eeeeee........eeeeeee............eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 1qnz L   1 DIVLTQSPASLAVSLGQRATISCKASQSVDYDGDSYMNWYQQKPGQPPKLLIYAASNLESGIPARFSGSGSRTDFTLNIHPVEEEDAATYYCQQSNEDPFTFGSGTKLEIKR 112
                                    10        20        30        40        50        60        70        80        90       100       110  


Chain P from PDB  Type:PROTEIN  Length:18
 aligned with Q79416_9HIV1 | Q79416 from UniProtKB/TrEMBL  Length:36

    Alignment length:18
                                    18        
         Q79416_9HIV1     9 RKSIRIQRGPGRAFVTIG  26
               SCOP domains ------------------ SCOP domains
               CATH domains ------------------ CATH domains
               Pfam domains GP120-1qnzP01      Pfam domains
         Sec.struct. author ..eee........eee.. Sec.struct. author
                 SAPs(SNPs) ------------------ SAPs(SNPs)
                    PROSITE ------------------ PROSITE
                 Transcript ------------------ Transcript
                 1qnz P 232 RKSIRIQRGPGRAFVTIG 249
                                   241
   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  (2, 2)

NMR Structure
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

NMR Structure
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (2, 3)

NMR Structure
(-)
Clan: Ig (577)
(-)
Family: V-set (144)
(-)
Clan: no clan defined [family: GP120] (26)

(-) Gene Ontology  (9, 10)

NMR Structure(hide GO term definitions)
Chain H   (HVM06_MOUSE | P01750)
molecular function
    GO:0003823    antigen binding    Interacting selectively and non-covalently with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen.

Chain L   (KV3AD_MOUSE | P01665)
molecular function
    GO:0003823    antigen binding    Interacting selectively and non-covalently with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen.

Chain P   (Q79416_9HIV1 | Q79416)
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: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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  Cis Peptide Bonds
    Asp L:98 - Pro L:99   [ RasMol ]  
    Gly P:240 - Pro P:241   [ RasMol ]  
 

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  1qnz
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  KV3AD_MOUSE | P01665
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  Q79416_9HIV1 | Q79416
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 Related Entries

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

UniProtKB/Swiss-Prot
        HVM06_MOUSE | P01750: 1qfw
        KV3AD_MOUSE | P01665: 1f11 2zch 2zck 2zcl

(-) Related Entries Specified in the PDB File

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