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(-) Description

Title :  TRIVALENT ANTIBODY FRAGMENT
 
Authors :  R. L. Williams, X. Y. Pei
Date :  04 Apr 97  (Deposition) - 20 Aug 97  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,C
Biol. Unit 1:  A,C  (3x)
Biol. Unit 2:  A  (3x)
Biol. Unit 3:  C  (3x)
Keywords :  Antibody Fragment, Multivalent Antibody, Diabody, Domain Swapping, Immunoglobulin (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  X. Y. Pei, P. Holliger, A. G. Murzin, R. L. Williams
The 2. 0-A Resolution Crystal Structure Of A Trimeric Antibody Fragment With Noncognate Vh-Vl Domain Pairs Shows Rearrangement Of Vh Cdr3.
Proc. Natl. Acad. Sci. Usa V. 94 9637 1997
PubMed-ID: 9275175  |  Reference-DOI: 10.1073/PNAS.94.18.9637

(-) Compounds

Molecule 1 - SINGLE-CHAIN ANTIBODY FRAGMENT
    Cell LineNQ11 MURINE-MURINE HYBRIDOMA, B1-8 MURINE-MURINE HYBRIDOMA
    ChainsA, C
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Cellular LocationSECRETED
    Expression System GeneB1-8 VH DOMAIN FUSED TO NQ11 VL DOMAIN
    Expression System PlasmidB18NQ11
    Expression System StrainTG1TR
    Expression System Taxid562
    Expression System VectorPUC119-MYC-HIS6
    Expression System Vector TypePLASMID
    FragmentVH DOMAIN RESIDUES 2 - 120, VL DOMAIN RESIDUES 121 - 233
    GeneB1-8 VH DOMAIN FUSED TO NQ11 V
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymVARIABLE HEAVY (VH) DOMAIN, VARIABLE LIGHT (VL) DOMAIN

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AC
Biological Unit 1 (3x)AC
Biological Unit 2 (3x)A 
Biological Unit 3 (3x) C

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1NQB)

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:22 -A:96
2A:143 -A:213
3C:22 -C:96
4C:143 -C:213

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Thr A:127 -Pro A:128
2Val A:219 -Pro A:220
3Thr C:127 -Pro C:128
4Val C:219 -Pro C:220

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1NQB)

(-) 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 A from PDB  Type:PROTEIN  Length:232
 aligned with HVM07_MOUSE | P01751 from UniProtKB/Swiss-Prot  Length:139

    Alignment length:232
                                                                                                                                                139                                                                                                                 
                                    30        40        50        60        70        80        90       100       110       120       130        |-         -         -         -         -         -         -         -         -         -         -         -  
          HVM07_MOUSE    21 VQLQQPGAELVKPGASVKLSCKASGYTFTSYWMHWVKQRPGRGLEWIGRIDPNSGGTKYNEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCARYDYYGSSYFDYWGQGTTLTVSS-----------------------------------------------------------------------------------------------------------------   -
               SCOP domains d1nqba1 A:2-120 Immunoglobulin heavy chain variable domain, VH                                                         d1nqba2 A:121-233 Immunoglobulin light chain kappa variable domain, VL-kappa                                      SCOP domains
               CATH domains -1nqbA01 A:3-120 Immunoglobulins                                                                                       1nqbA02 A:121-219 Immunoglobulins                                                                  -------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...eee.....eeeeeeee...hhh.eeeeeeee...eeeeeeeee.....eee.hhh...eeeeee....eeeeee....hhh.eeeeeee...............eeeee.....eeee..eeee.....eeeeeee............eeeeee.....eeeee.............eeeeee..eeeeee....hhh.eeeeeee...........eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nqb A   2 VQLQQSGAELVKPGASVKLSCKASGYTFTSYWMHWVKQRPGRGLEWIGRIDPNSGGTKYNEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCARYDYYGSSYFDYWGQGTTVTVSSDIELTQTPLSLPVSLGDQASISCRSSQSIVHSNGNTYLEWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPYTFGGGTKLEIKR 233
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231  

Chain C from PDB  Type:PROTEIN  Length:232
 aligned with HVM07_MOUSE | P01751 from UniProtKB/Swiss-Prot  Length:139

    Alignment length:232
                                                                                                                                                139                                                                                                                 
                                    30        40        50        60        70        80        90       100       110       120       130        |-         -         -         -         -         -         -         -         -         -         -         -  
          HVM07_MOUSE    21 VQLQQPGAELVKPGASVKLSCKASGYTFTSYWMHWVKQRPGRGLEWIGRIDPNSGGTKYNEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCARYDYYGSSYFDYWGQGTTLTVSS-----------------------------------------------------------------------------------------------------------------   -
               SCOP domains d1nqbc1 C:2-120 Immunoglobulin heavy chain variable domain, VH                                                         d1nqbc2 C:121-233 Immunoglobulin light chain kappa variable domain, VL-kappa                                      SCOP domains
               CATH domains -1nqbC01 C:3-120 Immunoglobulins                                                                                       1nqbC02 C:121-219 Immunoglobulins                                                                  -------------- CATH domains
           Pfam domains (1) V-set-1nqbC01 C:2-118                                                                                                ------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) V-set-1nqbC02 C:2-118                                                                                                ------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .eeee...eee.....eeeeeeee...hhh.eeeeeeee...eeeeeeeee.....eee.hhh...eeeeee....eeeeee....hhh.eeeeeee...............eeeee.....eeee..eeee.....eeeeeee............eeeeee.....eeeee.............eeeeee..eeeeee....hhh.eeeeeee...........eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nqb C   2 VQLQQSGAELVKPGASVKLSCKASGYTFTSYWMHWVKQRPGRGLEWIGRIDPNSGGTKYNEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCARYDYYGSSYFDYWGQGTTVTVSSDIELTQTPLSLPVSLGDQASISCRSSQSIVHSNGNTYLEWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPYTFGGGTKLEIKR 233
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231  

   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, 4)

Asymmetric Unit

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Ig (577)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,C   (HVM07_MOUSE | P01751)
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.
    GO:0034987    immunoglobulin receptor binding    Interacting selectively and non-covalently with one or more specific sites on an immunoglobulin receptor molecule.
biological process
    GO:0050853    B cell receptor signaling pathway    A series of molecular signals initiated by the cross-linking of an antigen receptor on a B cell.
    GO:0006958    complement activation, classical pathway    Any process involved in the activation of any of the steps of the classical pathway of the complement cascade which allows for the direct killing of microbes, the disposal of immune complexes, and the regulation of other immune processes.
    GO:0042742    defense response to bacterium    Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0006911    phagocytosis, engulfment    The internalization of bacteria, immune complexes and other particulate matter or of an apoptotic cell by phagocytosis, including the membrane and cytoskeletal processes required, which involves one of three mechanisms: zippering of pseudopods around a target via repeated receptor-ligand interactions, sinking of the target directly into plasma membrane of the phagocytosing cell, or induced uptake via an enhanced membrane ruffling of the phagocytosing cell similar to macropinocytosis.
    GO:0006910    phagocytosis, recognition    The initial step in phagocytosis involving adhesion to bacteria, immune complexes and other particulate matter, or an apoptotic cell and based on recognition of factors such as bacterial cell wall components, opsonins like complement and antibody or protein receptors and lipids like phosphatidyl serine, and leading to intracellular signaling in the phagocytosing cell.
    GO:0050871    positive regulation of B cell activation    Any process that activates or increases the frequency, rate or extent of B cell activation.
cellular component
    GO:0072562    blood microparticle    A phospholipid microvesicle that is derived from any of several cell types, such as platelets, blood cells, endothelial cells, or others, and contains membrane receptors as well as other proteins characteristic of the parental cell. Microparticles are heterogeneous in size, and are characterized as microvesicles free of nucleic acids.
    GO:0009897    external side of plasma membrane    The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
    GO:0042571    immunoglobulin complex, circulating    An immunoglobulin complex that is secreted into extracellular space and found in mucosal areas or other tissues or circulating in the blood or lymph. In its canonical form, a circulating immunoglobulin complex is composed of two identical heavy chains and two identical light chains, held together by disulfide bonds. Some forms of are polymers of the basic structure and contain additional components such as J-chain and the secretory component.

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    Thr A:127 - Pro A:128   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        HVM07_MOUSE | P017511a6u 1a6v 1a6w 1ngp 1ngq 1oaq 1oar 1oau 1oax 1oay 1oaz 1ocw 2bjm

(-) Related Entries Specified in the PDB File

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