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(-) Description

Title :  B1-8 FV FRAGMENT COMPLEXED WITH A (4-HYDROXY-3-NITROPHENYL) ACETATE COMPOUND
 
Authors :  T. Simon, K. Henrick, M. Hirshberg, G. Winter
Date :  03 Mar 98  (Deposition) - 15 Jul 98  (Release) - 14 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  H,I,J,L,M,N
Biol. Unit 1:  H,L  (1x)
Biol. Unit 2:  I,M  (1x)
Biol. Unit 3:  J,N  (1x)
Keywords :  Immunoglobulin, Hapten, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Simon, K. Henrick, M. Hirshberg, G. Winter
X-Ray Structures Of Fv Fragment And Its (4-Hydroxy-3-Nitrophenyl)Acetate Complex Of Murine B1-8 Antibody
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - B1-8 FV (LIGHT CHAIN)
    Cell LineJ558L
    ChainsL, M, N
    EngineeredYES
    Expression SystemMUS MUSCULUS
    Expression System Cell LineJ558L
    Expression System CommonHOUSE MOUSE
    Expression System Taxid10090
    Expression System VectorPEC-GAMMA3
    FragmentFV FRAGMENT
    OrganTAIL
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    StrainC57BL/6
 
Molecule 2 - B1-8 FV (HEAVY CHAIN)
    Cell LineJ558L
    ChainsH, I, J
    EngineeredYES
    Expression SystemMUS MUSCULUS
    Expression System Cell LineJ558L
    Expression System CommonHOUSE MOUSE
    Expression System Taxid10090
    Expression System VectorPEC-GAMMA3
    FragmentFV FRAGMENT
    OrganTAIL
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    StrainC57BL/6

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit HIJLMN
Biological Unit 1 (1x)H  L  
Biological Unit 2 (1x) I  M 
Biological Unit 3 (1x)  J  N

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1NPC3Ligand/Ion4-HYDROXY-3-NITROPHENYLACETYL-EPSILON-AMINOCAPROIC ACIDANION
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1NPC3Ligand/Ion4-HYDROXY-3-NITROPHENYLACETYL-EPSILON-AMINOCAPROIC ACIDANION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1NPC-1Ligand/Ion4-HYDROXY-3-NITROPHENYLACETYL-EPSILON-AMINOCAPROIC ACIDANION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1NPC-1Ligand/Ion4-HYDROXY-3-NITROPHENYLACETYL-EPSILON-AMINOCAPROIC ACIDANION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1unknownHOH H:73 , TRP H:333 , HIS H:335 , ARG H:350 , LYS H:359 , TYR H:401 , SER H:405 , TYR L:34 , TRP L:93 , TRP L:98NULL
2AC2unknownHOH H:73 , HOH H:141 , TRP H:333 , HIS H:335 , ARG H:350 , LYS H:359 , TYR H:399 , TYR H:401 , NPC H:430 , TRP L:93 , TRP L:98NULL
3AC3unknownTRP I:333 , HIS I:335 , ARG I:350 , LYS I:359 , TYR I:399 , TYR I:401 , TYR I:402 , SER I:405 , HOH I:512 , HOH I:513 , TYR M:34 , TRP M:93 , TRP M:98NULL
4AC4unknownTRP J:333 , HIS J:335 , ARG J:350 , LYS J:359 , TYR J:399 , TYR J:401 , HOH J:437 , HOH J:514 , THR N:31 , SER N:32 , TYR N:34 , TRP N:93NULL

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1H:322 -H:396
2I:322 -I:396
3J:322 -J:396
4L:22 -L:90
5M:22 -M:90
6N:22 -N:90

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1A6V)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1A6V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1A6V)

(-) Exons   (0, 0)

(no "Exon" information available for 1A6V)

(-) 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 H from PDB  Type:PROTEIN  Length:118
 aligned with HVM07_MOUSE | P01751 from UniProtKB/Swiss-Prot  Length:139

    Alignment length:118
                                    29        39        49        59        69        79        89        99       109       119       129        
          HVM07_MOUSE    20 QVQLQQPGAELVKPGASVKLSCKASGYTFTSYWMHWVKQRPGRGLEWIGRIDPNSGGTKYNEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCARYDYYGSSYFDYWGQGTTLTV 137
               SCOP domains d1a6vh_ H: Immunoglobulin heavy chain variable domain, VH                                                              SCOP domains
               CATH domains 1a6vH00 H:301-418 Immunoglobulins                                                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...eee......eeeeeeee...hhh.eeeeeee......eeeeeee....eeee.hhh...eeeeee....eeeeee........eeeeeeee..............eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 1a6v H 301 QVQLQQPGAELVKPGASVKLSCKASGYTFTSYWMHWVKQRPGRGLEWIGRIDPNSGGTKYNEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCARYDYYGSSYFDYWGQGTTVTV 418
                                   310       320       330       340       350       360       370       380       390       400       410        

Chain I from PDB  Type:PROTEIN  Length:119
 aligned with HVM07_MOUSE | P01751 from UniProtKB/Swiss-Prot  Length:139

    Alignment length:119
                                    29        39        49        59        69        79        89        99       109       119       129         
          HVM07_MOUSE    20 QVQLQQPGAELVKPGASVKLSCKASGYTFTSYWMHWVKQRPGRGLEWIGRIDPNSGGTKYNEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCARYDYYGSSYFDYWGQGTTLTVS 138
               SCOP domains d1a6vi_ I: Immunoglobulin heavy chain variable domain, VH                                                               SCOP domains
               CATH domains 1a6vI00 I:301-419 Immunoglobulins                                                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...eeee.....eeeeeeee.......eeeeeee.....eeeeeeee.....eee.hhh...eeeeee....eeeeee........eeeeeeee.......eeee...eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 1a6v I 301 QVQLQQPGAELVKPGASVKLSCKASGYTFTSYWMHWVKQRPGRGLEWIGRIDPNSGGTKYNEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCARYDYYGSSYFDYWGQGTTVTVS 419
                                   310       320       330       340       350       360       370       380       390       400       410         

Chain J from PDB  Type:PROTEIN  Length:120
 aligned with HVM07_MOUSE | P01751 from UniProtKB/Swiss-Prot  Length:139

    Alignment length:120
                                    29        39        49        59        69        79        89        99       109       119       129       139
          HVM07_MOUSE    20 QVQLQQPGAELVKPGASVKLSCKASGYTFTSYWMHWVKQRPGRGLEWIGRIDPNSGGTKYNEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCARYDYYGSSYFDYWGQGTTLTVSS 139
               SCOP domains d1a6vj_ J: Immunoglobulin heavy chain variable domain, VH                                                                SCOP domains
               CATH domains 1a6vJ00 J:301-420 Immunoglobulins                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee..eee..........eeee.......eeeeeee.....eeeeee.....................................hhh.eeeeeeee.......eeee...eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 1a6v J 301 QVQLQQPGAELVKPGASVKLSCKASGYTFTSYWMHWVKQRPGRGLEWIGRIDPNSGGTKYNEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCARYDYYGSSYFDYWGQGTTVTVSS 420
                                   310       320       330       340       350       360       370       380       390       400       410       420

Chain L from PDB  Type:PROTEIN  Length:110
 aligned with LV1B_MOUSE | P01724 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:110
                                    29        39        49        59        69        79        89        99       109       119       129
           LV1B_MOUSE    20 QAVVTQESALTTSPGETVTLTCRSSTGAVTTSNYANWVQQKPDHLFTGLIGGTNNRAPGVPARFSGSLIGNKAALTITGAQTEDEAIYFCALWYSNHWVFGGGTKLTVLG 129
               SCOP domains d1a6vl_ L: Immunoglobulin light chain lambda variable domain, VL-lambda                                        SCOP domains
               CATH domains 1a6vL00 L:1-110 Immunoglobulins                                                                                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee..eee.....eeeeeeee...........eeeeee...eeeeee.............eeeeee..eeeeeee...hhh.eeeeeeeee..eeee...eeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 1a6v L   1 QAVVTQESALTTSPGETVTLTCRSSTGAVTTSNYANWVQEKPDHLFTGLIGGTNNRAPGVPARFSGSLIGNKAALTITGAQTEDEAIYFCALWYSNHWVFGGGTKLTVLE 110
                                    10        20        30        40        50        60        70        80        90       100       110

Chain M from PDB  Type:PROTEIN  Length:109
 aligned with LV1B_MOUSE | P01724 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:109
                                    29        39        49        59        69        79        89        99       109       119         
           LV1B_MOUSE    20 QAVVTQESALTTSPGETVTLTCRSSTGAVTTSNYANWVQQKPDHLFTGLIGGTNNRAPGVPARFSGSLIGNKAALTITGAQTEDEAIYFCALWYSNHWVFGGGTKLTVL 128
               SCOP domains d1a6vm_ M: Immunoglobulin light chain lambda variable domain, VL-lambda                                       SCOP domains
               CATH domains 1a6vM00 M:1-109 Immunoglobulins                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee....eeeee........hhh..eeeeee...eeeeee.............eeeeee..eeeeee........eeeeeeee....eee...eeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 1a6v M   1 QAVVTQESALTTSPGETVTLTCRSSTGAVTTSNYANWVQEKPDHLFTGLIGGTNNRAPGVPARFSGSLIGNKAALTITGAQTEDEAIYFCALWYSNHWVFGGGTKLTVL 109
                                    10        20        30        40        50        60        70        80        90       100         

Chain N from PDB  Type:PROTEIN  Length:109
 aligned with LV1B_MOUSE | P01724 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:109
                                    29        39        49        59        69        79        89        99       109       119         
           LV1B_MOUSE    20 QAVVTQESALTTSPGETVTLTCRSSTGAVTTSNYANWVQQKPDHLFTGLIGGTNNRAPGVPARFSGSLIGNKAALTITGAQTEDEAIYFCALWYSNHWVFGGGTKLTVL 128
               SCOP domains d1a6vn_ N: Immunoglobulin light chain lambda variable domain, VL-lambda                                       SCOP domains
               CATH domains 1a6vN00 N:1-109 Immunoglobulins                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee....eeeeee............eeeeee...eeeeee.............eeeeee..eeeeee........eeeeeeeee..eeee...eeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 1a6v N   1 QAVVTQESALTTSPGETVTLTCRSSTGAVTTSNYANWVQEKPDHLFTGLIGGTNNRAPGVPARFSGSLIGNKAALTITGAQTEDEAIYFCALWYSNHWVFGGGTKLTVL 109
                                    10        20        30        40        50        60        70        80        90       100         

   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, 6)

Asymmetric Unit

(-) CATH Domains  (1, 6)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)
1a1a6vH00H:301-418
1b1a6vM00M:1-109
1c1a6vN00N:1-109
1d1a6vL00L:1-110
1e1a6vI00I:301-419
1f1a6vJ00J:301-420

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1A6V)

(-) Gene Ontology  (12, 13)

Asymmetric Unit(hide GO term definitions)
Chain H,I,J   (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.

Chain L,M,N   (LV1B_MOUSE | P01724)
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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        HVM07_MOUSE | P017511a6u 1a6w 1ngp 1ngq 1nqb 1oaq 1oar 1oau 1oax 1oay 1oaz 1ocw 2bjm
        LV1B_MOUSE | P017241a6u 1a6w 1dl7 1oaq 1oar 1oau 1oax 1oay 1oaz 1ocw 1q0y 2bjm

(-) Related Entries Specified in the PDB File

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