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(-) Description

Title :  THE STRUCTURAL BASIS OF REPERTOIRE SHIFT IN AN IMMUNE RESPONSE TO PHOSPHOCHOLINE
 
Authors :  M. Schumacher, M. Brown
Date :  08 Dec 99  (Deposition) - 13 Dec 00  (Release) - 02 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym./Biol. Unit :  H,L
Keywords :  Single Chain Fv, Repertoire Shift, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Brown, M. A. Schumacher, G. D. Wiens, R. G. Brennan, M. B. Rittenberg
The Structural Basis Of Repertoire Shift In An Immune Response To Phosphocholine.
J. Exp. Med. V. 191 2101 2000
PubMed-ID: 10859335  |  Reference-DOI: 10.1084/JEM.191.12.2101

(-) Compounds

Molecule 1 - PROTEIN (ANTIBODY M3C65 (LIGHT CHAIN))
    Chains: L
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET3D
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: FV (SINGLE CHAIN)
    Gene: HYBRIDOMA M3C65
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: COMBINED LIGHT AND HEAVY CHAIN VIA (G4S)3 LINKER
 
Molecule 2 - PROTEIN (ANTIBODY M3C65 (HEAVY CHAIN))
    Chains: H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET3D
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: FV (SINGLE CHAIN)
    Gene: HYBRIDOMA M3C65
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : HL

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1NCH1Ligand/IonP-NITROPHENYL-PHOSPHOCHOLINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP H:52 , TYR H:83 , ASP H:98 , TYR H:99 , TYR L:34 , ASN L:36 , GLY L:51 , GLY L:52 , HIS L:55 , TRP L:93 , HOH L:1023 , HOH L:1026BINDING SITE FOR RESIDUE NCH L 999

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:95
2L:22 -L:90

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly H:100 -Pro H:101

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1DL7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1DL7)

(-) Exons   (0, 0)

(no "Exon" information available for 1DL7)

(-) 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 H from PDB  Type:PROTEIN  Length:112
 aligned with HVM44_MOUSE | P01820 from UniProtKB/Swiss-Prot  Length:115

    Alignment length:112
                                                                                                                         115                
                                    29        39        49        59        69        79        89        99       109     |   -         -  
          HVM44_MOUSE    20 QVQLKESGPGLVAPSQSLSITCTVSGFSLTGYGVNWVRQPPGKGLEWLGMIWGDGSTDYNSALKSRLSISKDNSKSQVFLKMNSLQTDDTARYYCA----------------   -
               SCOP domains d1dl7h_ H: Immunoglobulin heavy chain variable domain, VH                                                        SCOP domains
               CATH domains 1dl7H00 H:1-112 Immunoglobulins                                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................eeeeee..........eeeeee......eeeeee.....eee.hhhh.....eee....eeeeee...hhhhheeeeeee..........ee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 1dl7 H   1 QVQLKESGPGLVAPSQSLSITCTVSGFSLTGYGVNWVRQPPGKGLEWLGMIWGDGSTDYNSALKSRLNISKDKSKSQVFLRMYSLQTDDTARYYCARDYGPYWGQGTLVTVS 112
                                    10        20        30        40        50        60        70        80        90       100       110  


Chain L 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 d1dl7l_ L: Immunoglobulin light chain lambda variable domain, VL-lambda                                       SCOP domains
               CATH domains 1dl7L00 L:1-109 Immunoglobulins                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee...eeee....eeee..ee...........eeeeee...eeeeeee...ee.......eeeeee..eeeeeee..hhhhheeeeeee......ee...eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 1dl7 L   1 QAVVTQESALTTSPGETVTLTCRSSTGAVTTSNYANWVQEKPDHLFTGLIGGTKHRTPGAPARFSGSLIGDKAALTITGAQTEDEAIYFCALWYSNHWVFGGGTKLTVL 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, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1DL7)

(-) Gene Ontology  (1, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain H   (HVM44_MOUSE | P01820)
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   (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
        HVM44_MOUSE | P01820: 1a2y 1a7n 1a7o 1a7p 1a7q 1a7r 1dvf 1g7h 1g7i 1g7j 1g7l 1g7m 1kir 1p4b 1p4i 1vfa 1vfb 43c9 43ca
        LV1B_MOUSE | P01724: 1a6u 1a6v 1a6w 1oaq 1oar 1oau 1oax 1oay 1oaz 1ocw 1q0y 2bjm

(-) Related Entries Specified in the PDB File

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