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(-) Description

Title :  CRYSTAL STRUCTURE OF THE UNLIGANDED FV-FRAGMENT OF THE ANTI-CYTOCHROME C OXIDASE ANTIBODY 7E2
 
Authors :  L. -O. Essen, A. Harrenga, C. Ostermeier, H. Michel
Date :  16 Sep 02  (Deposition) - 01 Apr 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.28
Chains :  Asym./Biol. Unit :  H,L
Keywords :  Antibody, Membrane Protein, Cytochrome C Oxidase, High- Resolution Structure, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. O. Essen, A. Harrenga, C. Ostermeier, H. Michel
1. 3 A X-Ray Structure Of An Antibody Fv Fragment Used For Induced Membrane-Protein Crystallization.
Acta Crystallogr. , Sect. D V. 59 677 2003
PubMed-ID: 12657787  |  Reference-DOI: 10.1107/S0907444903002233
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ANTIBODY 7E2 FV FRAGMENT, LIGHT CHAIN
    Chains: L
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PASK68
    Expression System Strain: JM83
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - ANTIBODY 7E2 FV FRAGMENT, HEAVY CHAIN
    Chains: H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PASK68
    Expression System Strain: JM83
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Common: HOUSE 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  (0, 0)

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

(-) Sites  (0, 0)

(no "Site" information available for 1MQK)

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:96
2L:23 -L:88

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Thr L:7 -Pro L:8
2Pro L:95 -Pro L:96

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1MQK)

(-) 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:123
 aligned with HVM54_MOUSE | P18525 from UniProtKB/Swiss-Prot  Length:117

    Alignment length:123
                                                                                                                           117                         
                                    29        39        49        59        69        79        89        99       109       | -         -         -   
          HVM54_MOUSE    20 EVKLVESGGGLVQPGGSLKLSCAASGFTFSSYTMSWVRQTPEKRLEWVAYISNGGGSTYYPDTVKGRFTISRDNAKNNLYLQMSSLKSEDTAMYYCAR-------------------------   -
               SCOP domains d1mqkh_ H: Immunoglobulin heavy chain variable domain, VH                                                                   SCOP domains
               CATH domains 1mqkH00 H:1-123 Immunoglobulins                                                                                             CATH domains
               Pfam domains V-set-1mqkH01 H:1-96                                                                            --------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......ee........eeeeeehhh.eeeeee...hhhhheeeeeeeee...eeeee...eeeee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mqk H   1 EVKLQESGGDLVQPGGSLKLSCAASGFTFSSYTMSWVRQTPEKRLEWVASINNGGGRTYYPDTVKGRFTISRDNAKNTLYLQMSSLKSEDTAMYYCVRHEYYYAMDYWGQGTTVTVSSAWRHP 123
                                    10        20        30        40        50        60        70        80        90       100       110       120   


Chain L from PDB  Type:PROTEIN  Length:109
 aligned with KV5A4_MOUSE | P01636 from UniProtKB/Swiss-Prot  Length:108

    Alignment length:109
                                                                                                                           96            
                                                                                                                         95 |            
                                    10        20        30        40        50        60        70        80        90    | | 99         
          KV5A4_MOUSE     1 DIQMTQSPDYLSASVGETVTITCRASENIYSYLAWYQQKQGKSPQLLVYDAKTLVEGVPSRFSGSGSGTQFSLKINSLQPEDFGSYYCQHHYGIP-FTFGSGTKLEIKR 108
               SCOP domains d1mqkl_ L: Immunoglobulin light chain kappa variable domain, VL-kappa                                         SCOP domains
               CATH domains 1mqkL00 L:1-109 Immunoglobulins                                                                               CATH domains
               Pfam domains ----------V-set-1mqkL01 L:11-107                                                                           -- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee............eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 1mqk L   1 DIELTQTPVSLSASVGETVTITCRASENIYSYLAWYQQKQGKSPQFLVYNAKTLGEGVPSRFSGSGSGTQFSLKINSLLPEDFGSYYCQHHYGTPPLTFGGGTKLEIKR 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  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: Ig (577)

(-) Gene Ontology  (1, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain H   (HVM54_MOUSE | P18525)
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   (KV5A4_MOUSE | P01636)
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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  Cis Peptide Bonds
    Pro L:95 - Pro L:96   [ RasMol ]  
    Thr L:7 - Pro L:8   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        HVM54_MOUSE | P18525: 1ar1 3ehb 3hb3
        KV5A4_MOUSE | P01636: 1ar1 3ehb 3hb3

(-) Related Entries Specified in the PDB File

1ar1 7E2 ANTIBODY COCRYSTALLIZED WITH THE PARACOCCUS DENITRIFICANS TWO-SUBUNIT CYTOCHROME C OXIDASE
1qle 7E2 ANTIBODY COCRYSTALLIZED WITH THE PARACOCCUS DENITRIFICANS FOUR-SUBUNIT CYTOCHROME C OXIDASE