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(-) Description

Title :  VARIABLE LIGHT CHAIN DIMER OF ANTI-FERRITIN ANTIBODY
 
Authors :  Y. Nymalm, Z. Kravchuk, T. Salminen, A. A. Chumanevich, A. P. Dubnovitsky, J. Kankare, O. Pentikainen, J. Lehtonen, P. Arosio S. Martsev, M. S. Johnson
Date :  22 Jun 00  (Deposition) - 23 Oct 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  L
Biol. Unit 1:  L  (2x)
Keywords :  Immunoglobulin Fold, Variable Light Chain, Dimer, Anti- Ferritin Antibody, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Nymalm, Z. Kravchuk, T. Salminen, A. A. Chumanevich, A. P. Dubnovitsky, J. Kankare, O. Pentikainen, J. Lehtonen, P. Arosio, S. Martsev, M. S. Johnson
Antiferritin Vl Homodimer Binds Human Spleen Ferritin With High Specificity
J. Struct. Biol. V. 138 171 2002
PubMed-ID: 12217656  |  Reference-DOI: 10.1016/S1047-8477(02)00015-1
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ANTI-FERRITIN IMMUNOGLOBULIN LIGHT CHAIN
    ChainsL
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPETVL
    Expression System Taxid562
    FragmentVARIABLE LIGHT CHAIN
    OrganSPLEEN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit L
Biological Unit 1 (2x)L

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1F6L)

(-) Sites  (0, 0)

(no "Site" information available for 1F6L)

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1L:23 -L:88

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ser L:7 -Pro L:8
2Thr L:94 -Pro L:95

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1F6L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1F6L)

(-) Exons   (0, 0)

(no "Exon" information available for 1F6L)

(-) 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 L from PDB  Type:PROTEIN  Length:106
 aligned with KV139_HUMAN | P01597 from UniProtKB/Swiss-Prot  Length:117

    Alignment length:106
                                                                                                                        117           
                                    32        42        52        62        72        82        92       102       112    |    -      
          KV139_HUMAN    23 DIQMTQSPSSLSASVGDRVTITCRASQSISSYLNWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSYSTP-----------   -
               SCOP domains d1f6ll_ L: Immunoglobulin light chain kappa variable domain, VL-kappa                                      SCOP domains
               CATH domains 1f6lL00 L:1-106 Immunoglobulins                                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eee......eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee...........eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 1f6l L   1 DIQMTQSPASLSASVGETVTITCRASENIYSYLAWYQQKQGKSPQLLVYNAKTLAEGVPSRFSGSGSGTQFSLKINSLQPEDFGSYYCQHHYGTPFTFGSGTKLEI 106
                                    10        20        30        40        50        60        70        80        90       100      

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  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  (1, 1)

Asymmetric Unit

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1F6L)

(-) Gene Ontology  (14, 27)

Asymmetric Unit(hide GO term definitions)
Chain L   (KV139_HUMAN | P01597)
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:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
    GO:0038095    Fc-epsilon receptor signaling pathway    A series of molecular signals initiated by the binding of the Fc portion of immunoglobulin E (IgE) to an Fc-epsilon receptor on the surface of a signal-receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription. The Fc portion of an immunoglobulin is its C-terminal constant region.
    GO:0038096    Fc-gamma receptor signaling pathway involved in phagocytosis    An Fc-gamma receptor signaling pathway that contributes to the endocytic engulfment of external particulate material by phagocytes.
    GO:0006956    complement activation    Any process involved in the activation of any of the steps of the complement cascade, which allows for the direct killing of microbes, the disposal of immune complexes, and the regulation of other immune processes; the initial steps of complement activation involve one of three pathways, the classical pathway, the alternative pathway, and the lectin pathway, all of which lead to the terminal complement pathway.
    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:0006955    immune response    Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0006898    receptor-mediated endocytosis    An endocytosis process in which cell surface receptors ensure specificity of transport. A specific receptor on the cell surface binds tightly to the extracellular macromolecule (the ligand) that it recognizes; the plasma-membrane region containing the receptor-ligand complex then undergoes endocytosis, forming a transport vesicle containing the receptor-ligand complex and excluding most other plasma-membrane proteins. Receptor-mediated endocytosis generally occurs via clathrin-coated pits and vesicles.
    GO:0050776    regulation of immune response    Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
cellular component
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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    Ser L:7 - Pro L:8   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        KV139_HUMAN | P015971dgx 3upa

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