Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Theoretical Model
collapse expand < >
Image Theoretical Model
Theoretical Model  (Jmol Viewer)

(-) Description

Title :  THEORETICAL MODEL OF THE UNMUTATED, MAJOR CANONICAL ANTIBODY SPECIFIC FOR HAEMOPHILUS INFLUENZAE TYPE B CAPSULAR POLYSACCHARIDE.
 
Authors :  L. Hougs, L. Juul, A. Svejgaard, T. Barington
Date :  26 Feb 99  (Deposition) - 11 Mar 99  (Release) - 11 Mar 03  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  H,L
Keywords :  Immunoglobulin Fv, Anti Haemophilus Influenzae Type B Capcular Polysaccharide, Igvh3-23, Igk A2, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Hougs, L. Juul, A. Svejgaard, T. Barington
Structural Requirements Of The Major Protective Antibody To Haemophilus Influenzae Type B.
Infect. Immun. V. 67 2503 1999
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (IG)
    CellB-CELL
    ChainsL
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Cellular LocationPERIPLASMIC SPACE
    Expression System CommonBACTERIA
    Expression System GeneIMMUNOGLOBULIN
    Expression System StrainTOP-10-TET
    Expression System Vector TypePHAGMIDE EXPRESSION
    FragmentANTIGEN BINDING DOMAIN
    GeneVK A2A, JK1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Other DetailsFRANEWORK REGION (FR) 1: A 1 - A 23 COMPLEMENTARITY DETERMINING REGION (CDR) 1 A 24 - A 34 FR2 A 35 - A 49 CDR2 A 50 - A 65 FR3 A 66 - A 88 CDR3 A 89 - A 97 FR4 A 98 - A 106
    Other Details - SourceHEALTHY ADULT HUMAN MALE. PREDICTED GERM- LINE OF A KNOWN REARRANGED ANTIBODY
    TissueBLOOD
 
Molecule 2 - PROTEIN (IG)
    CellB-CELL
    ChainsH
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Cellular LocationPERIPLASMATIC SPACE
    Expression System CommonBACTERIA
    Expression System GeneIMMUNOGLOBULIN
    Expression System StrainTOP-10-TET
    Expression System Vector TypePHAGEMID EXPRESSION
    FragmentANTIGEN BINDING DOMAIN
    GeneVH3-23, JH6B1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Other DetailsFRANEWORK REGION (FR) 1: A 1 - A 30 COMPLEMENTARITY DETERMINING REGION (CDR) 1 A 31 - A 35 FR2 A 36 - A 49 CDR2 A 50 - A 65 FR3 A 66 - A 94 CDR3 A 95 - A 102 FR4 A 102 - A 113
    Other Details - SourceHEALTHY ADULT HUMAN MALE. PREDICTED GERM- LINE OF A KNOWN REARRANGED ANTIBODY
    TissueBLOOD

 Structural Features

(-) Chains, Units

  
Theoretical Model 

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1HOU)

(-) SS Bonds  (2, 2)

Theoretical Model
No.Residues
1H:22 -H:92
2L:23 -L:88

(-) Cis Peptide Bonds  (3, 3)

Theoretical Model
No.Residues
1Thr L:7 -Pro L:8
2Pro L:95 -Arg L:95F
3Tyr H:96 -Gly H:97

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Theoretical Model (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_073326V24LHV323_HUMANPolymorphism  ---HL5L
2UniProtVAR_073327A80GHV323_HUMANPolymorphism  ---HA60G

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (1, 1)

Theoretical Model (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003906091ENSE00002048341chr14:106725733-106725609125HV323_HUMAN1-16160--
1.2ENST000003906092ENSE00001851371chr14:106725505-106725201305HV323_HUMAN16-1161011H:1-9397

(-) Sequences/Alignments

Theoretical Model
   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:115
 aligned with HV323_HUMAN | P01764 from UniProtKB/Swiss-Prot  Length:117

    Alignment length:115
                                                                                                                           117                 
                                    29        39        49        59        69        79        89        99       109       | -         -     
          HV323_HUMAN    20 EVQLVESGGGLVQPGGSLRLSCAASGFTFSSYAMSWVRQAPGKGLEWVSAISGSGGSTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAK-----------------   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..........eeeeee.....hhh.eeeeeee.....eeeeeeee.....eee.......eeeeee....eeeeee....hhh.eeeeeee..........eee.... Sec.struct. author
                 SAPs(SNPs) ----L-------------------------------------------------------G------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.2  PDB: H:1-93 UniProt: 16-116 [INCOMPLETE]                                               ------------------ Transcript 1
                 1hou H   1 EVQLLESGGGLVQPGGSLRLSCAASGFTFSSYAMSWVRQAPGKGLEWVSAISGSGGSTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKGYGMDVWGQGTTVTVSS 113
                                    10        20        30        40        50  |     59        69        79   |||  86        96||     108     
                                                                              52C                            82A||             97|             
                                                                                                              82B|             100             
                                                                                                               82C                             

Chain L from PDB  Type:PROTEIN  Length:112
                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..eee......eeeeee............eeeeeee.......................eeeeee..eeeeee....hhh..eeeeeee............eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 1hou L   1 DIVMTQTPLSLSVTPGQPASISCKSSQSLLHSDGKTYLYWYLQKPGQPPQLLIYEVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCMQSIQLPRWTFGQGTKVEI 106
                                    10        20       27C||      35        45        55        65        75        85        95|      104  
                                                     27A||||                                                                  95F           
                                                      27B|||                                                                                
                                                       27C||                                                                                
                                                        27D|                                                                                
                                                         27E                                                                                

   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  (0, 0)

(no "SCOP Domain" information available for 1HOU)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1HOU)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (23, 23)

Theoretical Model(hide GO term definitions)
Chain H   (HV323_HUMAN | P01764)
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.
    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: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: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:0042742    defense response to bacterium    Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
    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: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.
    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: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: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: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.
    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.

 Visualization

(-) Interactive Views

Theoretical Model
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1hou)
 
  Sites
(no "Sites" information available for 1hou)
 
  Cis Peptide Bonds
    Pro L:95 - Arg L:95F  [ RasMol ]  
    Thr L:7 - Pro L:8   [ RasMol ]  
    Tyr H:96 - Gly H:97   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1hou
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  HV323_HUMAN | P01764
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  HV323_HUMAN | P01764
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        HV323_HUMAN | P017641ohq 3bn9 3upc 3zhd 3zhk 3zhl 4kfz

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1HOU)