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(-) Description

Title :  SOLUTION STRUCTURE OF HUMAN BETA-DEFENSIN 1
 
Authors :  D. J. Schibli, H. N. Hunter, V. Aseyev, T. D. Starner, J. M. Wiencek, P. B. Mccray Jr. , B. F. Tack, H. J. Vogel
Date :  04 Dec 01  (Deposition) - 20 Mar 02  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Defensin, Antimicrobial Protein, Human Beta-Defensin 1, Beta-Defensin, Hbd1, Antibiotic (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. J. Schibli, H. N. Hunter, V. Aseyev, T. D. Starner, J. M. Wiencek, P. B. Mccray Jr. , B. F. Tack, H. J. Vogel
The Solution Structures Of The Human Beta-Defensins Lead To A Better Understanding Of The Potent Bactericidal Activity Of Hbd3 Against Staphylococcus Aureus.
J. Biol. Chem. V. 277 8279 2002
PubMed-ID: 11741980  |  Reference-DOI: 10.1074/JBC.M108830200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BETA-DEFENSIN 1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHBD-1, DEFENSIN, BETA 1

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1KJ5)

(-) Sites  (0, 0)

(no "Site" information available for 1KJ5)

(-) SS Bonds  (3, 3)

NMR Structure
No.Residues
1A:5 -A:34
2A:12 -A:27
3A:17 -A:35

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1KJ5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 3)

NMR Structure (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_018405V38IDEFB1_HUMANPolymorphism2738047AV6I
2UniProtVAR_014925A48VDEFB1_HUMANPolymorphism1800967AA16V
3UniProtVAR_014926C67SDEFB1_HUMANPolymorphism1800968AC35S

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1KJ5)

(-) Exons   (1, 1)

NMR Structure (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002974391ENSE00001087806chr8:6735544-6735319226DEFB1_HUMAN1-21210--
1.2ENST000002974392ENSE00001087807chr8:6728348-6728097252DEFB1_HUMAN21-68481A:1-3636

(-) Sequences/Alignments

NMR Structure
   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 A from PDB  Type:PROTEIN  Length:36
 aligned with DEFB1_HUMAN | P60022 from UniProtKB/Swiss-Prot  Length:68

    Alignment length:36
                                    42        52        62      
           DEFB1_HUMAN   33 DHYNCVSSGGQCLYSACPIFTKIQGTCYRGKAKCCK 68
               SCOP domains d1kj5a_ A: Beta-defensin, BD         SCOP domains
               CATH domains ------------------------------------ CATH domains
               Pfam domains Defensin_beta-1kj5A01 A:1-36         Pfam domains
         Sec.struct. author ..........eee.........eeee......eee. Sec.struct. author
                 SAPs(SNPs) -----I---------V------------------S- SAPs(SNPs)
                    PROSITE ------------------------------------ PROSITE
               Transcript 1 Exon 1.2  PDB: A:1-36 UniProt: 21-68 Transcript 1
                  1kj5 A  1 DHYNCVSSGGQCLYSACPIFTKIQGTCYRGKAKCCK 36
                                    10        20        30      

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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)

NMR Structure

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1KJ5)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: Defensin (30)

(-) Gene Ontology  (16, 16)

NMR Structure(hide GO term definitions)
Chain A   (DEFB1_HUMAN | P60022)
biological process
    GO:0007186    G-protein coupled receptor signaling pathway    A series of molecular signals that proceeds with an activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction, or for basal GPCR signaling the pathway begins with the receptor activating its G protein in the absence of an agonist, and ends with regulation of a downstream cellular process, e.g. transcription. The pathway can start from the plasma membrane, Golgi or nuclear membrane (PMID:24568158 and PMID:16902576).
    GO:0002526    acute inflammatory response    Inflammation which comprises a rapid, short-lived, relatively uniform response to acute injury or antigenic challenge and is characterized by accumulations of fluid, plasma proteins, and granulocytic leukocytes. An acute inflammatory response occurs within a matter of minutes or hours, and either resolves within a few days or becomes a chronic inflammatory response.
    GO:0019731    antibacterial humoral response    An immune response against bacteria mediated through a body fluid. Examples of this process are the antibacterial humoral responses in Mus musculus and Drosophila melanogaster.
    GO:0006935    chemotaxis    The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
    GO:0006952    defense response    Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
    GO:0050830    defense response to Gram-positive bacterium    Reactions triggered in response to the presence of a Gram-positive bacterium that act to protect the cell or organism.
    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:0002227    innate immune response in mucosa    Any process of the innate immune response that takes place in the mucosal tissues.
    GO:0009617    response to bacterium    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a bacterium.
    GO:0033574    response to testosterone    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a testosterone stimulus.
cellular component
    GO:0005796    Golgi lumen    The volume enclosed by the membranes of any cisterna or subcompartment of the Golgi apparatus, including the cis- and trans-Golgi networks.
    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:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DEFB1_HUMAN | P600221e4s 1iju 1ijv 2nlb 2nlc 2nld 2nle 2nlf 2nlg 2nlh 2nlp 2nlq 2nls 2plz

(-) Related Entries Specified in the PDB File

1kj6 SOLUTION STRUCTURE OF HUMAN BETA-DEFENSIN 3