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(-) Description

Title :  HUMAN BETA-DEFENSIN-1 (MUTANT LYS22GLU)
 
Authors :  J. Lubkowski, M. Pazgier
Date :  20 Oct 06  (Deposition) - 31 Oct 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  A (1x),B (1x),C (1x),D (1x)
Biol. Unit 6:  C (1x),D (1x)
Biol. Unit 7:  A (1x),B (1x)
Keywords :  Antimicrobial, Chemotactic, Defensin, Mutant, Antimicrobial Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Pazgier, A. Prahl, D. M. Hoover, J. Lubkowski
Studies Of The Biological Properties Of Human Beta-Defensin 1.
J. Biol. Chem. V. 282 1819 2007
PubMed-ID: 17071614  |  Reference-DOI: 10.1074/JBC.M607210200

(-) Compounds

Molecule 1 - BETA-DEFENSIN 1
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPAED4
    Expression System StrainBL21(DE3)PLYSE
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentHUMAN BETA-DEFENSIN 1, RESIDUES 33-68
    GeneDEFB1, BD1, HBD1
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymBD-1, DEFENSIN, BETA 1, HBD-1

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A   
Biological Unit 2 (1x) B  
Biological Unit 3 (1x)  C 
Biological Unit 4 (1x)   D
Biological Unit 5 (1x)A (1x)B (1x)C (1x)D (1x)
Biological Unit 6 (1x)  C (1x)D (1x)
Biological Unit 7 (1x)A (1x)B (1x)  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric Unit (1, 8)
No.NameCountTypeFull Name
1SO48Ligand/IonSULFATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 3 (1, 3)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION
Biological Unit 4 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 5 (1, 3)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION
Biological Unit 6 (1, 3)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION
Biological Unit 7 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:3 , HOH A:303 , HOH A:314 , ASP B:1 , HIS B:2 , CYS B:27 , TYR B:28 , ARG B:29 , HOH B:310 , HOH C:344BINDING SITE FOR RESIDUE SO4 B 301
2AC2SOFTWAREASP A:1 , HIS A:2 , CYS A:27 , TYR A:28 , ARG A:29 , HOH A:303 , HOH A:311 , HOH A:344 , HOH A:353 , TYR B:3 , HOH B:310BINDING SITE FOR RESIDUE SO4 A 302
3AC3SOFTWAREASP A:1 , GLY A:25 , THR A:26 , HOH A:348 , ARG C:29 , ASN D:4 , HOH D:315 , HOH D:341BINDING SITE FOR RESIDUE SO4 D 303
4AC4SOFTWARETYR C:3 , HOH C:310 , ASP D:1 , HIS D:2 , CYS D:27 , TYR D:28 , ARG D:29 , HOH D:307 , HOH D:310 , HOH D:313 , HOH D:358BINDING SITE FOR RESIDUE SO4 D 304
5AC5SOFTWAREHOH A:318 , HOH B:328 , ASP C:1 , HIS C:2 , CYS C:27 , TYR C:28 , ARG C:29 , HOH C:310 , HOH C:328 , TYR D:3 , HOH D:307BINDING SITE FOR RESIDUE SO4 C 305
6AC6SOFTWAREHOH A:304 , ARG B:29 , HOH B:313 , HOH B:314 , ASP C:1 , GLY C:25 , THR C:26 , HOH C:311 , HOH C:318 , HOH C:334BINDING SITE FOR RESIDUE SO4 C 306
7AC7SOFTWAREASP B:1 , GLY B:25 , THR B:26 , HOH B:349 , HOH B:354BINDING SITE FOR RESIDUE SO4 B 307
8AC8SOFTWARESER C:8 , LYS C:31 , LYS C:36 , HOH C:340 , HOH C:343BINDING SITE FOR RESIDUE SO4 C 308

(-) SS Bonds  (12, 12)

Asymmetric Unit
No.Residues
1A:5 -A:34
2A:12 -A:27
3A:17 -A:35
4B:5 -B:34
5B:12 -B:27
6B:17 -B:35
7C:5 -C:34
8C:12 -C:27
9C:17 -C:35
10D:5 -D:34
11D:12 -D:27
12D:17 -D:35

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2NLG)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 12)

Asymmetric Unit (3, 12)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_018405V38IDEFB1_HUMANPolymorphism2738047A/B/C/DV6I
2UniProtVAR_014925A48VDEFB1_HUMANPolymorphism1800967A/B/C/DA16V
3UniProtVAR_014926C67SDEFB1_HUMANPolymorphism1800968A/B/C/DC35S

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_018405V38IDEFB1_HUMANPolymorphism2738047AV6I
2UniProtVAR_014925A48VDEFB1_HUMANPolymorphism1800967AA16V
3UniProtVAR_014926C67SDEFB1_HUMANPolymorphism1800968AC35S

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_018405V38IDEFB1_HUMANPolymorphism2738047BV6I
2UniProtVAR_014925A48VDEFB1_HUMANPolymorphism1800967BA16V
3UniProtVAR_014926C67SDEFB1_HUMANPolymorphism1800968BC35S

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 3 (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_018405V38IDEFB1_HUMANPolymorphism2738047CV6I
2UniProtVAR_014925A48VDEFB1_HUMANPolymorphism1800967CA16V
3UniProtVAR_014926C67SDEFB1_HUMANPolymorphism1800968CC35S

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 4 (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_018405V38IDEFB1_HUMANPolymorphism2738047DV6I
2UniProtVAR_014925A48VDEFB1_HUMANPolymorphism1800967DA16V
3UniProtVAR_014926C67SDEFB1_HUMANPolymorphism1800968DC35S

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 5 (3, 12)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_018405V38IDEFB1_HUMANPolymorphism2738047A/B/C/DV6I
2UniProtVAR_014925A48VDEFB1_HUMANPolymorphism1800967A/B/C/DA16V
3UniProtVAR_014926C67SDEFB1_HUMANPolymorphism1800968A/B/C/DC35S

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 6 (3, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_018405V38IDEFB1_HUMANPolymorphism2738047C/DV6I
2UniProtVAR_014925A48VDEFB1_HUMANPolymorphism1800967C/DA16V
3UniProtVAR_014926C67SDEFB1_HUMANPolymorphism1800968C/DC35S

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 7 (3, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_018405V38IDEFB1_HUMANPolymorphism2738047A/BV6I
2UniProtVAR_014925A48VDEFB1_HUMANPolymorphism1800967A/BA16V
3UniProtVAR_014926C67SDEFB1_HUMANPolymorphism1800968A/BC35S

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2NLG)

(-) Exons   (1, 4)

Asymmetric Unit (1, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002974391ENSE00001087806chr8:6735544-6735319226DEFB1_HUMAN1-21210--
1.2ENST000002974392ENSE00001087807chr8:6728348-6728097252DEFB1_HUMAN21-68484A:1-36
B:1-36
C:1-36
D:1-36
36
36
36
36

(-) 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 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 d2nlga_ A: automated matches         SCOP domains
               CATH domains ------------------------------------ CATH domains
               Pfam domains ------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhh..eee.........eeeee....eeee. 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
                  2nlg A  1 DHYNCVSSGGQCLYSACPIFTEIQGTCYRGKAKCCK 36
                                    10        20        30      

Chain B 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 d2nlgb_ B: automated matches         SCOP domains
               CATH domains ------------------------------------ CATH domains
               Pfam domains ------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhh..eee.........eeeee....eeee. Sec.struct. author
                 SAPs(SNPs) -----I---------V------------------S- SAPs(SNPs)
                    PROSITE ------------------------------------ PROSITE
               Transcript 1 Exon 1.2  PDB: B:1-36 UniProt: 21-68 Transcript 1
                  2nlg B  1 DHYNCVSSGGQCLYSACPIFTEIQGTCYRGKAKCCK 36
                                    10        20        30      

Chain C 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 d2nlgc_ C: automated matches         SCOP domains
               CATH domains ------------------------------------ CATH domains
               Pfam domains ------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhh..eee.........eeeee....eeee. Sec.struct. author
                 SAPs(SNPs) -----I---------V------------------S- SAPs(SNPs)
                    PROSITE ------------------------------------ PROSITE
               Transcript 1 Exon 1.2  PDB: C:1-36 UniProt: 21-68 Transcript 1
                  2nlg C  1 DHYNCVSSGGQCLYSACPIFTEIQGTCYRGKAKCCK 36
                                    10        20        30      

Chain D 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 d2nlgd_ D: automated matches         SCOP domains
               CATH domains ------------------------------------ CATH domains
           Pfam domains (1) Defensin_beta-2nlgD01 D:1-36         Pfam domains (1)
           Pfam domains (2) Defensin_beta-2nlgD02 D:1-36         Pfam domains (2)
           Pfam domains (3) Defensin_beta-2nlgD03 D:1-36         Pfam domains (3)
           Pfam domains (4) Defensin_beta-2nlgD04 D:1-36         Pfam domains (4)
         Sec.struct. author hhhhhhhh..eee.........eeeee....eeee. Sec.struct. author
                 SAPs(SNPs) -----I---------V------------------S- SAPs(SNPs)
                    PROSITE ------------------------------------ PROSITE
               Transcript 1 Exon 1.2  PDB: D:1-36 UniProt: 21-68 Transcript 1
                  2nlg D  1 DHYNCVSSGGQCLYSACPIFTEIQGTCYRGKAKCCK 36
                                    10        20        30      

   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  (1, 4)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2NLG)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: Defensin (30)

(-) Gene Ontology  (16, 16)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (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 1kj5 2nlb 2nlc 2nld 2nle 2nlf 2nlh 2nlp 2nlq 2nls 2plz

(-) Related Entries Specified in the PDB File

2nlb HUMAN BETA-DEFENSIN-1 (MUTANT ASN4ALA)
2nlc HUMAN BETA-DEFENSIN-1 (MUTANT SER8ALA)
2nld HUMAN BETA-DEFENSIN-1 (MUTANT GLN11ALA)
2nle HUMAN BETA-DEFENSIN-1 (MUTANT GLN11ALA)
2nlf HUMAN BETA-DEFENSIN-1 (MUTANT LEU13GLU)
2nlh HUMAN BETA-DEFENSIN-1 (MUTANT GLN24ALA)
2nlp
2nlq
2nls