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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN ALPHA-DEFENSIN 1 (HNP1)
 
Authors :  M. Pazgier, W-Y. Lu
Date :  18 Mar 09  (Deposition) - 28 Jul 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.56
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Biol. Unit 2:  A,B  (1x)
Keywords :  Antimicrobial Peptide, Human Alpha Defensin 1, Human Neutrophil Peptide 1, Hnp1, Antibiotic, Antimicrobial, Antiviral Defense, Defensin, Disulfide Bond, Fungicide, Phosphoprotein, Secreted, Antimicrobial Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. Wei, E. De Leeuw, M. Pazgier, W. Yuan, G. Zou, J. Wang, B. Ericksen, W. Y. Lu, R. I. Lehrer, W. Lu
Through The Looking Glass, Mechanistic Insights From Enantiomeric Human Defensins.
J. Biol. Chem. V. 284 29180 2009
PubMed-ID: 19640840  |  Reference-DOI: 10.1074/JBC.M109.018085

(-) Compounds

Molecule 1 - NEUTROPHIL DEFENSIN 1
    ChainsA, B
    EngineeredYES
    Other DetailsTHE PEPTIDE IS NATURALLY FOUND IN HOMO SAPIENS (HUMAN).
    SynonymHNP-1, HP-1, HP1, DEFENSIN, ALPHA 1, HP 1-56, NEUTROPHIL DEFENSIN 2, HNP-2, HP-2, HP2
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (2x)AB
Biological Unit 2 (1x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2GOL2Ligand/IonGLYCEROL
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL4Ligand/IonGLYCEROL
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL2Ligand/IonGLYCEROL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG B:14 , HOH B:51BINDING SITE FOR RESIDUE CL A 31
2AC2SOFTWAREPRO A:7 , ARG A:15 , LEU A:25 , HOH A:57BINDING SITE FOR RESIDUE GOL A 32
3AC3SOFTWAREPRO B:7 , ARG B:15 , LEU B:25 , TRP B:26 , ALA B:27 , HOH B:63BINDING SITE FOR RESIDUE GOL B 31

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1A:2 -A:30
2A:4 -A:19
3A:9 -A:29
4B:2 -B:30
5B:4 -B:19
6B:9 -B:29

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ile A:6 -Pro A:7
2Ile B:6 -Pro B:7

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3GNY)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DEFENSINPS00269 Mammalian defensins signature.DEF1_HUMAN66-94
 
  2A:2-30
B:2-30
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DEFENSINPS00269 Mammalian defensins signature.DEF1_HUMAN66-94
 
  4A:2-30
B:2-30
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DEFENSINPS00269 Mammalian defensins signature.DEF1_HUMAN66-94
 
  2A:2-30
B:2-30

(-) Exons   (1, 2)

Asymmetric Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.4ENST000003826924ENSE00001493017chr8:6837602-683753568DEF1_HUMAN-00--
1.5aENST000003826925aENSE00001645348chr8:6836168-6835982187DEF1_HUMAN1-59590--
1.6aENST000003826926aENSE00001493014chr8:6835401-6835172230DEF1_HUMAN59-94362A:1-30
B:1-30
30
30

(-) 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:30
 aligned with DEF1_HUMAN | P59665 from UniProtKB/Swiss-Prot  Length:94

    Alignment length:30
                                    74        84        94
            DEF1_HUMAN   65 ACYCRIPACIAGERRYGTCIYQGRLWAFCC 94
               SCOP domains ------------------------------ SCOP domains
               CATH domains ------------------------------ CATH domains
               Pfam domains ------------------------------ Pfam domains
         Sec.struct. author ..eee........eeeeeeee..eeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------ SAPs(SNPs)
                    PROSITE -DEFENSIN  PDB: A:2-30         PROSITE
               Transcript 1 Exon 1.6a  PDB: A:1-30         Transcript 1
                  3gny A  1 ACYCRIPACIAGERRYGTCIYQGRLWAFCC 30
                                    10        20        30

Chain B from PDB  Type:PROTEIN  Length:30
 aligned with DEF1_HUMAN | P59665 from UniProtKB/Swiss-Prot  Length:94

    Alignment length:30
                                    74        84        94
            DEF1_HUMAN   65 ACYCRIPACIAGERRYGTCIYQGRLWAFCC 94
               SCOP domains ------------------------------ SCOP domains
               CATH domains ------------------------------ CATH domains
               Pfam domains ------------------------------ Pfam domains
         Sec.struct. author ..eee........eeeeeeee..eeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------ SAPs(SNPs)
                    PROSITE -DEFENSIN  PDB: B:2-30         PROSITE
               Transcript 1 Exon 1.6a  PDB: B:1-30         Transcript 1
                  3gny B  1 ACYCRIPACIAGERRYGTCIYQGRLWAFCC 30
                                    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  (0, 0)

(no "SCOP Domain" information available for 3GNY)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3GNY)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3GNY)

(-) Gene Ontology  (18, 18)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (DEF1_HUMAN | P59665)
biological process
    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:0050832    defense response to fungus    Reactions triggered in response to the presence of a fungus that act to protect the cell or organism.
    GO:0051607    defense response to virus    Reactions triggered in response to the presence of a virus 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:0030520    intracellular estrogen receptor signaling pathway    Any series of molecular signals generated as a consequence of an intracellular estrogen receptor binding to one of its physiological ligands. The pathway begins with receptor-ligand binding, and ends with regulation of a downstream cellular process (e.g. transcription).
    GO:0031640    killing of cells of other organism    Any process in an organism that results in the killing of cells of another organism, including in some cases the death of the other organism. Killing here refers to the induction of death in one cell by another cell, not cell-autonomous death due to internal or other environmental conditions.
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:0035578    azurophil granule lumen    The volume enclosed by the membrane of an azurophil granule, a primary lysosomal granule found in neutrophil granulocytes that contains a wide range of hydrolytic enzymes and is released into the extracellular fluid.
    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:0031012    extracellular matrix    A structure lying external to one or more cells, which provides structural support for cells or tissues.
    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
        DEF1_HUMAN | P596651dfn 2kht 2pm1 2pm4 2pm5 3h6c 3hj2 3hjd 3lo1 3lo2 3lo4 3lo6 3lo9 3loe 3lvx 4du0 4lb1 4lb7 4lbb 4lbf

(-) Related Entries Specified in the PDB File

1dfn CRYSTAL STRUCTURE OF HUMAN ALPHA-DEFENSIN 3 (HNP3)
2pm1 DERIVATIVE OF HUMAN ALPHA-DEFENSIN 1
2pm4 HUMAN ALPHA-DEFENSIN 1 (MULTIPLE ARG TO LYS MUTANT)
2pm5 HUMAN ALPHA-DEFENSIN 1 DERIVATIVE
3go0 CRYSTAL STRUCTURE OF D-ENANTIOMER OF HUMAN ALPHA-DEFENSIN 1 (D-HNP1)