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(-) Description

Title :  THE CRYSTAL STRUCTURE OF RECOMBINANT HUMAN NEUTROPHIL-ACTIVATING PEPTIDE-2 (M6L) AT 1.9-ANGSTROMS RESOLUTION
 
Authors :  M. G. Malkowski, B. F. P. Edwards
Date :  19 Dec 94  (Deposition) - 19 Dec 95  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Cytokine (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. G. Malkowski, J. Y. Wu, J. B. Lazar, P. H. Johnson, B. F. Edwards
The Crystal Structure Of Recombinant Human Neutrophil-Activating Peptide-2 (M6L) At 1. 9-A Resolution.
J. Biol. Chem. V. 270 7077 1995
PubMed-ID: 7706245  |  Reference-DOI: 10.1074/JBC.270.13.7077
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NEUTROPHIL ACTIVATING PEPTIDE-2
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPBR-CRM-CTAP-MET20,LEU26
    Expression System Taxid562
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymNAP-2

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1NAP)

(-) SS Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1A:25 -A:51
2A:27 -A:67
3B:25 -B:51
4B:27 -B:67
5C:25 -C:51
6C:27 -C:67
7D:25 -D:51
8D:27 -D:67

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 4)

Asymmetric/Biological Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SMALL_CYTOKINES_CXCPS00471 Small cytokines (intercrine/chemokine) C-x-C subfamily signature.CXCL7_HUMAN63-107
 
 
 
  4A:25-69
B:25-69
C:25-69
D:25-69

(-) Exons   (2, 8)

Asymmetric/Biological Unit (2, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002960281ENSE00001077818chr4:74853914-74853673242CXCL7_HUMAN1-50500--
1.2ENST000002960282ENSE00001077819chr4:74853369-74853234136CXCL7_HUMAN50-95464A:21-57
B:21-57
C:24-57
D:21-57
37
37
34
37
1.3ENST000002960283ENSE00001077820chr4:74853091-74852755337CXCL7_HUMAN95-128344A:57-86
B:57-86
C:57-86
D:57-86
30
30
30
30

(-) Sequences/Alignments

Asymmetric/Biological 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:66
 aligned with CXCL7_HUMAN | P02775 from UniProtKB/Swiss-Prot  Length:128

    Alignment length:66
                                    68        78        88        98       108       118      
          CXCL7_HUMAN    59 AELRCMCIKTTSGIHPKNIQSLEVIGKGTHCNQVEVIATLKDGRKICLDPDAPRIKKIVQKKLAGD 124
               SCOP domains d1napa_ A: Platelet basic protein, PBP                             SCOP domains
               CATH domains 1napA00 A:21-86  [code=2.40.50.40, no name defined]                CATH domains
               Pfam domains ------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...............hhheeeeeee.........eeeeee....eeee....hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----SMALL_CYTOKINES_CXC  PDB: A:25-69            ----------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: A:21-57 UniProt: 50-95----------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------Exon 1.3  PDB: A:57-86         Transcript 1 (2)
                 1nap A  21 AELRCLCIKTTSGIHPKNIQSLEVIGKGTHCNQVEVIATLKDGRKICLDPDAPRIKKIVQKKLAGD  86
                                    30        40        50        60        70        80      

Chain B from PDB  Type:PROTEIN  Length:66
 aligned with CXCL7_HUMAN | P02775 from UniProtKB/Swiss-Prot  Length:128

    Alignment length:66
                                    68        78        88        98       108       118      
          CXCL7_HUMAN    59 AELRCMCIKTTSGIHPKNIQSLEVIGKGTHCNQVEVIATLKDGRKICLDPDAPRIKKIVQKKLAGD 124
               SCOP domains d1napb_ B: Platelet basic protein, PBP                             SCOP domains
               CATH domains 1napB00 B:21-86  [code=2.40.50.40, no name defined]                CATH domains
               Pfam domains ------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...............hhheeeeeee.........eeeeee....eeee....hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----SMALL_CYTOKINES_CXC  PDB: B:25-69            ----------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: B:21-57 UniProt: 50-95----------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------Exon 1.3  PDB: B:57-86         Transcript 1 (2)
                 1nap B  21 AELRCLCIKTTSGIHPKNIQSLEVIGKGTHCNQVEVIATLKDGRKICLDPDAPRIKKIVQKKLAGD  86
                                    30        40        50        60        70        80      

Chain C from PDB  Type:PROTEIN  Length:63
 aligned with CXCL7_HUMAN | P02775 from UniProtKB/Swiss-Prot  Length:128

    Alignment length:63
                                    71        81        91       101       111       121   
          CXCL7_HUMAN    62 RCMCIKTTSGIHPKNIQSLEVIGKGTHCNQVEVIATLKDGRKICLDPDAPRIKKIVQKKLAGD 124
               SCOP domains d1napc_ C: Platelet basic protein, PBP                          SCOP domains
               CATH domains 1napC00 C:24-86  [code=2.40.50.40, no name defined]             CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhheeeeeee.........eeeeee....eeee....hhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -SMALL_CYTOKINES_CXC  PDB: C:25-69            ----------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: C:24-57            ----------------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------Exon 1.3  PDB: C:57-86         Transcript 1 (2)
                 1nap C  24 RCLCIKTTSGIHPKNIQSLEVIGKGTHCNQVEVIATLKDGRKICLDPDAPRIKKIVQKKLAGD  86
                                    33        43        53        63        73        83   

Chain D from PDB  Type:PROTEIN  Length:66
 aligned with CXCL7_HUMAN | P02775 from UniProtKB/Swiss-Prot  Length:128

    Alignment length:66
                                    68        78        88        98       108       118      
          CXCL7_HUMAN    59 AELRCMCIKTTSGIHPKNIQSLEVIGKGTHCNQVEVIATLKDGRKICLDPDAPRIKKIVQKKLAGD 124
               SCOP domains d1napd_ D: Platelet basic protein, PBP                             SCOP domains
               CATH domains 1napD00 D:21-86  [code=2.40.50.40, no name defined]                CATH domains
               Pfam domains ------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...............hhheeeeeee.........eeeeee....eeee....hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----SMALL_CYTOKINES_CXC  PDB: D:25-69            ----------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: D:21-57 UniProt: 50-95----------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------Exon 1.3  PDB: D:57-86         Transcript 1 (2)
                 1nap D  21 AELRCLCIKTTSGIHPKNIQSLEVIGKGTHCNQVEVIATLKDGRKICLDPDAPRIKKIVQKKLAGD  86
                                    30        40        50        60        70        80      

   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/Biological Unit

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (24, 24)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (CXCL7_HUMAN | P02775)
molecular function
    GO:0045236    CXCR chemokine receptor binding    Interacting selectively and non-covalently with a chemokine receptor in the CXCR family.
    GO:0008009    chemokine activity    The function of a family of small chemotactic cytokines; their name is derived from their ability to induce directed chemotaxis in nearby responsive cells. All chemokines possess a number of conserved cysteine residues involved in intramolecular disulfide bond formation. Some chemokines are considered pro-inflammatory and can be induced during an immune response to recruit cells of the immune system to a site of infection, while others are considered homeostatic and are involved in controlling the migration of cells during normal processes of tissue maintenance or development. Chemokines are found in all vertebrates, some viruses and some bacteria.
    GO:0005125    cytokine activity    Functions to control the survival, growth, differentiation and effector function of tissues and cells.
    GO:0005355    glucose transmembrane transporter activity    Enables the transfer of the hexose monosaccharide glucose from one side of the membrane to the other.
    GO:0008083    growth factor activity    The function that stimulates a cell to grow or proliferate. Most growth factors have other actions besides the induction of cell growth or proliferation.
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:0070098    chemokine-mediated signaling pathway    A series of molecular signals initiated by the binding of a chemokine to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    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:0042742    defense response to bacterium    Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
    GO:1904659    glucose transmembrane transport    The directed movement of glucose across a membrane.
    GO:0015758    glucose transport    The directed movement of the hexose monosaccharide glucose into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    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:0006954    inflammatory response    The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
    GO:0002523    leukocyte migration involved in inflammatory response    The movement of a leukocyte within or between different tissues and organs of the body contributing to an inflammatory response.
    GO:0030593    neutrophil chemotaxis    The directed movement of a neutrophil cell, the most numerous polymorphonuclear leukocyte found in the blood, in response to an external stimulus, usually an infection or wounding.
    GO:0043312    neutrophil degranulation    The regulated exocytosis of secretory granules containing preformed mediators such as proteases, lipases, and inflammatory mediators by a neutrophil.
    GO:0002576    platelet degranulation    The regulated exocytosis of secretory granules containing preformed mediators such as histamine and serotonin by a platelet.
    GO:0051781    positive regulation of cell division    Any process that activates or increases the frequency, rate or extent of cell division.
    GO:0002690    positive regulation of leukocyte chemotaxis    Any process that activates or increases the frequency, rate, or extent of leukocyte chemotaxis.
    GO:0042127    regulation of cell proliferation    Any process that modulates the frequency, rate or extent of cell proliferation.
    GO:0032496    response to lipopolysaccharide    Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
cellular component
    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.
    GO:0031093    platelet alpha granule lumen    The volume enclosed by the membrane of the platelet alpha granule.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CXCL7_HUMAN | P027751f9p 1tvx

(-) Related Entries Specified in the PDB File

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