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(-) Description

Title :  PF4-M2 CHIMERIC MUTANT WITH THE FIRST 10 N-TERMINAL RESIDUES OF R-PF4 REPLACED BY THE N-TERMINAL RESIDUES OF THE IL8 SEQUENCE. MODELS 1-15 OF A 27-MODEL SET.
 
Authors :  K. H. Mayo, V. Roongta, E. Ilyina, R. Milius, S. Barker, C. Quinlan, G. La Rosa, T. J. Daly
Date :  18 Jul 95  (Deposition) - 29 Jan 96  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B,C,D  (15x)
Keywords :  Cytokine (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. H. Mayo, V. Roongta, E. Ilyina, R. Milius, S. Barker, C. Quinlan, G. La Rosa, T. J. Daly
Nmr Solution Structure Of The 32-Kda Platelet Factor 4 Elr-Motif N-Terminal Chimera: A Symmetric Tetramer.
Biochemistry V. 34 11399 1995
PubMed-ID: 7547867  |  Reference-DOI: 10.1021/BI00036A012
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PF4-M2 CHIMERA
    Cell Line: BL21
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: BL21
    Expression System Taxid: 562
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PLATELET FACTOR 4, PLATELET FACTOR M2

 Structural Features

(-) Chains, Units

  
NMR Structure (15x): 

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1PFM)

(-) SS Bonds  (8, 8)

NMR Structure
No.Residues
1A:10 -A:36
2A:12 -A:52
3B:10 -B:36
4B:12 -B:52
5C:10 -C:36
6C:12 -C:52
7D:10 -D:36
8D:12 -D:52

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 4)

NMR Structure (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SMALL_CYTOKINES_CXCPS00471 Small cytokines (intercrine/chemokine) C-x-C subfamily signature.PLF4_HUMAN41-85
 
 
 		  4A:10-54
B:10-54
C:10-54
D:10-54

(-) Exons   (3, 12)

NMR Structure (3, 12)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002960291ENSE00001077823chr4:74847841-74847580262PLF4_HUMAN1-31314A:3-4
B:3-4
C:3-4
D:3-4		2
2
2
2
1.2ENST000002960292ENSE00001756309chr4:74847260-74847134127PLF4_HUMAN31-73434A:5-42 (gaps)
B:5-42 (gaps)
C:5-42 (gaps)
D:5-42 (gaps)		41
41
41
41
1.3ENST000002960293ENSE00001077821chr4:74847008-74846794215PLF4_HUMAN73-101294A:42-70
B:42-70
C:42-70
D:42-70		29
29
29
29

(-) 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:68
 aligned with PLF4_HUMAN | P02776 from UniProtKB/Swiss-Prot  Length:101

    Alignment length:101
                                    10        20        30        40        50        60        70        80        90       100 
           PLF4_HUMAN     1 MSSAAGFCASRPGLLFLGLLLLPLVVAFASAEAEEDGDLQCLCVKTTSQVRPRHITSLEVIKAGPHCPTAQLIATLKNGRKICLDLQAPLYKKIIKKLLES 101
               SCOP domains d1                              pfm   a_ A: Platelet factor 4, PF4                                    SCOP domains
               CATH domains 1p                              fmA   00 A:3-70  [code=2.40.50.40, no name defined]                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..------------------------------...---..................eeeee.........eeeee.............hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------SMALL_CYTOKINES_CXC  PDB: A:10-54            ---------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: A:3-4           -----------------------------------------Exon 1.3  PDB: A:42-70        Transcript 1 (1)
           Transcript 1 (2) ------------------------------Exon 1.2  PDB: A:5-42 (gaps) UniProt: 31-73---------------------------- Transcript 1 (2)
                 1pfm A   3 MS------------------------------AKE---LRCQCVKTTSQVRPRHITSLEVIKAGPHCPTAQLIATLKNGRKICLDLQAPLYKKIIKKLLES  70
                             |       -         -         -  | |   |9        19        29        39        49        59        69 
                             4                              5 7   8                                                              


Chain B from PDB  Type:PROTEIN  Length:68
 aligned with PLF4_HUMAN | P02776 from UniProtKB/Swiss-Prot  Length:101

    Alignment length:101
                                    10        20        30        40        50        60        70        80        90       100 
           PLF4_HUMAN     1 MSSAAGFCASRPGLLFLGLLLLPLVVAFASAEAEEDGDLQCLCVKTTSQVRPRHITSLEVIKAGPHCPTAQLIATLKNGRKICLDLQAPLYKKIIKKLLES 101
               SCOP domains d1                              pfm   b_ B: Platelet factor 4, PF4                                    SCOP domains
               CATH domains 1p                              fmB   00 B:3-70  [code=2.40.50.40, no name defined]                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..------------------------------...---..................eeeee.........eeeee.............hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------SMALL_CYTOKINES_CXC  PDB: B:10-54            ---------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: B:3-4           -----------------------------------------Exon 1.3  PDB: B:42-70        Transcript 1 (1)
           Transcript 1 (2) ------------------------------Exon 1.2  PDB: B:5-42 (gaps) UniProt: 31-73---------------------------- Transcript 1 (2)
                 1pfm B   3 MS------------------------------AKE---LRCQCVKTTSQVRPRHITSLEVIKAGPHCPTAQLIATLKNGRKICLDLQAPLYKKIIKKLLES  70
                             |       -         -         -  | |   |9        19        29        39        49        59        69 
                             4                              5 7   8                                                              


Chain C from PDB  Type:PROTEIN  Length:68
 aligned with PLF4_HUMAN | P02776 from UniProtKB/Swiss-Prot  Length:101

    Alignment length:101
                                    10        20        30        40        50        60        70        80        90       100 
           PLF4_HUMAN     1 MSSAAGFCASRPGLLFLGLLLLPLVVAFASAEAEEDGDLQCLCVKTTSQVRPRHITSLEVIKAGPHCPTAQLIATLKNGRKICLDLQAPLYKKIIKKLLES 101
               SCOP domains d1                              pfm   c_ C: Platelet factor 4, PF4                                    SCOP domains
               CATH domains 1p                              fmC   00 C:3-70  [code=2.40.50.40, no name defined]                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..------------------------------...---..................eeeee.........eeeee.............hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------SMALL_CYTOKINES_CXC  PDB: C:10-54            ---------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: C:3-4           -----------------------------------------Exon 1.3  PDB: C:42-70        Transcript 1 (1)
           Transcript 1 (2) ------------------------------Exon 1.2  PDB: C:5-42 (gaps) UniProt: 31-73---------------------------- Transcript 1 (2)
                 1pfm C   3 MS------------------------------AKE---LRCQCVKTTSQVRPRHITSLEVIKAGPHCPTAQLIATLKNGRKICLDLQAPLYKKIIKKLLES  70
                             |       -         -         -  | |   |9        19        29        39        49        59        69 
                             4                              5 7   8                                                              


Chain D from PDB  Type:PROTEIN  Length:68
 aligned with PLF4_HUMAN | P02776 from UniProtKB/Swiss-Prot  Length:101

    Alignment length:101
                                    10        20        30        40        50        60        70        80        90       100 
           PLF4_HUMAN     1 MSSAAGFCASRPGLLFLGLLLLPLVVAFASAEAEEDGDLQCLCVKTTSQVRPRHITSLEVIKAGPHCPTAQLIATLKNGRKICLDLQAPLYKKIIKKLLES 101
               SCOP domains d1                              pfm   d_ D: Platelet factor 4, PF4                                    SCOP domains
               CATH domains 1p                              fmD   00 D:3-70  [code=2.40.50.40, no name defined]                   CATH domains
           Pfam domains (1) ------------------------------------------IL8-1pfmD01 D:12-67                                     --- Pfam domains (1)
           Pfam domains (2) ------------------------------------------IL8-1pfmD02 D:12-67                                     --- Pfam domains (2)
           Pfam domains (3) ------------------------------------------IL8-1pfmD03 D:12-67                                     --- Pfam domains (3)
           Pfam domains (4) ------------------------------------------IL8-1pfmD04 D:12-67                                     --- Pfam domains (4)
         Sec.struct. author ..------------------------------...---..................eeeee.........eeeee.............hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------SMALL_CYTOKINES_CXC  PDB: D:10-54            ---------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: D:3-4           -----------------------------------------Exon 1.3  PDB: D:42-70        Transcript 1 (1)
           Transcript 1 (2) ------------------------------Exon 1.2  PDB: D:5-42 (gaps) UniProt: 31-73---------------------------- Transcript 1 (2)
                 1pfm D   3 MS------------------------------AKE---LRCQCVKTTSQVRPRHITSLEVIKAGPHCPTAQLIATLKNGRKICLDLQAPLYKKIIKKLLES  70
                             |       -         -         -  | |   |9        19        29        39        49        59        69 
                             4                              5 7   8
   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)

NMR Structure
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 4)

NMR Structure
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 4)

NMR Structure
(-)
Clan: no clan defined [family: IL8] (55)
(-)
Family: IL8 (55)
(-)
Homo sapiens (Human) (49)
1aIL8-1pfmD01D:12-67
1bIL8-1pfmD02D:12-67
1cIL8-1pfmD03D:12-67
1dIL8-1pfmD04D:12-67

(-) Gene Ontology  (31, 31)

NMR Structure(hide GO term definitions)
Chain A,B,C,D   (PLF4_HUMAN | P02776)
molecular function
    GO:0048248    CXCR3 chemokine receptor binding    Interacting selectively and non-covalently with a the CXCR3 chemokine receptor.
    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:0008201    heparin binding    Interacting selectively and non-covalently with heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells and which consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues.
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:0019221    cytokine-mediated signaling pathway    A series of molecular signals initiated by the binding of a cytokine to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    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:0030595    leukocyte chemotaxis    The movement of a leukocyte in response to an external stimulus.
    GO:0045347    negative regulation of MHC class II biosynthetic process    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of MHC class II.
    GO:0016525    negative regulation of angiogenesis    Any process that stops, prevents, or reduces the frequency, rate or extent of angiogenesis.
    GO:0045918    negative regulation of cytolysis    Any process that stops, prevents, or reduces the frequency, rate or extent of cytolysis.
    GO:2001240    negative regulation of extrinsic apoptotic signaling pathway in absence of ligand    Any process that stops, prevents or reduces the frequency, rate or extent of extrinsic apoptotic signaling pathway in absence of ligand.
    GO:0045653    negative regulation of megakaryocyte differentiation    Any process that stops, prevents, or reduces the frequency, rate or extent of megakaryocyte differentiation.
    GO:0030168    platelet activation    A series of progressive, overlapping events triggered by exposure of the platelets to subendothelial tissue. These events include shape change, adhesiveness, aggregation, and release reactions. When carried through to completion, these events lead to the formation of a stable hemostatic plug.
    GO:0002576    platelet degranulation    The regulated exocytosis of secretory granules containing preformed mediators such as histamine and serotonin by a platelet.
    GO:0030816    positive regulation of cAMP metabolic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving the nucleotide cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate).
    GO:0043950    positive regulation of cAMP-mediated signaling    Any process which activates, maintains or increases the frequency, rate or extent of cAMP-mediated signaling, a series of molecular signals in which a cell uses cyclic AMP to convert an extracellular signal into a response.
    GO:0010628    positive regulation of gene expression    Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0002690    positive regulation of leukocyte chemotaxis    Any process that activates or increases the frequency, rate, or extent of leukocyte chemotaxis.
    GO:0010744    positive regulation of macrophage derived foam cell differentiation    Any process that increases the rate, frequency or extent of macrophage derived foam cell differentiation. Macrophage derived foam cell differentiation is the process in which a macrophage acquires the specialized features of a foam cell. A foam cell is a type of cell containing lipids in small vacuoles and typically seen in atherosclerotic lesions, as well as other conditions.
    GO:0045651    positive regulation of macrophage differentiation    Any process that activates or increases the frequency, rate or extent of macrophage differentiation.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0032760    positive regulation of tumor necrosis factor production    Any process that activates or increases the frequency, rate, or extent of tumor necrosis factor production.
    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
        PLF4_HUMAN | P02776: 1dn3 1f9q 1f9r 1f9s 1pfn 1rhp 4r9w 4r9y 4rau

(-) Related Entries Specified in the PDB File

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