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(-) Description

Title :  CRYSTAL STRUCTURE OF THE MOUSE COLONY-STIMULATING FACTOR 1 (MCSF-1) CYTOKINE
 
Authors :  J. Elegheert, N. Bracke, A. Bekaert, S. N. Savvides
Date :  31 Oct 11  (Deposition) - 22 Aug 12  (Release) - 17 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hematopoietic Cytokine, Rtkiii, Four-Helix Bundle, Cytokine (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Elegheert, N. Bracke, P. Pouliot, I. Gutsche, A. V. Shkumatov, N. Tarbouriech, K. Verstraete, A. Bekaert, W. P. Burmeister, D. I. Svergun, B. N. Lambrecht, B. Vergauwen, S. N. Savvides
Allosteric Competitive Inactivation Of Hematopoietic Csf-1 Signaling By The Viral Decoy Receptor Barf1
Nat. Struct. Mol. Biol. V. 19 938 2012
PubMed-ID: 22902366  |  Reference-DOI: 10.1038/NSMB.2367

(-) Compounds

Molecule 1 - MACROPHAGE COLONY-STIMULATING FACTOR 1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3) CODONPLUS RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 33-181
    Gene: CSF1, CSFM
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: CSF-1, MCSF, PROCESSED MACROPHAGE COLONY-STIMULATING FACTOR 1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:5 , THR A:105BINDING SITE FOR RESIDUE CA A 200
2AC2SOFTWAREHIS A:9 , SER A:147BINDING SITE FOR RESIDUE CA A 201
3AC3SOFTWAREASP B:59 , ASP B:62 , THR B:105BINDING SITE FOR RESIDUE CA B 200
4AC4SOFTWAREASP A:131 , ASN A:133 , ASN B:138 , ASN B:140 , ASN B:141BINDING SITE FOR RESIDUE CA B 201

(-) SS Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1A:7 -A:90
2A:31 -B:31
3A:48 -A:139
4A:102 -A:146
5B:7 -B:90
6B:48 -B:139
7B:102 -B:146

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3UF5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3UF5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3UF5)

(-) Exons   (0, 0)

(no "Exon" information available for 3UF5)

(-) 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:145
 aligned with CSF1_MOUSE | P07141 from UniProtKB/Swiss-Prot  Length:552

    Alignment length:147
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       
           CSF1_MOUSE    33 KEVSEHCSHMIGNGHLKVLQQLIDSQMETSCQIAFEFVDQEQLDDPVCYLKKAFFLVQDIIDETMRFKDNTPNANATERLQELSNNLNSCFTKDYEEQNKACVRTFHETPLQLLEKIKNFFNETKNLLEKDWNIFTKNCNNSFAKCS 179
               SCOP domains d3uf5a_ A: automated matches                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh..hhhhhhhhhhhhhh.......eeeeee......hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh.....--....eeeeeehhhhhhhhhhhhhhhhhhhhhhh.hhhhh.hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3uf5 A   1 KEVSEHCSHMIGNGHLKVLQQLIDSQMETSCQIAFEFVDQEQLDDPVCYLKKAFFLVQDIIDETMRFKDNTPNANATERLQELSNNLNSCFTKDYE--NKACVRTFHETPLQLLEKIKNFFNETKNLLEKDWNIFTKNCNNSFAKCS 147
                                    10        20        30        40        50        60        70        80        90     | 100       110       120       130       140       
                                                                                                                          96 99                                                


Chain B from PDB  Type:PROTEIN  Length:144
 aligned with CSF1_MOUSE | P07141 from UniProtKB/Swiss-Prot  Length:552

    Alignment length:146
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172      
           CSF1_MOUSE    33 KEVSEHCSHMIGNGHLKVLQQLIDSQMETSCQIAFEFVDQEQLDDPVCYLKKAFFLVQDIIDETMRFKDNTPNANATERLQELSNNLNSCFTKDYEEQNKACVRTFHETPLQLLEKIKNFFNETKNLLEKDWNIFTKNCNNSFAKC 178
               SCOP domains d3uf5b_ B: automated matches                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhh.hhhhhhhhhhhhhhh......eeeeee.hhhh.hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh.....--....eeeeeehhhhhhhhhhhhhhhhhhhhhhh.hhhhh.hhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3uf5 B   1 KEVSEHCSHMIGNGHLKVLQQLIDSQMETSCQIAFEFVDQEQLDDPVCYLKKAFFLVQDIIDETMRFKDNTPNANATERLQELSNNLNSCFTKDYE--NKACVRTFHETPLQLLEKIKNFFNETKNLLEKDWNIFTKNCNNSFAKC 146
                                    10        20        30        40        50        60        70        80        90     | 100       110       120       130       140      
                                                                                                                          96 99
   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, 2)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3UF5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3UF5)

(-) Gene Ontology  (47, 47)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (CSF1_MOUSE | P07141)
molecular function
    GO:0005125    cytokine activity    Functions to control the survival, growth, differentiation and effector function of tissues and cells.
    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.
    GO:0005157    macrophage colony-stimulating factor receptor binding    Interacting selectively and non-covalently with the macrophage colony-stimulating factor receptor.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
    GO:0060444    branching involved in mammary gland duct morphogenesis    The process in which the branching structure of the mammary gland duct is generated and organized. The mammary gland is a large compound sebaceous gland that in female mammals is modified to secrete milk.
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0003006    developmental process involved in reproduction    A developmental process in which a progressive change in the state of some part of an organism specifically contributes to its ability to form offspring.
    GO:0048873    homeostasis of number of cells within a tissue    Any biological process involved in the maintenance of the steady-state number of cells within a population of cells in a tissue.
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    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:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0038145    macrophage colony-stimulating factor signaling pathway    A series of molecular signals initiated by the binding of the cytokine macrophage colony-stimulating factor (M-CSF) to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0030225    macrophage differentiation    The process in which a relatively unspecialized monocyte acquires the specialized features of a macrophage.
    GO:0060763    mammary duct terminal end bud growth    The morphogenetic growth of the large, club-shaped terminal end of a mammary gland duct during prepubertal growth and during puberty.
    GO:0060611    mammary gland fat development    The progression of the mammary gland fat over time, from its formation to the mature structure. The mammary fat is an adipose structure in the gland that is invaded by the mammary ducts.
    GO:0042476    odontogenesis    The process whose specific outcome is the progression of a tooth or teeth over time, from formation to the mature structure(s). A tooth is any hard bony, calcareous, or chitinous organ found in the mouth or pharynx of an animal and used in procuring or masticating food.
    GO:0001503    ossification    The formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance.
    GO:0030316    osteoclast differentiation    The process in which a relatively unspecialized monocyte acquires the specialized features of an osteoclast. An osteoclast is a specialized phagocytic cell associated with the absorption and removal of the mineralized matrix of bone tissue.
    GO:0002158    osteoclast proliferation    The multiplication or reproduction of osteoclasts, resulting in the expansion of an osteoclast cell population. An osteoclast is a specialized phagocytic cell associated with the absorption and removal of the mineralized matrix of bone tissue, which typically differentiates from monocytes.
    GO:0046579    positive regulation of Ras protein signal transduction    Any process that activates or increases the frequency, rate or extent of Ras protein signal transduction.
    GO:0030335    positive regulation of cell migration    Any process that activates or increases the frequency, rate or extent of cell migration.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    GO:0001954    positive regulation of cell-matrix adhesion    Any process that activates or increases the rate or extent of cell adhesion to an extracellular matrix.
    GO:0032270    positive regulation of cellular protein metabolic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving a protein, occurring at the level of an individual cell.
    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:0010759    positive regulation of macrophage chemotaxis    Any process that increases the rate, frequency or extent of macrophage chemotaxis. Macrophage chemotaxis is the movement of a macrophage in response to an external stimulus.
    GO:1902228    positive regulation of macrophage colony-stimulating factor signaling pathway    Any process that activates or increases the frequency, rate or extent of macrophage colony-stimulating factor signaling pathway.
    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:1904141    positive regulation of microglial cell migration    Any process that activates or increases the frequency, rate or extent of microglial cell migration.
    GO:0045657    positive regulation of monocyte differentiation    Any process that activates or increases the frequency, rate or extent of monocyte differentiation.
    GO:0032946    positive regulation of mononuclear cell proliferation    Any process that activates or increases the frequency, rate or extent of mononuclear cell proliferation.
    GO:0040018    positive regulation of multicellular organism growth    Any process that activates or increases the frequency, rate or extent of growth of an organism to reach its usual body size.
    GO:0042488    positive regulation of odontogenesis of dentin-containing tooth    Any process that activates or increases the frequency, rate or extent of the formation and development of teeth, the hard, bony appendages that are borne on the jaws, or on other bones in the walls of the mouth or pharynx of most vertebrates.
    GO:0045672    positive regulation of osteoclast differentiation    Any process that activates or increases the frequency, rate or extent of osteoclast differentiation.
    GO:0045860    positive regulation of protein kinase activity    Any process that activates or increases the frequency, rate or extent of protein kinase activity.
    GO:0030278    regulation of ossification    Any process that modulates the frequency, rate or extent of bone formation.
    GO:0007169    transmembrane receptor protein tyrosine kinase signaling pathway    A series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell where the receptor possesses tyrosine kinase activity, and ending with regulation of a downstream cellular process, e.g. transcription.
cellular component
    GO:1990682    CSF1-CSF1R complex    A protein complex consisting of a macrophage colony-stimulating factor (CSF1, also called M-CSF) dimer bound to a dimerized receptor (CSF1R, also called FMS). Receptor dimerization requires the presence of the ligand.
    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.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CSF1_MOUSE | P07141: 3ejj 4adq

(-) Related Entries Specified in the PDB File

3ejj 3uez 3uf2