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(-) Description

Title :  THREE-DIMENSIONAL STRUCTURE OF RECOMBINANT HUMAN GRANULOCYTE-MACROPHAGE COLONY-STIMULATING FACTOR
 
Authors :  M. R. Walter, W. J. Cook, S. E. Ealick
Date :  23 Nov 92  (Deposition) - 31 Oct 93  (Release) - 20 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Cytokine (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. R. Walter, W. J. Cook, S. E. Ealick, T. L. Nagabhushan, P. P. Trotta, C. E. Bugg
Three-Dimensional Structure Of Recombinant Human Granulocyte-Macrophage Colony-Stimulating Factor.
J. Mol. Biol. V. 224 1075 1992
PubMed-ID: 1569568  |  Reference-DOI: 10.1016/0022-2836(92)90470-5

(-) Compounds

Molecule 1 - GRANULOCYTE-MACROPHAGE COLONY-STIMULATING FACTOR
    Chains: A, B
    Engineered: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1CSG)

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:54 -A:96
2A:88 -A:121
3B:54 -B:96
4B:88 -B:121

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ser A:5 -Pro A:6
2Ser B:5 -Pro B:6

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 4)

Asymmetric/Biological Unit (2, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_013089T115ICSF2_HUMANPolymorphism2069640A/BT98I
2UniProtVAR_001975I117TCSF2_HUMANPolymorphism25882A/BI100T
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GM_CSFPS00702 Granulocyte-macrophage colony-stimulating factor signature.CSF2_HUMAN105-113
 		  2A:88-96
B:88-96

(-) Exons   (4, 8)

Asymmetric/Biological Unit (4, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002968711ENSE00001124351chr5:131409483-131409675193CSF2_HUMAN1-53532A:5-36
B:5-36		32
32
1.2ENST000002968712ENSE00001084066chr5:131409774-13140981542CSF2_HUMAN54-67142A:37-50
B:37-50		14
14
1.3ENST000002968713ENSE00001084068chr5:131410503-131410628126CSF2_HUMAN68-109422A:51-92
B:51-92		42
42
1.4ENST000002968714ENSE00001124346chr5:131411438-131411859422CSF2_HUMAN110-144352A:93-124
B:93-124		32
32

(-) 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:120
 aligned with CSF2_HUMAN | P04141 from UniProtKB/Swiss-Prot  Length:144

    Alignment length:120
                                    31        41        51        61        71        81        91       101       111       121       131       141
           CSF2_HUMAN    22 SPSPSTQPWEHVNAIQEARRLLNLSRDTAAEMNETVEVISEMFDLQEPTCLQTRLELYKQGLRGSLTKLKGPLTMMASHYKQHCPPTPETSCATQIITFESFKENLKDFLLVIPFDCWEP 141
               SCOP domains d1csga_ A: Granulocyte-macrophage colony-stimulating factor (GM-CSF)                                                     SCOP domains
               CATH domains 1csgA00 A:5-124  [code=1.20.1250.10, no name defined]                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhh..........eeeeee...........hhhhhhhhhh.........hhhhhhhhhhhhh...........eeeeehhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------I-T------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------GM_CSF   ---------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:5-36           Exon 1.2      Exon 1.3  PDB: A:51-92 UniProt: 68-109    Exon 1.4  PDB: A:93-124          Transcript 1
                 1csg A   5 SPSPSTQPWEHVNAIQEARRLLNLSRDTAAEMNETVEVISEMFDLQEPTCLQTRLELYKQGLRGSLTKLKGPLTMMASHYKQHCPPTPETSCATQIITFESFKENLKDFLLVIPFDCWEP 124
                                    14        24        34        44        54        64        74        84        94       104       114       124


Chain B from PDB  Type:PROTEIN  Length:120
 aligned with CSF2_HUMAN | P04141 from UniProtKB/Swiss-Prot  Length:144

    Alignment length:120
                                    31        41        51        61        71        81        91       101       111       121       131       141
           CSF2_HUMAN    22 SPSPSTQPWEHVNAIQEARRLLNLSRDTAAEMNETVEVISEMFDLQEPTCLQTRLELYKQGLRGSLTKLKGPLTMMASHYKQHCPPTPETSCATQIITFESFKENLKDFLLVIPFDCWEP 141
               SCOP domains d1csgb_ B: Granulocyte-macrophage colony-stimulating factor (GM-CSF)                                                     SCOP domains
               CATH domains 1csgB00 B:5-124  [code=1.20.1250.10, no name defined]                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhh..........eeeeee...........hhhhhhhhhh.........hhhhhhhhhhhhh...........eeeeehhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------I-T------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------GM_CSF   ---------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:5-36           Exon 1.2      Exon 1.3  PDB: B:51-92 UniProt: 68-109    Exon 1.4  PDB: B:93-124          Transcript 1
                 1csg B   5 SPSPSTQPWEHVNAIQEARRLLNLSRDTAAEMNETVEVISEMFDLQEPTCLQTRLELYKQGLRGSLTKLKGPLTMMASHYKQHCPPTPETSCATQIITFESFKENLKDFLLVIPFDCWEP 124
                                    14        24        34        44        54        64        74        84        94       104       114       124
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (29, 29)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (CSF2_HUMAN | P04141)
molecular function
    GO:0005088    Ras guanyl-nucleotide exchange factor activity    Stimulates the exchange of guanyl nucleotides associated with a GTPase of the Ras superfamily. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
    GO:0005125    cytokine activity    Functions to control the survival, growth, differentiation and effector function of tissues and cells.
    GO:0005129    granulocyte macrophage colony-stimulating factor receptor binding    Interacting selectively and non-covalently with the granulocyte macrophage colony-stimulating factor receptor.
    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: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:0004713    protein tyrosine kinase activity    Catalysis of the reaction: ATP + a protein tyrosine = ADP + protein tyrosine phosphate.
biological process
    GO:0000165    MAPK cascade    An intracellular protein kinase cascade containing at least a MAPK, a MAPKK and a MAP3K. The cascade can also contain two additional tiers: the upstream MAP4K and the downstream MAP Kinase-activated kinase (MAPKAPK). The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell.
    GO:0071222    cellular response to lipopolysaccharide    Any process that results in a change in state or activity of a cell (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.
    GO:0097028    dendritic cell differentiation    The process in which a precursor cell type acquires the specialized features of a dendritic cell. A dendritic cell is a leukocyte of dendritic lineage specialized in the uptake, processing, and transport of antigens to lymph nodes for the purpose of stimulating an immune response via T cell activation.
    GO:0001892    embryonic placenta development    The embryonically driven process whose specific outcome is the progression of the placenta over time, from its formation to the mature structure. The placenta is an organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin.
    GO:0042045    epithelial fluid transport    The directed movement of fluid across epithelia.
    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:0042116    macrophage activation    A change in morphology and behavior of a macrophage resulting from exposure to a cytokine, chemokine, cellular ligand, or soluble factor.
    GO:0043011    myeloid dendritic cell differentiation    The process in which a monocyte acquires the specialized features of a dendritic cell, an immunocompetent cell of the lymphoid and hemopoietic systems and skin.
    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:0018108    peptidyl-tyrosine phosphorylation    The phosphorylation of peptidyl-tyrosine to form peptidyl-O4'-phospho-L-tyrosine.
    GO:0045740    positive regulation of DNA replication    Any process that activates or increases the frequency, rate or extent of DNA replication.
    GO:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    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:0032747    positive regulation of interleukin-23 production    Any process that activates or increases the frequency, rate, or extent of interleukin-23 production.
    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:0071803    positive regulation of podosome assembly    Any process that activates or increases the rate or extent of podosome assembly.
    GO:0042127    regulation of cell proliferation    Any process that modulates the frequency, rate or extent of cell proliferation.
    GO:0010468    regulation of gene expression    Any process that modulates 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.
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:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CSF2_HUMAN | P04141: 2gmf 4nkq 4rs1 5c7x 5d70 5d71 5d72

(-) Related Entries Specified in the PDB File

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