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(-) Description

Title :  THE STRUCTURE OF GRANULOCYTE-COLONY-STIMULATING FACTOR AND ITS RELATIONSHIP TO THOSE OF OTHER GROWTH FACTORS
 
Authors :  C. P. Hill, T. D. Osslund, D. Eisenberg
Date :  29 Jan 93  (Deposition) - 31 Jan 94  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Growth Factor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. P. Hill, T. D. Osslund, D. Eisenberg
The Structure Of Granulocyte-Colony-Stimulating Factor And Its Relationship To Other Growth Factors.
Proc. Natl. Acad. Sci. Usa V. 90 5167 1993
PubMed-ID: 7685117  |  Reference-DOI: 10.1073/PNAS.90.11.5167
(for further references see the PDB file header)

(-) Compounds

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

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1RHG)

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:36 -A:42
2B:36 -B:42
3B:64 -B:74
4C:36 -C:42

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 5)

Asymmetric/Biological Unit (2, 5)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_013073L157MCSF3_HUMANPolymorphism2227329A/CL124M
2UniProtVAR_013074A174TCSF3_HUMANPolymorphism2227330A/B/CA141T
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 3)

Asymmetric/Biological Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1INTERLEUKIN_6PS00254 Interleukin-6 / G-CSF / MGF signature.CSF3_HUMAN97-122
 
 		  3A:71-89
B:64-89
C:71-89

(-) Exons   (4, 12)

Asymmetric/Biological Unit (4, 12)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000002254741bENSE00001309996chr17:38171697-3817176771CSF3_HUMAN1-14140--
1.1fENST000002254741fENSE00000950689chr17:38171944-38172107164CSF3_HUMAN14-68553A:9-35
B:9-35
C:9-35		27
27
27
1.2aENST000002254742aENSE00000950690chr17:38172486-38172593108CSF3_HUMAN69-104363A:36-71 (gaps)
B:36-71 (gaps)
C:36-71 (gaps)		36
36
36
1.2cENST000002254742cENSE00000950691chr17:38172738-38172884147CSF3_HUMAN105-153493A:72-120
B:72-120
C:72-120		49
49
49
1.3cENST000002254743cENSE00001268721chr17:38173048-381740661019CSF3_HUMAN154-207543A:121-172 (gaps)
B:121-172 (gaps)
C:121-172 (gaps)		52
52
52

(-) 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 CSF3_HUMAN | P09919 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:167
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       
           CSF3_HUMAN    39 LPQSFLLKCLEQVRKIQGDGAALQEKLVSECATYKLCHPEELVLLGHSLGIPWAPLSSCPSQALQLAGCLSQLHSGLFLYQGLLQALEGISPELGPTLDTLQLDVADFATTIWQQMEELGMAPALQPTQGAMPAFASAFQRRAGGVLVASHLQSFLEVSYRVLRHLA 205
               SCOP domains d1rhga_ A: Granulocyte-colo   ny stimulating factor (G-C         SF)                                                                                                    SCOP domains
               CATH domains 1rhgA00 A:9-172  [code=1.20   .1250.10, no name defined]                                                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhh---hhhh....hhhhh.............---------hhhhhhhhhhhhhhhhhhhhh.hhh....hhhhhhhhhhhhhhhhhhhhhhhh...----------......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------M----------------T------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------INTERLEUKIN_6  PDB: A:71-8----------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1f  PDB: A:9-35        Exon 1.2a  PDB: A:36-71 (gaps)      Exon 1.2c  PDB: A:72-120 UniProt: 105-153        Exon 1.3c  PDB: A:121-172 (gaps) UniProt: 154-207    Transcript 1
                 1rhg A   9 LPQSFLLKCLEQVRKIQGDGAALQEKL---CATYKLCHPEELVLLGHSLGIPWAPL---------LAGCLSQLHSGLFLYQGLLQALEGISPELGPTLDTLQLDVADFATTIWQQMEELGM----------MPAFASAFQRRAGGVLVASHLQSFLEVSYRVLRHLA 172
                                    18        28      |  -|       45        55     |   -     |  75        85        95       105       115       125|        - |     145       155       165       
                                                     35  36                       61        71                                                    126        137                                   


Chain B from PDB  Type:PROTEIN  Length:144
 aligned with CSF3_HUMAN | P09919 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:167
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       
           CSF3_HUMAN    39 LPQSFLLKCLEQVRKIQGDGAALQEKLVSECATYKLCHPEELVLLGHSLGIPWAPLSSCPSQALQLAGCLSQLHSGLFLYQGLLQALEGISPELGPTLDTLQLDVADFATTIWQQMEELGMAPALQPTQGAMPAFASAFQRRAGGVLVASHLQSFLEVSYRVLRHLA 205
               SCOP domains d1rhgb_ B: Granulocyte-colo   ny stimulating factor (G-CSF)                                                                                                             SCOP domains
               CATH domains 1rhgB00 B:9-172  [code=1.20   .1250.10, no name defined]                                                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhh---hhhh....hhhhh................------hhhhhhhhhhhhhhhhhhhhh.hhh...........................--------------......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------T------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------INTERLEUKIN_6  PDB: B:64-8----------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1f  PDB: B:9-35        Exon 1.2a  PDB: B:36-71 (gaps)      Exon 1.2c  PDB: B:72-120 UniProt: 105-153        Exon 1.3c  PDB: B:121-172 (gaps) UniProt: 154-207    Transcript 1
                 1rhg B   9 LPQSFLLKCLEQVRKIQGDGAALQEKL---CATYKLCHPEELVLLGHSLGIPWAPLSSC------LAGCLSQLHSGLFLYQGLLQALEGISPELGPTLDTLQLDVADFATTIWQQME--------------MPAFASAFQRRAGGVLVASHLQSFLEVSYRVLRHLA 172
                                    18        28      |  -|       45        55        |-     |  75        85        95       105       115      |  -         - |     145       155       165       
                                                     35  36                          64     71                                                122            137                                   


Chain C from PDB  Type:PROTEIN  Length:145
 aligned with CSF3_HUMAN | P09919 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:167
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       
           CSF3_HUMAN    39 LPQSFLLKCLEQVRKIQGDGAALQEKLVSECATYKLCHPEELVLLGHSLGIPWAPLSSCPSQALQLAGCLSQLHSGLFLYQGLLQALEGISPELGPTLDTLQLDVADFATTIWQQMEELGMAPALQPTQGAMPAFASAFQRRAGGVLVASHLQSFLEVSYRVLRHLA 205
               SCOP domains d1rhgc_ C: Granulocyte-colo   ny stimulating factor (G-C         SF)                                                                                                    SCOP domains
               CATH domains 1rhgC00 C:9-172  [code=1.20   .1250.10, no name defined]                                                                                                                CATH domains
           Pfam domains (1) ------------IL6-1rhgC01 C:2   1-169                                                                                                                                 --- Pfam domains (1)
           Pfam domains (2) ------------IL6-1rhgC02 C:2   1-169                                                                                                                                 --- Pfam domains (2)
           Pfam domains (3) ------------IL6-1rhgC03 C:2   1-169                                                                                                                                 --- Pfam domains (3)
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhh---hhhh....hhhhh.............---------hhhhhhhhhhhhhhhhhhhhh.hhh....hhhhhhhhhhhhhhhhhhhhhhhh...----------......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------M----------------T------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------INTERLEUKIN_6  PDB: C:71-8----------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1f  PDB: C:9-35        Exon 1.2a  PDB: C:36-71 (gaps)      Exon 1.2c  PDB: C:72-120 UniProt: 105-153        Exon 1.3c  PDB: C:121-172 (gaps) UniProt: 154-207    Transcript 1
                 1rhg C   9 LPQSFLLKCLEQVRKIQGDGAALQEKL---CATYKLCHPEELVLLGHSLGIPWAPL---------LAGCLSQLHSGLFLYQGLLQALEGISPELGPTLDTLQLDVADFATTIWQQMEELGM----------MPAFASAFQRRAGGVLVASHLQSFLEVSYRVLRHLA 172
                                    18        28      |  -|       45        55     |   -     |  75        85        95       105       115       125|        - |     145       155       165       
                                                     35  36                       61        71                                                    126        137
   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, 3)

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

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Clan: 4H_Cytokine (48)
(-)
Family: IL6 (3)
(-)
Homo sapiens (Human) (3)
1aIL6-1rhgC01C:21-169
1bIL6-1rhgC02C:21-169
1cIL6-1rhgC03C:21-169

(-) Gene Ontology  (24, 24)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (CSF3_HUMAN | P09919)
molecular function
    GO:0005125    cytokine activity    Functions to control the survival, growth, differentiation and effector function of tissues and cells.
    GO:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    GO:0005130    granulocyte colony-stimulating factor receptor binding    Interacting selectively and non-covalently with the granulocyte 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.
biological process
    GO:0071345    cellular response to cytokine stimulus    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 cytokine stimulus.
    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: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:0030851    granulocyte differentiation    The process in which a myeloid precursor cell acquires the specialized features of a granulocyte. Granulocytes are a class of leukocytes characterized by the presence of granules in their cytoplasm. These cells are active in allergic immune reactions such as arthritic inflammation and rashes. This class includes basophils, eosinophils and neutrophils.
    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:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:1901215    negative regulation of neuron death    Any process that stops, prevents or reduces the frequency, rate or extent of neuron death.
    GO:2000251    positive regulation of actin cytoskeleton reorganization    Any process that activates or increases the frequency, rate or extent of actin cytoskeleton reorganization.
    GO:0030838    positive regulation of actin filament polymerization    Any process that activates or increases the frequency, rate or extent of actin polymerization.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    GO:0045639    positive regulation of myeloid cell differentiation    Any process that activates or increases the frequency, rate or extent of myeloid cell differentiation.
    GO:0033138    positive regulation of peptidyl-serine phosphorylation    Any process that activates or increases the frequency, rate or extent of the phosphorylation of peptidyl-serine.
    GO:0050731    positive regulation of peptidyl-tyrosine phosphorylation    Any process that activates or increases the frequency, rate or extent of the phosphorylation of peptidyl-tyrosine.
    GO:0014068    positive regulation of phosphatidylinositol 3-kinase signaling    Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the phosphatidylinositol 3-kinase cascade.
    GO:0032092    positive regulation of protein binding    Any process that activates or increases the frequency, rate or extent of protein binding.
    GO:0051897    positive regulation of protein kinase B signaling    Any process that activates or increases the frequency, rate or extent of protein kinase B signaling, a series of reactions mediated by the intracellular serine/threonine kinase protein kinase B.
    GO:0042993    positive regulation of transcription factor import into nucleus    Any process that activates or increases the frequency, rate or extent of the movement of a transcription factor from the cytoplasm to the nucleus.
    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.
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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CSF3_HUMAN | P09919: 1cd9 1gnc 1pgr 2d9q

(-) Related Entries Specified in the PDB File

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