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(-) Description

Title :  STRUCTURE OF A CLASS III RTK SIGNALING ASSEMBLY
 
Authors :  H. Liu, X. Chen, P. Focia, X. He
Date :  29 Nov 06  (Deposition) - 13 Mar 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A (1x),B (1x)
Keywords :  Stem Cell Factor, Receptor Tyrosine Kinase, Class Iii, Receptor/Ligand Complex, Growth Factor, Cytokine, 4-Helix Bundle, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Liu, X. Chen, P. J. Focia, X. He
Structural Basis For Stem Cell Factor-Kit Signaling And Activation Of Class Iii Receptor Tyrosine Kinases.
Embo J. V. 26 891 2007
PubMed-ID: 17255936  |  Reference-DOI: 10.1038/SJ.EMBOJ.7601545
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - KIT LIGAND
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPGEX-4T-1
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentRESIDUES 28-166
    GeneKITLG, KITL, MGF, SL, SLF
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymC-KIT LIGAND, STEM CELL FACTOR, SCF, MAST CELL GROWTH FACTOR, MGF, HEMATOPOIETIC GROWTH FACTOR KL, STEEL FACTOR

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)AB
Biological Unit 2 (1x)A (1x)B (1x)

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2O27)

(-) Sites  (0, 0)

(no "Site" information available for 2O27)

(-) SS Bonds  (3, 3)

Asymmetric Unit
No.Residues
1A:4 -A:89
2A:43 -A:138
3B:43 -B:138

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2O27)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_SCF_MOUSE_001 *N122SSCF_MOUSE  ---  ---A/BN97S
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_SCF_MOUSE_001 *N122SSCF_MOUSE  ---  ---A/BN97S
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_SCF_MOUSE_001 *N122SSCF_MOUSE  ---  ---A/BN97S
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2O27)

(-) Exons   (0, 0)

(no "Exon" information available for 2O27)

(-) Sequences/Alignments

Asymmetric 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:126
 aligned with SCF_MOUSE | P20826 from UniProtKB/Swiss-Prot  Length:273

    Alignment length:138
                                    38        48        58        68        78        88        98       108       118       128       138       148       158        
            SCF_MOUSE    29 CGNPVTDNVKDITKLVANLPNDYMITLNYVAGMDVLPSHCWLRDMVIQLSLSLTTLLDKFSNISEGLSNYSIIDKLGKIVDDLVLCMEENAPKNIKESPKRPETRSFTPEEFFSIFNRSIDAFKDFMVASDTSDCVLS 166
               SCOP domains d2o    27a_ A: automated matches                                                                                                           SCOP domains
               CATH domains 2o2    7A00 A:4-141  [code=1.20.1250.10, no name defined]                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...----...hhhhhhhh......eeeee.......hhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhh....--.....eeeeehhhhhhhhhhhhhhhhh..------...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------S-------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2o27 A   4 CGN----NVKDITKLVANLPNDYMITLNYVAGMDVLPSHCWLRDMVIQLSLSLTTLLDKFSNISEGLSNYSIIDKLGKIVDDLVLCMEENAPKNI--SPKRPETRSFTPEEFFSIFNRSIDAFKDF------SDCVLS 141
                              |    |13        23        33        43        53        63        73        83        93    |  103       113       123     |   -  |     
                              6   11                                                                                     98  |                         129    136     
                                                                                                                           101                                        

Chain B from PDB  Type:PROTEIN  Length:125
 aligned with SCF_MOUSE | P20826 from UniProtKB/Swiss-Prot  Length:273

    Alignment length:133
                                    43        53        63        73        83        93       103       113       123       133       143       153       163   
            SCF_MOUSE    34 TDNVKDITKLVANLPNDYMITLNYVAGMDVLPSHCWLRDMVIQLSLSLTTLLDKFSNISEGLSNYSIIDKLGKIVDDLVLCMEENAPKNIKESPKRPETRSFTPEEFFSIFNRSIDAFKDFMVASDTSDCVLS 166
               SCOP domains d2o27b_ B: automated matches                                                                                                          SCOP domains
               CATH domains 2o27B00 B:9-141  [code=1.20.1250.10, no name defined]                                                                                 CATH domains
           Pfam domains (1) SCF-2o27B01 B:9-141                                                                                                                   Pfam domains (1)
           Pfam domains (2) SCF-2o27B02 B:9-141                                                                                                                   Pfam domains (2)
         Sec.struct. author .....hhhhhhhh......eeeee.......hhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh......--.....eeeeehhhhhhhhhhhhhhhhh...------..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------S-------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2o27 B   9 TDNVKDITKLVANLPNDYMITLNYVAGMDVLPSHCWLRDMVIQLSLSLTTLLDKFSNISEGLSNYSIIDKLGKIVDDLVLCMEENAPKNI--SPKRPETRSFTPEEFFSIFNRSIDAFKDFM------DCVLS 141
                                    18        28        38        48        58        68        78        88        98  |    108       118       128 |     138   
                                                                                                                    98  |                          130    137    
                                                                                                                      101                                        

   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 Unit

(-) CATH Domains  (1, 2)

Asymmetric Unit

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (31, 31)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (SCF_MOUSE | P20826)
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: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:0005173    stem cell factor receptor binding    Interacting selectively and non-covalently with the stem cell factor receptor (SCFR), a type III transmembrane kinase receptor.
biological process
    GO:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
    GO:0035234    ectopic germ cell programmed cell death    Programmed cell death of an errant germ line cell that is outside the normal migratory path or ectopic to the gonad. This is an important mechanism of regulating germ cell survival within the embryo.
    GO:0035162    embryonic hemopoiesis    The stages of blood cell formation that take place within the embryo.
    GO:0097192    extrinsic apoptotic signaling pathway in absence of ligand    A series of molecular signals in which a signal is conveyed from the cell surface to trigger the apoptotic death of a cell. The pathway starts with withdrawal of a ligand from a cell surface receptor, and ends when the execution phase of apoptosis is triggered.
    GO:0007281    germ cell development    The process whose specific outcome is the progression of an immature germ cell over time, from its formation to the mature structure (gamete). A germ cell is any reproductive cell in a multicellular organism.
    GO:0008584    male gonad development    The process whose specific outcome is the progression of the male gonad over time, from its formation to the mature structure.
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:0033026    negative regulation of mast cell apoptotic process    Any process that stops, prevents, or reduces the frequency, rate, or extent of mast cell apoptotic process.
    GO:0001755    neural crest cell migration    The characteristic movement of cells from the dorsal ridge of the neural tube to a variety of locations in a vertebrate embryo.
    GO:0001541    ovarian follicle development    The process whose specific outcome is the progression of the ovarian follicle over time, from its formation to the mature structure.
    GO:0045740    positive regulation of DNA replication    Any process that activates or increases the frequency, rate or extent of DNA replication.
    GO:0043406    positive regulation of MAP kinase activity    Any process that activates or increases the frequency, rate or extent of MAP kinase activity.
    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:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    GO:1902035    positive regulation of hematopoietic stem cell proliferation    Any process that activates or increases the frequency, rate or extent of hematopoietic stem cell proliferation.
    GO:0002687    positive regulation of leukocyte migration    Any process that activates or increases the frequency, rate, or extent of leukocyte migration.
    GO:0070668    positive regulation of mast cell proliferation    Any process that activates or increases the rate or extent of mast cell proliferation.
    GO:0045636    positive regulation of melanocyte differentiation    Any process that activates or increases the frequency, rate or extent of melanocyte differentiation.
    GO:0002763    positive regulation of myeloid leukocyte differentiation    Any process that activates or increases the frequency, rate, or extent of myeloid leukocyte differentiation.
    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    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: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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        SCF_MOUSE | P208262o26

(-) Related Entries Specified in the PDB File

2o26 STRUCTURE OF A CLASS III RTK SIGNALING ASSEMBLY