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(-) Description

Title :  CRYSTAL STRUCTURE OF CATALYTIC DOMAIN OF SON OF SEVENLESS (REM-CDC25) IN THE ABSENCE OF RAS
 
Authors :  T. S. Freedman, H. Sondermann, G. D. Friedland, T. Kortemme, D. Bar- Sagi, S. Marqusee, J. Kuriyan
Date :  27 Sep 06  (Deposition) - 31 Oct 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.02
Chains :  Asym./Biol. Unit :  A
Keywords :  Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. S. Freedman, H. Sondermann, G. D. Friedland, T. Kortemme, D. Bar-Sagi, S. Marqusee, J. Kuriyan
A Ras-Induced Conformational Switch In The Ras Activator Son Of Sevenless.
Proc. Natl. Acad. Sci. Usa V. 103 16692 2006
PubMed-ID: 17075039  |  Reference-DOI: 10.1073/PNAS.0608127103
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SON OF SEVENLESS HOMOLOG 1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPPROEXHT
    Expression System StrainBL21*
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentCATALYTIC DOMAIN, RASGEF (RESIDUES 564-1049)
    GeneSOS1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymSOS-1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2II0)

(-) Sites  (0, 0)

(no "Site" information available for 2II0)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2II0)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Pro A:924 -Pro A:925

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (12, 12)

Asymmetric/Biological Unit (12, 12)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_066051L569VSOS1_HUMANPolymorphism200786705AL569V
02UniProtVAR_066052F623ISOS1_HUMANDisease (NS4)  ---AF623I
03UniProtVAR_030437P655LSOS1_HUMANPolymorphism56219475AP655L
04UniProtVAR_030438Y702HSOS1_HUMANDisease (NS4)727505381AY702H
05UniProtVAR_066053A708TSOS1_HUMANPolymorphism140811086AA708T
06UniProtVAR_030439W729LSOS1_HUMANDisease (NS4)  ---AW729L
07UniProtVAR_030440I733FSOS1_HUMANDisease (NS4)574088829AI733F
08UniProtVAR_066054I784TSOS1_HUMANUnclassified  ---AI784T
09UniProtVAR_030441E846KSOS1_HUMANDisease (NS4)397517159AE846K
10UniProtVAR_066055P894RSOS1_HUMANDisease (NS4)  ---AP894R
11UniProtVAR_030442Q977RSOS1_HUMANPolymorphism  ---AQ977R
12UniProtVAR_066056N1011SSOS1_HUMANPolymorphism8192671AN1011S

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

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RASGEF_NTERPS50212 Ras guanine-nucleotide exchange factors N-terminal domain profile.SOS1_HUMAN597-741  1A:597-741
2RASGEF_CATPS50009 Ras guanine-nucleotide exchange factors catalytic domain profile.SOS1_HUMAN780-1019  1A:780-1019
3RASGEFPS00720 Ras Guanine-nucleotide exchange factors domain signature.SOS1_HUMAN927-960  1A:927-960

(-) Exons   (0, 0)

(no "Exon" information available for 2II0)

(-) 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:463
 aligned with SOS1_HUMAN | Q07889 from UniProtKB/Swiss-Prot  Length:1333

    Alignment length:480
                                   575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795       805       815       825       835       845       855       865       875       885       895       905       915       925       935       945       955       965       975       985       995      1005      1015      1025      1035      1045
          SOS1_HUMAN    566 QMRLPSADVYRFAEPDSEENIIFEENMQPKAGIPIIKAGTVIKLIERLTYHMYADPNFVRTFLTTYRSFCKPQELLSLIIERFEIPEPEPTEADRIAIENGDQPLSAELKRFRKEYIQPVQLRVLNVCRHWVEHHFYDFERDAYLLQRMEEFIGTVRGKAMKKWVESITKIIQRKKIARDNGPGHNITFQSSPPTVEWHISRPGHIETFDLLTLHPIEIARQLTLLESDLYRAVQPSELVGSVWTKEDKEINSPNLLKMIRHTTNLTLWFEKCIVETENLEERVAVVSRIIEILQVFQELNNFNGVLEVVSAMNSSPVYRLDHTFEQIPSRQKKILEEAHELSEDHYKKYLAKLRSINPPCVPFFGIYLTNILKTEEGNPEVLKRHGKELINFSKRRKVAEITGEIQQYQNQPYCLRVESDIKRFFENLNPMGNSMEKEFTDYLFNKSLEIEPRNPKPLPRFPKKYSYPLKSPGVRPSNP 1045
               SCOP domains d2ii0a_ A: Son of sevenl       ess protein homolog 1 (sos-1)                                                                                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains --2ii0A01 A:568-741,A:93       1-973 Son of sevenless (SoS) protein Chain: S domain 1                                                                                           --          -----2ii0A02 A:759-930,A:974-1043 Son of sevenless (Sos) protein Chain                                                                                                           2ii0A01 A:568-741,A:931-973                2ii0A02 A:759-930,A:974-1043 Son of sevenless (Sos) protein Chain     -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........hhhhh......eee.-------....eeeehhhhhhhhhh.....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhh......hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh----------................hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh...eeee..eeeeehhhhhhhhhhhhhhhhhh........hhhhhhhhhh.......hhhhhhhhhhhhhhhhh............................ Sec.struct. author
                 SAPs(SNPs) ---V-----------------------------------------------------I-------------------------------L----------------------------------------------H-----T--------------------L---F--------------------------------------------------T-------------------------------------------------------------K-----------------------------------------------R----------------------------------------------------------------------------------R---------------------------------S---------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------------------RASGEF_NTER  PDB: A:597-741 UniProt: 597-741                                                                                                     --------------------------------------RASGEF_CAT  PDB: A:780-1019 UniProt: 780-1019                                                                                                                                                                                                   -------------------------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RASGEF  PDB: A:927-960            ------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                2ii0 A  566 QMRLPSADVYRFAEPDSEENIIFE-------GIPIIKAGTVIKLIERLTYHMYADPNFVRTFLTTYRSFCKPQELLSLIIERFEIPEPEPTEADRIAIENGDQPLSAELKRFRKEYIQPVQLRVLNVCRHWVEHHFYDFERDAYLLQRMEEFIGTVRGKAMKKWVESITKIIQRKKIA----------FQSSPPTVEWHISRPGHIETFDLLTLHPIEIARQLTLLESDLYRAVQPSELVGSVWTKEDKEINSPNLLKMIRHTTNLTLWFEKCIVETENLEERVAVVSRIIEILQVFQELNNFNGVLEVVSAMNSSPVYRLDHTFEQIPSRQKKILEEAHELSEDHYKKYLAKLRSINPPCVPFFGIYLTNILKTEEGNPEVLKRHGKELINFSKRRKVAEITGEIQQYQNQPYCLRVESDIKRFFENLNPMGNSMEKEFTDYLFNKSLEIEPRNPKPLPRFPKKYSYPLKSPGVRPSNP 1045
                                   575       585   |     - |     605       615       625       635       645       655       665       675       685       695       705       715       725       735       | -       755       765       775       785       795       805       815       825       835       845       855       865       875       885       895       905       915       925       935       945       955       965       975       985       995      1005      1015      1025      1035      1045
                                                 589     597                                                                                                                                               743        754                                                                                                                                                                                                                                                                                                   

   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, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2II0)

(-) Gene Ontology  (46, 52)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SOS1_HUMAN | Q07889)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0005096    GTPase activator activity    Binds to and increases the activity of a GTPase, an enzyme that catalyzes the hydrolysis of GTP.
    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:0005089    Rho guanyl-nucleotide exchange factor activity    Stimulates the exchange of guanyl nucleotides associated with a GTPase of the Rho family. 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:0017124    SH3 domain binding    Interacting selectively and non-covalently with a SH3 domain (Src homology 3) of a protein, small protein modules containing approximately 50 amino acid residues found in a great variety of intracellular or membrane-associated proteins.
    GO:0005085    guanyl-nucleotide exchange factor activity    Stimulates the exchange of guanyl nucleotides associated with a GTPase. 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: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:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
biological process
    GO:0001782    B cell homeostasis    The process of regulating the proliferation and elimination of B cells such that the total number of B cells within a whole or part of an organism is stable over time in the absence of an outside stimulus.
    GO:0038128    ERBB2 signaling pathway    A series of molecular signals initiated by binding of a ligand to a member of the ERBB family of receptors on the surface of a cell, where the signal is transmitted by ERBB2. The pathway ends with regulation of a downstream cellular process, e.g. transcription. ERBB2 receptors are themselves unable to bind to ligands, but act as a signal-amplifying tyrosine kinase within a heterodimeric pair.
    GO:0038095    Fc-epsilon receptor signaling pathway    A series of molecular signals initiated by the binding of the Fc portion of immunoglobulin E (IgE) to an Fc-epsilon receptor on the surface of a signal-receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription. The Fc portion of an immunoglobulin is its C-terminal constant region.
    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:0007265    Ras protein signal transduction    A series of molecular signals within the cell that are mediated by a member of the Ras superfamily of proteins switching to a GTP-bound active state.
    GO:0007411    axon guidance    The chemotaxis process that directs the migration of an axon growth cone to a specific target site in response to a combination of attractive and repulsive cues.
    GO:0048514    blood vessel morphogenesis    The process in which the anatomical structures of blood vessels are generated and organized. The blood vessel is the vasculature carrying blood.
    GO:0003209    cardiac atrium morphogenesis    The process in which the cardiac atrium is generated and organized. A cardiac atrium receives blood from a vein and pumps it to a cardiac ventricle.
    GO:0007173    epidermal growth factor receptor signaling pathway    A series of molecular signals initiated by binding of a ligand to the tyrosine kinase receptor EGFR (ERBB1) on the surface of a cell. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
    GO:0061029    eyelid development in camera-type eye    The progression of the eyelid in a camera-type eye from its formation to the mature state. The eyelid is a membranous cover that helps protect and lubricate the eye.
    GO:0001942    hair follicle development    The process whose specific outcome is the progression of the hair follicle over time, from its formation to the mature structure. A hair follicle is a tube-like opening in the epidermis where the hair shaft develops and into which the sebaceous glands open.
    GO:0003007    heart morphogenesis    The developmental process in which the heart is generated and organized. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
    GO:0061384    heart trabecula morphogenesis    The process of shaping a trabecula in the heart. A trabecula is a small, often microscopic, tissue element in the form of a small beam, strut or rod, which generally has a mechanical function. Trabecula are usually but not necessarily, composed of dense collagenous tissue.
    GO:0008286    insulin receptor signaling pathway    The series of molecular signals generated as a consequence of the insulin receptor binding to insulin.
    GO:0050900    leukocyte migration    The movement of a leukocyte within or between different tissues and organs of the body.
    GO:0002260    lymphocyte homeostasis    The process of regulating the proliferation and elimination of lymphocytes such that the total number of lymphocytes within a whole or part of an organism is stable over time in the absence of an outside stimulus.
    GO:1904693    midbrain morphogenesis    The developmental process by which a midbrain is generated and organized.
    GO:0035264    multicellular organism growth    The increase in size or mass of an entire multicellular organism, as opposed to cell growth.
    GO:0048011    neurotrophin TRK receptor signaling pathway    A series of molecular signals initiated by the binding of a neurotrophin 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.
    GO:0060021    palate development    The biological process whose specific outcome is the progression of the palate from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure. The palate is the partition that separates the nasal and oral cavities.
    GO:0003344    pericardium morphogenesis    The process in which the anatomical structure of the pericardium is generated and organized.
    GO:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:0043065    positive regulation of apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
    GO:0045742    positive regulation of epidermal growth factor receptor signaling pathway    Any process that activates or increases the frequency, rate or extent of epidermal growth factor receptor signaling pathway activity.
    GO:0051057    positive regulation of small GTPase mediated signal transduction    Any process that activates or increases the frequency, rate or extent of small GTPase mediated signal transduction.
    GO:0035023    regulation of Rho protein signal transduction    Any process that modulates the frequency, rate or extent of Rho protein signal transduction.
    GO:0033081    regulation of T cell differentiation in thymus    Any process that modulates the frequency, rate or extent of T cell differentiation in the thymus.
    GO:0042129    regulation of T cell proliferation    Any process that modulates the frequency, rate or extent of T cell proliferation.
    GO:2000973    regulation of pro-B cell differentiation    Any process that modulates the frequency, rate or extent of pro-B cell differentiation.
    GO:0051056    regulation of small GTPase mediated signal transduction    Any process that modulates the frequency, rate or extent of small GTPase mediated signal transduction.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0007264    small GTPase mediated signal transduction    Any series of molecular signals in which a small monomeric GTPase relays one or more of the signals.
    GO:0007296    vitellogenesis    The production of yolk. Yolk is a mixture of materials used for embryonic nutrition.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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.
    GO:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
    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.
    GO:0014069    postsynaptic density of dendrite    An electron dense network of proteins within and adjacent to the postsynaptic membrane of the dendrite of asymetric synapses. Its major components include neurotransmitter receptors and the proteins that spatially and functionally organize them such as anchoring and scaffolding molecules, signaling enzymes and cytoskeletal components.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SOS1_HUMAN | Q078891awe 1bkd 1dbh 1nvu 1nvv 1nvw 1nvx 1q9c 1xd2 1xd4 1xdv 3ksy 4nyi 4nyj 4nym 4uru 4urv 4urw 4urx 4ury 4urz 4us0 4us1 4us2

(-) Related Entries Specified in the PDB File

1bkd RAS:SOSCAT COMPLEX
1nvv TERNARY RAS:SOSCAT COMPLEX