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(-) Description

Title :  CRYSTAL STRUCTURE OF SH2 DOMAIN OF HUMAN CSK (CARBOXYL-TERMINAL SRC KINASE), C122S MUTANT.
 
Authors :  D. Liu, R. D. Seidel, D. Cowburn
Date :  26 Aug 08  (Deposition) - 10 Nov 09  (Release) - 14 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.31
Chains :  Asym./Biol. Unit :  A
Keywords :  Sh2, Csk, Disulfide, Oxidized Reduced, Atp-Binding, Cell Membrane, Kinase, Membrane, Nucleotide-Binding, Phosphoprotein, Sh2 Domain, Sh3 Domain, Transferase, Tyrosine-Protein Kinase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. Liu, D. Cowburn
Combining Biophysical Methods To Analyze The Disulfide Bond In Sh2 Domain Of C-Terminal Src Kinase.
Biophys Rep V. 2 33 2016
PubMed-ID: 27819029  |  Reference-DOI: 10.1007/S41048-016-0025-4

(-) Compounds

Molecule 1 - TYROSINE-PROTEIN KINASE CSK
    ChainsA
    EC Number2.7.10.2
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPTWIN1
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentCSK, SH2 DOMAIN (UNP RESIDUES 73 TO 178)
    GeneCSK
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    StrainBL21(DE3)
    SynonymC-SRC KINASE, PROTEIN-TYROSINE KINASE CYL

 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 3EAZ)

(-) Sites  (0, 0)

(no "Site" information available for 3EAZ)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3EAZ)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Tyr A:97 -Pro A:98

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH2PS50001 Src homology 2 (SH2) domain profile.CSK_HUMAN82-171  1A:82-171

(-) Exons   (3, 3)

Asymmetric/Biological Unit (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000002200031bENSE00001357268chr15:75074425-75075061637CSK_HUMAN-00--
1.2ENST000002200032ENSE00001357265chr15:75090574-7509065380CSK_HUMAN1-550--
1.3ENST000002200033ENSE00001326572chr15:75090956-75091069114CSK_HUMAN6-43380--
1.4ENST000002200034ENSE00001245986chr15:75091167-75091279113CSK_HUMAN44-81381A:73-819
1.5bENST000002200035bENSE00001245980chr15:75091613-75091832220CSK_HUMAN81-154741A:81-15474
1.6ENST000002200036ENSE00001245972chr15:75092753-7509284694CSK_HUMAN155-186321A:155-17420
1.7ENST000002200037ENSE00001245968chr15:75093022-7509308766CSK_HUMAN186-208230--
1.8ENST000002200038ENSE00001245963chr15:75093164-75093263100CSK_HUMAN208-241340--
1.9ENST000002200039ENSE00001245953chr15:75093353-7509344391CSK_HUMAN241-271310--
1.10ENST0000022000310ENSE00001245942chr15:75093863-7509393674CSK_HUMAN272-296250--
1.11ENST0000022000311ENSE00001163016chr15:75094036-75094231196CSK_HUMAN296-361660--
1.12ENST0000022000312ENSE00001245924chr15:75094338-7509442487CSK_HUMAN362-390290--
1.13bENST0000022000313bENSE00001870511chr15:75094672-75095539868CSK_HUMAN391-450600--

(-) 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:102
 aligned with CSK_HUMAN | P41240 from UniProtKB/Swiss-Prot  Length:450

    Alignment length:102
                                    82        92       102       112       122       132       142       152       162       172  
            CSK_HUMAN    73 AGTKLSLMPWFHGKITREQAERLLYPPETGLFLVRESTNYPGDYTLCVSCDGKVEHYRIMYHASKLSIDEEVYFENLMQLVEHYTSDADGLCTRLIKPKVME 174
               SCOP domains d3eaza_ A: automated matches                                                                           SCOP domains
               CATH domains 3eazA00 A:73-174 SHC Adaptor Protein                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhh.......hhhhhhhhh......eeeeee.......eeeeeee..eeeeee.eee..eee........hhhhhhhhhhhh.........ee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------SH2  PDB: A:82-171 UniProt: 82-171                                                        --- PROSITE
           Transcript 1 (1) Exon 1.4 -------------------------------------------------------------------------Exon 1.6             Transcript 1 (1)
           Transcript 1 (2) --------Exon 1.5b  PDB: A:81-154 UniProt: 81-154                                  -------------------- Transcript 1 (2)
                 3eaz A  73 AGTKLSLMPWFHGKITREQAERLLYPPETGLFLVRESTNYPGDYTLCVSSDGKVEHYRIMYHASKLSIDEEVYFENLMQLVEHYTSDADGLCTRLIKPKVME 174
                                    82        92       102       112       122       132       142       152       162       172  

   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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (53, 53)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CSK_HUMAN | P41240)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004715    non-membrane spanning protein tyrosine kinase activity    Catalysis of the reaction: ATP + protein L-tyrosine = ADP + protein L-tyrosine phosphate by a non-membrane spanning protein.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0070064    proline-rich region binding    Interacting selectively and non-covalently with a proline-rich region, i.e. a region that contains a high proportion of proline residues, in a protein.
    GO:0008022    protein C-terminus binding    Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
    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:0034236    protein kinase A catalytic subunit binding    Interacting selectively and non-covalently with one or both of the catalytic subunits of protein kinase A.
    GO:0004672    protein kinase activity    Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
    GO:0019903    protein phosphatase binding    Interacting selectively and non-covalently with any protein phosphatase.
    GO:0004713    protein tyrosine kinase activity    Catalysis of the reaction: ATP + a protein tyrosine = ADP + protein tyrosine phosphate.
    GO:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0031295    T cell costimulation    The process of providing, via surface-bound receptor-ligand pairs, a second, antigen-independent, signal in addition to that provided by the T cell receptor to augment T cell activation.
    GO:0050852    T cell receptor signaling pathway    A series of molecular signals initiated by the cross-linking of an antigen receptor on a T cell.
    GO:0002250    adaptive immune response    An immune response mediated by cells expressing specific receptors for antigen produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory).
    GO:0034332    adherens junction organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an adherens junction. An adherens junction is a cell junction at which the cytoplasmic face of the plasma membrane is attached to actin filaments.
    GO:0007420    brain development    The process whose specific outcome is the progression of the brain over time, from its formation to the mature structure. Brain development begins with patterning events in the neural tube and ends with the mature structure that is the center of thought and emotion. The brain is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.).
    GO:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0016477    cell migration    The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms.
    GO:0071375    cellular response to peptide hormone 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 peptide hormone stimulus. A peptide hormone is any of a class of peptides that are secreted into the blood stream and have endocrine functions in living animals.
    GO:0007417    central nervous system development    The process whose specific outcome is the progression of the central nervous system over time, from its formation to the mature structure. The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the brain and spinal cord. In those invertebrates with a central nervous system it typically consists of a brain, cerebral ganglia and a nerve cord.
    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: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:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0070373    negative regulation of ERK1 and ERK2 cascade    Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade.
    GO:0042997    negative regulation of Golgi to plasma membrane protein transport    Any process that stops, prevents, or reduces the frequency, rate or extent of the transport of proteins from the Golgi to the plasma membrane.
    GO:0045779    negative regulation of bone resorption    Any process that stops, prevents, or reduces the frequency, rate or extent of bone resorption.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:0032715    negative regulation of interleukin-6 production    Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-6 production.
    GO:0033673    negative regulation of kinase activity    Any process that stops, prevents, or reduces the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0010989    negative regulation of low-density lipoprotein particle clearance    Any process that decreases the rate, frequency or extent of low-density lipoprotein particle clearance. Low-density lipoprotein particle clearance is the process in which a low-density lipoprotein particle is removed from the blood via receptor-mediated endocytosis and its constituent parts degraded.
    GO:0050765    negative regulation of phagocytosis    Any process that stops, prevents, or reduces the frequency, rate or extent of phagocytosis.
    GO:0048709    oligodendrocyte differentiation    The process in which a relatively unspecialized cell acquires the specialized features of an oligodendrocyte. An oligodendrocyte is a type of glial cell involved in myelinating the axons of neurons in the central nervous system.
    GO:0038083    peptidyl-tyrosine autophosphorylation    The phosphorylation by a protein of one or more of its own tyrosine amino acid residues, or a tyrosine residue on an identical protein.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0043406    positive regulation of MAP kinase activity    Any process that activates or increases the frequency, rate or extent of MAP kinase activity.
    GO:0046777    protein autophosphorylation    The phosphorylation by a protein of one or more of its own amino acid residues (cis-autophosphorylation), or residues on an identical protein (trans-autophosphorylation).
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0060368    regulation of Fc receptor mediated stimulatory signaling pathway    Any process that modulates the rate, frequency or extent of the Fc receptor mediated stimulatory signaling pathway. The Fc receptor mediated stimulatory signaling pathway is a series of molecular signals generated as a consequence of a the binding of the Fc portion of an immunoglobulin by an Fc receptor capable of activating or perpetuating an immune response. The Fc portion of an immunoglobulin is its C-terminal constant region.
    GO:0042127    regulation of cell proliferation    Any process that modulates the frequency, rate or extent of cell proliferation.
    GO:0001817    regulation of cytokine production    Any process that modulates the frequency, rate, or extent of production of a cytokine.
    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:0005911    cell-cell junction    A cell junction that forms a connection between two or more cells in a multicellular organism; excludes direct cytoplasmic junctions such as ring canals.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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: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:0031234    extrinsic component of cytoplasmic side of plasma membrane    The component of a plasma membrane consisting of gene products and protein complexes that are loosely bound to its cytoplasmic surface, but not integrated into the hydrophobic region.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0045121    membrane raft    Any of the small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions.
    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
        CSK_HUMAN | P412401byg 1csk 3d7t 3d7u 3eac

(-) Related Entries Specified in the PDB File

1k9a
3eac CRYSTAL STRUCTURE OF SH2 DOMAIN OF HUMAN CSK (CARBOXYL- TERMINAL SRC KINASE), OXIDIZED FORM.