2RSY - JenaLib

NMR Structure - model 1 (Jmol Viewer)

NMR Structure - all models (Jmol Viewer)

Title :   SOLUTION STRUCTURE OF THE SH2 DOMAIN OF CSK IN COMPLEX WITH A PHOSPHOPEPTIDE FROM CBP

Authors :   H. Tanaka, K. Akagi, C. Oneyama, M. Tanaka, Y. Sasaki, T. Kanou, Y. Lee, D. Yokogawa, M. Debenecker, A. Nakagawa, M. Okada, T. Ikegami

Date :   10 Sep 12 (Deposition) - 10 Apr 13 (Release) - 10 Apr 13 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A,B  (20x)
NMR Structure *: A,B  (1x)

Keywords :   Sh2 Domain, Csk, Cbp, Solution Structure, Transferase-Signaling Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Tanaka, K. Akagi, C. Oneyama, M. Tanaka, Y. Sasaki, T. Kanou, Y. Lee, D. Yokogawa, M. Debenecker, A. Nakagawa, M. Okada, T. Ikegami
Identification Of A New Interaction Mode Between The Src Homology 2 (Sh2) Domain Of C-Terminal Src Kinase (Csk) And Csk-Binding Protein (Cbp)/Phosphoprotein Associated With Glycosphingolipid Microdomains (Pag)
J. Biol. Chem. 2013
PubMed: search | Reference-DOI: 10.1074/JBC.M112.439075

Molecule 1 - TYROSINE-PROTEIN KINASE CSK
	Chains	:	A
	EC Number	:	2.7.10.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	ORIGAMI B (DE3)
	Expression System Taxid	:	562
	Expression System Vector	:	PGEX-6P-1
	Expression System Vector Type	:	VECTOR
	Fragment	:	SRC HOMOLOGY 2 DOMAIN, UNP RESIDUES 80-173
	Gene	:	CSK
	Organism Common	:	RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116
	Synonym	:	C-SRC KINASE

Molecule 2 - PHOSPHOPROTEIN ASSOCIATED WITH GLYCOSPHINGOLIPID-ENRICHED MICRODOMAINS 1
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21
	Expression System Taxid	:	562
	Expression System Vector	:	PGEX-6P-1
	Expression System Vector Type	:	VECTOR
	Fragment	:	CBP, UNP RESIDUES 288-321
	Gene	:	PAG1, CBP, PAG
	Organism Common	:	RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116
	Synonym	:	CSK-BINDING PROTEIN, TRANSMEMBRANE PHOSPHOPROTEIN CBP

		1	2
NMR Structure (20x)	:	A	B
NMR Structure * (1x)	:	A	B

Summary Information (see also Sequences/Alignments below)

NMR Structure (1, 1)

No.	Name	Count	Type	Full Name
1	PTR	1	Mod. Amino Acid	O-PHOSPHOTYROSINE

NMR Structure * (1, 1)

No.	Name	Count	Type	Full Name
1	PTR	1	Mod. Amino Acid	O-PHOSPHOTYROSINE

(no "Site" information available for 2RSY)

NMR Structure

No.	Residues
1	A:122	-	A:164

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

(no "SAP(SNP)/Variant" information available for 2RSY)

NMR Structure (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SH2	PS50001	Src homology 2 (SH2) domain profile.	CSK_RAT	82-171	1	A:82-171

NMR Structure * (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SH2	PS50001	Src homology 2 (SH2) domain profile.	CSK_RAT	82-171	1	A:82-171

NMR Structure (3, 3)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENSRNOT00000026358	1	ENSRNOE00000336163	chr8:61386013-61385952	62	CSK_RAT	1-5	5	0	-	-
1.2	ENSRNOT00000026358	2	ENSRNOE00000188473	chr8:61385625-61385512	114	CSK_RAT	6-43	38	0	-	-
1.3	ENSRNOT00000026358	3	ENSRNOE00000188547	chr8:61385399-61385287	113	CSK_RAT	44-81	38	1	A:75-81 (gaps)	8
1.4	ENSRNOT00000026358	4	ENSRNOE00000188616	chr8:61384997-61384778	220	CSK_RAT	81-154	74	1	A:81-154	74
1.5	ENSRNOT00000026358	5	ENSRNOE00000188677	chr8:61383988-61383895	94	CSK_RAT	155-186	32	1	A:155-173	19
1.6	ENSRNOT00000026358	6	ENSRNOE00000188731	chr8:61383701-61383636	66	CSK_RAT	186-208	23	0	-	-
1.7	ENSRNOT00000026358	7	ENSRNOE00000188789	chr8:61383555-61383456	100	CSK_RAT	208-241	34	0	-	-
1.8	ENSRNOT00000026358	8	ENSRNOE00000188836	chr8:61383310-61383220	91	CSK_RAT	241-271	31	0	-	-
1.9	ENSRNOT00000026358	9	ENSRNOE00000188062	chr8:61382971-61382898	74	CSK_RAT	272-296	25	0	-	-
1.10	ENSRNOT00000026358	10	ENSRNOE00000188106	chr8:61382797-61382602	196	CSK_RAT	296-361	66	0	-	-
1.11	ENSRNOT00000026358	11	ENSRNOE00000188155	chr8:61382524-61382438	87	CSK_RAT	362-390	29	0	-	-
1.12	ENSRNOT00000026358	12	ENSRNOE00000217789	chr8:61382198-61381337	862	CSK_RAT	391-450	60	0	-	-

NMR Structure

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
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Chain A from PDB  Type:PROTEIN  Length:99
 aligned with CSK_RAT | P32577 from UniProtKB/Swiss-Prot  Length:450

    Alignment length:100
                                    83        93       103       113       123       133       143       153       163       173
              CSK_RAT    74 GTKLSLMPWFHGKITREQAERLLYPPETGLFLVRESTNYPGDYTLCVSCEGKVEHYRIMYHASKLSIDEEVYFENLMQLVEHYTTDADGLCTRLIKPKVM 173
               SCOP domains d 2rsya_ A: automated matches                                                                        SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .-............hhhhhhhhh......eeeeee.......eeeeeee..eeeeeeeeee..eee........hhhhhhhhhhhh.........ee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------SH2  PDB: A:82-171 UniProt: 82-171                                                        -- PROSITE
           Transcript 1 (1) Exon 1.3-------------------------------------------------------------------------Exon 1.5            Transcript 1 (1)
           Transcript 1 (2) -------Exon 1.4  PDB: A:81-154 UniProt: 81-154                                   ------------------- Transcript 1 (2)
                 2rsy A  75 G-PLGSMPWFHGKITREQAERLLYPPETGLFLVRESTNYPGDYTLCVSCEGKVEHYRIMYHASKLSIDEEVYFENLMQLVEHYTTDADGLCTRLIKPKVM 173
                            | |     83        93       103       113       123       133       143       153       163       173
                            | |                                                                                                 
                           75 |                                                                                                 
                             76

Chain B from PDB  Type:PROTEIN  Length:38
 aligned with PHAG1_RAT | Q9JM80 from UniProtKB/Swiss-Prot  Length:424

    Alignment length:47
                                   284       294       304       314       
            PHAG1_RAT   275 GAEEQAPEAPSGHSKRFSSLSYKSREEDPTLTEEEISAMYSSVNKPG 321
               SCOP domains ----------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------- Pfam domains
         Sec.struct. author .--------...-..................hhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------- PROSITE
                 Transcript ----------------------------------------------- Transcript
                 2rsy B 284 G--------PLG-SKRFSSLSYKSREEDPTLTEEEISAMySSVNKPG 321
                            |      285 | |   294       304       314       
                          284      285 | |                       314-PTR   
                                     287 |                                 
                                       288

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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 '\|'

NMR Structure

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: SH2-like (260)

Superfamily: SH2 domain (260)

Family: automated matches (35)

Protein domain: automated matches (35)

Norway rat (Rattus norvegicus) [TaxId: 10116] (2)

d2rsya_

(no "CATH Domain" information available for 2RSY)

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

NMR Structure(hide GO term definitions)

Chain A (CSK_RAT | P32577)

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: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: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: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: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: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: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.

Chain B (PHAG1_RAT | Q9JM80)

molecular function
	GO:0042169	SH2 domain binding	Interacting selectively and non-covalently with a SH2 domain (Src homology 2) of a protein, a protein domain of about 100 amino-acid residues and belonging to the alpha + beta domain class.
	GO:0005068	transmembrane receptor protein tyrosine kinase adaptor activity	The binding activity of a molecule that brings together a transmembrane receptor protein tyrosine kinase and one or more other molecules, permitting them to function in a coordinated way.
biological process
	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: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:0035556	intracellular signal transduction	The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
	GO:0050868	negative regulation of T cell activation	Any process that stops, prevents, or reduces the frequency, rate or extent of T cell activation.
	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: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: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:0005887	integral component of plasma membrane	The component of the plasma 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: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: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.

NMR Structure
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