2OJ2 - JenaLib

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Title :   NMR STRUCTURE ANALYSIS OF THE HEMATOPOETIC CELL KINASE SH3 DOMAIN COMPLEXED WITH AN ARTIFICIAL HIGH AFFINITY LIGAND (PD1)

Authors :   H. Schmidt, S. Hoffmann, T. Tran, M. Stoldt, T. Stangler, K. Wiesehan, D. Willbold

Date :   12 Jan 07 (Deposition) - 30 Jan 07 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

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

Keywords :   Human Hck; Sh3; Src-Type Tyrosine Kinase; Nmr, Signaling Protein, Transferase/Inhibitor Complex, Signaling Protein, Transferase/Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Schmidt, S. Hoffmann, T. Tran, M. Stoldt, T. Stangler, K. Wiesehan, D. Willbold
Solution Structure Of A Hck Sh3 Domain Ligand Complex Reveals Novel Interaction Modes
J. Mol. Biol. V. 365 1517 2007
PubMed-ID: 17141806 | Reference-DOI: 10.1016/J.JMB.2006.11.013
(for further references see the PDB file header)

Molecule 1 - HEMATOPOETIC CELL KINASE, SH3 DOMAIN
	Chains	:	A
	EC Number	:	2.7.1.112
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PGEX6P2
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Fragment	:	SH3
	Gene	:	HCK
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	TYROSINE-PROTEIN KINASE HCK; P59-HCK/P60-HCK

Molecule 2 - ARTIFICIAL PEPTIDE PD1
	Chains	:	B
	Engineered	:	YES
	Other Details	:	THE PEPTIDE WAS IDENTIFIED AS HIGH AFFINITY LIGAND OF HCK-SH3 FROM SCREENING A PHAGE DISPLAYED PEPTIDE LIBARY, ACETYLATED AND AMIDATED
	Synthetic	:	YES


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

NMR Structure (2, 2)

No.	Name	Count	Type	Full Name
1	ACE	1	Mod. Amino Acid	ACETYL GROUP
2	NH2	1	Mod. Amino Acid	AMINO GROUP

NMR Structure (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:56 , TRP A:59 , TRP A:60 , TYR A:72	BINDING SITE FOR RESIDUE ACE B 119
2	AC2	SOFTWARE	LEU B:131	BINDING SITE FOR RESIDUE NH2 B 132

(no "SS Bond" information available for 2OJ2)

(no "Cis Peptide Bond" information available for 2OJ2)

NMR Structure (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_041708	M	105	L	HCK_HUMAN	Polymorphism	55722810	A	M	50	L

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

NMR Structure (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SH3	PS50002	Src homology 3 (SH3) domain profile.	HCK_HUMAN	78-138	1	A:23-83

NMR Structure (5, 5)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1c	ENST00000375852	1c	ENSE00002183369	chr20:30640064-30640289	226	HCK_HUMAN	1-21	21	1	A:1-2	2
1.4a	ENST00000375852	4a	ENSE00001592701	chr20:30659465-30659585	121	HCK_HUMAN	21-61	41	1	A:3-6 (gaps)	30
1.5	ENST00000375852	5	ENSE00000661152	chr20:30661122-30661164	43	HCK_HUMAN	62-76	15	1	A:7-21	15
1.6a	ENST00000375852	6a	ENSE00000661153	chr20:30661519-30661621	103	HCK_HUMAN	76-110	35	1	A:21-55	35
1.7	ENST00000375852	7	ENSE00000661154	chr20:30662426-30662524	99	HCK_HUMAN	110-143	34	1	A:55-86	32
1.8	ENST00000375852	8	ENSE00000661155	chr20:30667577-30667680	104	HCK_HUMAN	143-178	36	0	-	-
1.9	ENST00000375852	9	ENSE00000661156	chr20:30671697-30671846	150	HCK_HUMAN	178-228	51	0	-	-
1.10	ENST00000375852	10	ENSE00000661157	chr20:30672194-30672346	153	HCK_HUMAN	228-279	52	0	-	-
1.11	ENST00000375852	11	ENSE00000661158	chr20:30674431-30674610	180	HCK_HUMAN	279-339	61	0	-	-
1.12	ENST00000375852	12	ENSE00000661159	chr20:30676371-30676447	77	HCK_HUMAN	339-364	26	0	-	-
1.13	ENST00000375852	13	ENSE00001612642	chr20:30681666-30681819	154	HCK_HUMAN	365-416	52	0	-	-
1.14	ENST00000375852	14	ENSE00001636203	chr20:30686807-30686938	132	HCK_HUMAN	416-460	45	0	-	-
1.15d	ENST00000375852	15d	ENSE00001468583	chr20:30689120-30689659	540	HCK_HUMAN	460-526	67	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:86
 aligned with HCK_HUMAN | P08631 from UniProtKB/Swiss-Prot  Length:526

    Alignment length:123
                                    28        38        48        58        68        78        88        98       108       118       128       138   
            HCK_HUMAN    19 APRMGCMKSKFLQVGGNTFSKTETSASPHCPVYVPDPTSTIKPGPNSHNSNTPGIREAGSEDIIVVALYDYEAIHHEDLSFQKGDQMVVLEESGEWWKARSLATRKEGYIPSNYVARVDSLET 141
               SCOP domains --------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------2oj2A01 A:24-86 SH3 Domains                                     CATH domains
               Pfam domains -----------------------------------------------------------------SH3_1-2oj2A01 A:29-75                          ----------- Pfam domains
         Sec.struct. author ..-----------...--------------------------....................eeeee...ee.......ee....eeeeee.....eeeee......eee....eee.hhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------L------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------SH3  PDB: A:23-83 UniProt: 78-138                            --- PROSITE
           Transcript 1 (1) 1.1----------------------------------------Exon 1.5       ---------------------------------Exon 1.7  PDB: A:55-86           Transcript 1 (1)
           Transcript 1 (2) --Exon 1.4a  PDB: A:3-6 (gaps) [INCOMPLETE]--------------Exon 1.6a  PDB: A:21-55            ------------------------------- Transcript 1 (2)
                 2oj2 A   1 GP-----------LGS--------------------------PGPNSHNSNTPGIREAGSEDIIVVALYDYEAIHHEDLSFQKGDQMVVLEESGEWWKARSLATRKEGYIPSNYVARVDSLET  86
                             |       -   | |   -         -         -  |     13        23        33        43        53        63        73        83   
                             2           3 5                          6

Chain B from PDB  Type:PROTEIN  Length:14
                                              
               SCOP domains -------------- SCOP domains
               CATH domains -------------- CATH domains
               Pfam domains -------------- Pfam domains
         Sec.struct. author .............. Sec.struct. author
                 SAPs(SNPs) -------------- SAPs(SNPs)
                    PROSITE -------------- PROSITE
                 Transcript -------------- Transcript
                 2oj2 B 119 xHSKYPLPPLPSLx 132
                            |      128   |
                          119-ACE      132-NH2

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 '\|'

(no "SCOP Domain" information available for 2OJ2)

NMR Structure

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Roll (1513)

Topology: SH3 type barrels. (648)

Homologous Superfamily: SH3 Domains (267)

Human (Homo sapiens) (133)

2oj2A01

A:24-86

NMR Structure

Clans(

)

Families(

)

Organisms( (-)

)

Clan: SH3 (175)

Family: SH3_1 (141)

Homo sapiens (Human) (69)

SH3_1-2oj2A01

A:29-75

NMR Structure(hide GO term definitions)

Chain A (HCK_HUMAN | P08631)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	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: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: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: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:0038096	Fc-gamma receptor signaling pathway involved in phagocytosis	An Fc-gamma receptor signaling pathway that contributes to the endocytic engulfment of external particulate material by phagocytes.
	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: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: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:0006887	exocytosis	A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for exemple of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell.
	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:0006954	inflammatory response	The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
	GO:0045087	innate immune response	Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
	GO:0002758	innate immune response-activating signal transduction	The cascade of processes by which a signal interacts with a receptor, causing a change in the level or activity of a second messenger or other downstream target, and ultimately leading to activation or perpetuation of an innate immune response.
	GO:0007229	integrin-mediated signaling pathway	A series of molecular signals initiated by the binding of extracellular ligand to an integrin on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
	GO:0060333	interferon-gamma-mediated signaling pathway	A series of molecular signals initiated by the binding of interferon-gamma to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription. Interferon gamma is the only member of the type II interferon found so far.
	GO:0043299	leukocyte degranulation	The regulated exocytosis of secretory granules by a leukocyte.
	GO:0002522	leukocyte migration involved in immune response	The movement of a leukocyte within or between different tissues and organs of the body as part of an immune response.
	GO:0031663	lipopolysaccharide-mediated signaling pathway	A series of molecular signals initiated by the binding of a lipopolysaccharide (LPS) to a receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription. Lipopolysaccharides are major components of the outer membrane of Gram-negative bacteria, making them prime targets for recognition by the immune system.
	GO:0007498	mesoderm development	The process whose specific outcome is the progression of the mesoderm over time, from its formation to the mature structure. The mesoderm is the middle germ layer that develops into muscle, bone, cartilage, blood and connective tissue.
	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: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:0018108	peptidyl-tyrosine phosphorylation	The phosphorylation of peptidyl-tyrosine to form peptidyl-O4'-phospho-L-tyrosine.
	GO:0006909	phagocytosis	An endocytosis process that results in the engulfment of external particulate material by phagocytes. The particles are initially contained within phagocytic vacuoles (phagosomes), which then fuse with primary lysosomes to effect digestion of the particles.
	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: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: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:0008360	regulation of cell shape	Any process that modulates the surface configuration of a cell.
	GO:0050690	regulation of defense response to virus by virus	Any viral process that modulates the frequency, rate, or extent of the antiviral response of the host cell or organism.
	GO:0050727	regulation of inflammatory response	Any process that modulates the frequency, rate or extent of the inflammatory response, the immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents.
	GO:0050764	regulation of phagocytosis	Any process that modulates the frequency, rate or extent of phagocytosis, the process in which phagocytes engulf external particulate material.
	GO:0071801	regulation of podosome assembly	Any process that modulates the frequency, rate or extent of podosome assembly.
	GO:0051090	regulation of sequence-specific DNA binding transcription factor activity	Any process that modulates the frequency, rate or extent of the activity of a transcription factor, any factor involved in the initiation or regulation of transcription.
	GO:0045728	respiratory burst after phagocytosis	A phase of elevated metabolic activity, during which oxygen consumption increases, that occurs in neutrophils, monocytes, and macrophages shortly after phagocytosing material. An enhanced uptake of oxygen leads to the production, by an NADH dependent system, of hydrogen peroxide (H2O2), superoxide anions and hydroxyl radicals, which play a part in microbiocidal activity.
	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.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
	GO:0005794	Golgi apparatus	A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
	GO:0005884	actin filament	A filamentous structure formed of a two-stranded helical polymer of the protein actin and associated proteins. Actin filaments are a major component of the contractile apparatus of skeletal muscle and the microfilaments of the cytoskeleton of eukaryotic cells. The filaments, comprising polymerized globular actin molecules, appear as flexible structures with a diameter of 5-9 nm. They are organized into a variety of linear bundles, two-dimensional networks, and three dimensional gels. In the cytoskeleton they are most highly concentrated in the cortex of the cell just beneath the plasma membrane.
	GO:0005901	caveola	A membrane raft that forms small pit, depression, or invagination that communicates with the outside of a cell and extends inward, indenting the cytoplasm and the cell membrane. Examples include flask-shaped invaginations of the plasma membrane in adipocytes associated with caveolin proteins, and minute pits or incuppings of the cell membrane formed during pinocytosis. Caveolae may be pinched off to form free vesicles within the cytoplasm.
	GO:0030054	cell junction	A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
	GO:0042995	cell projection	A prolongation or process extending from a cell, e.g. a flagellum or axon.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0031410	cytoplasmic vesicle	A vesicle found in the cytoplasm of a cell.
	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:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	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:0005925	focal adhesion	Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
	GO:0005764	lysosome	A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
	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:0030133	transport vesicle	Any of the vesicles of the constitutive secretory pathway, which carry cargo from the endoplasmic reticulum to the Golgi, between Golgi cisternae, from the Golgi to the ER (retrograde transport) or to destinations within or outside the cell.

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6581	SEQUENCE-SPECIFIC 1H, 13C AND 15N RESONANCE ASSIGNMENTS OF HEMOPOIETIC CELL KINASE SH3 DOMAINS IN COMPLEX WITH A SYNTHETIC PEPTIDE

Description

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Ligands, Modified Residues, Ions (2, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

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Exons (5, 5)

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