1KA7 - JenaLib

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NMR Structure - model 1 (Jmol Viewer)

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Title :   SAP/SH2D1A BOUND TO PEPTIDE N-Y-C

Authors :   P. M. Hwang, C. Li, M. Morra, J. Lillywhite, F. Gertler, C. Terhorst, L. E. Kay, T. Pawson, J. Forman-Kay, S. -C. Li

Date :   31 Oct 01 (Deposition) - 07 Nov 01 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A,B

Keywords :   Sh2 Domain, Protein-Peptide Complex, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. M. Hwang, C. Li, M. Morra, J. Lillywhite, D. R. Muhandiram, F. Gertler, C. Terhorst, L. E. Kay, T. Pawson, J. D. Forman-Kay, S. C. Li
A "Three-Pronged" Binding Mechanism For The Sap/Sh2D1A Sh2 Domain: Structural Basis And Relevance To The Xlp Syndrome.
Embo J. V. 21 314 2002
PubMed-ID: 11823424 | Reference-DOI: 10.1093/EMBOJ/21.3.314
(for further references see the PDB file header)

Molecule 1 - SH2 DOMAIN PROTEIN 1A
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET3A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	SLAM-ASSOCIATED PROTEIN

Molecule 2 - PEPTIDE N-Y-C
	Chains	:	B
	Engineered	:	YES
	Fragment	:	CYTOPLASMIC REGION (RESIDUES 275-286)
	Mutation	:	YES
	Other Details	:	THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED (SOLID PHASE SYNTHESIS). THE SEQUENCE OF THE PEPTIDE IS NATURALLY FOUND IN HOMO SAPIENS (HUMAN).
	Synonym	:	SIGNALING LYMPHOCYTIC ACTIVATION MOLECULE
	Synthetic	:	YES


NMR Structure	:

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1KA7)

(no "Site" information available for 1KA7)

(no "SS Bond" information available for 1KA7)

(no "Cis Peptide Bond" information available for 1KA7)

NMR Structure (20, 20)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_048005	Y	7	C	SH21A_HUMAN	Disease (XLP1)	---	A	Y	7	C
02	UniProt	VAR_048006	H	8	D	SH21A_HUMAN	Disease (XLP1)	---	A	H	8	D
03	UniProt	VAR_048007	G	16	D	SH21A_HUMAN	Disease (XLP1)	---	A	G	16	D
04	UniProt	VAR_048008	G	27	S	SH21A_HUMAN	Disease (XLP1)	---	A	G	27	S
05	UniProt	VAR_048009	S	28	R	SH21A_HUMAN	Disease (XLP1)	---	A	S	28	R
06	UniProt	VAR_048010	L	31	P	SH21A_HUMAN	Disease (XLP1)	---	A	L	31	P
07	UniProt	VAR_005612	R	32	T	SH21A_HUMAN	Disease (XLP1)	111033624	A	R	32	T
08	UniProt	VAR_048011	D	33	Y	SH21A_HUMAN	Disease (XLP1)	---	A	D	33	Y
09	UniProt	VAR_048012	C	42	W	SH21A_HUMAN	Disease (XLP1)	---	A	C	42	W
10	UniProt	VAR_048013	G	49	V	SH21A_HUMAN	Disease (XLP1)	---	A	G	49	V
11	UniProt	VAR_048014	T	53	I	SH21A_HUMAN	Disease (XLP1)	---	A	T	53	I
12	UniProt	VAR_048015	Y	54	C	SH21A_HUMAN	Disease (XLP1)	---	A	Y	54	C
13	UniProt	VAR_018307	R	55	L	SH21A_HUMAN	Disease (XLP1)	111033630	A	R	55	L
14	UniProt	VAR_048016	S	57	P	SH21A_HUMAN	Unclassified	---	A	S	57	P
15	UniProt	VAR_005613	T	68	I	SH21A_HUMAN	Disease (XLP1)	111033627	A	T	68	I
16	UniProt	VAR_048017	I	84	T	SH21A_HUMAN	Disease (XLP1)	---	A	I	84	T
17	UniProt	VAR_048018	F	87	S	SH21A_HUMAN	Disease (XLP1)	---	A	F	87	S
18	UniProt	VAR_048019	Q	99	P	SH21A_HUMAN	Disease (XLP1)	---	A	Q	99	P
19	UniProt	VAR_005614	P	101	L	SH21A_HUMAN	Disease (XLP1)	28935184	A	P	101	L
20	UniProt	VAR_048020	V	102	G	SH21A_HUMAN	Disease (XLP1)	---	A	V	102	G

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

NMR Structure (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SH2	PS50001	Src homology 2 (SH2) domain profile.	SH21A_HUMAN	6-102	1	A:6-102

NMR Structure (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000302035	1a	ENSE00001850818	chr1:160617085-160616660	426	SLAF1_HUMAN	1-26	26	0	-	-
1.2c	ENST00000302035	2c	ENSE00001166217	chr1:160607319-160606981	339	SLAF1_HUMAN	26-139	114	0	-	-
1.3	ENST00000302035	3	ENSE00001166212	chr1:160604687-160604403	285	SLAF1_HUMAN	139-234	96	0	-	-
1.4	ENST00000302035	4	ENSE00001166202	chr1:160593975-160593886	90	SLAF1_HUMAN	234-264	31	0	-	-
1.5	ENST00000302035	5	ENSE00001166196	chr1:160589639-160589566	74	SLAF1_HUMAN	264-288	25	1	B:275-286	12
1.7	ENST00000302035	7	ENSE00001166189	chr1:160582370-160582278	93	SLAF1_HUMAN	289-319	31	0	-	-
1.8b	ENST00000302035	8b	ENSE00001820545	chr1:160580588-160577890	2699	SLAF1_HUMAN	320-335	16	0	-	-

2.1a	ENST00000371139	1a	ENSE00001920695	X:123480194-123480629	436	SH21A_HUMAN	1-46	46	1	A:1-46	46
2.3a	ENST00000371139	3a	ENSE00001327828	X:123499611-123499674	64	SH21A_HUMAN	46-67	22	1	A:46-67	22
2.4b	ENST00000371139	4b	ENSE00001306519	X:123504026-123504170	145	SH21A_HUMAN	68-116	49	1	A:68-107	40
2.5c	ENST00000371139	5c	ENSE00001917567	X:123505201-123507005	1805	SH21A_HUMAN	116-128	13	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
	(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:107
 aligned with SH21A_HUMAN | O60880 from UniProtKB/Swiss-Prot  Length:128

    Alignment length:107
                                    10        20        30        40        50        60        70        80        90       100       
          SH21A_HUMAN     1 MDAVAVYHGKISRETGEKLLLATGLDGSYLLRDSESVPGVYCLCVLYHGYIYTYRVSQTETGSWSAETAPGVHKRYFRKIKNLISAFQKPDQGIVIPLQYPVEKKSS 107
               SCOP domains d1ka7a_ A: The Xlp protein Sap                                                                              SCOP domains
               CATH domains 1ka7A00 A:1-107 SHC Adaptor Protein                                                                         CATH domains
               Pfam domains -----SH2-1ka7A01 A:6-87                                                                -------------------- Pfam domains
         Sec.struct. author ......eee..hhhhhhhhhhhhh...eeeeee.......eeeeeee..eeeeeeeee.....eee..............hhhhhhhh...........ee...... Sec.struct. author
                 SAPs(SNPs) ------CD-------D----------SR--PTY--------W------V---ICL-P----------I---------------T--S-----------P-LG----- SAPs(SNPs)
                    PROSITE -----SH2  PDB: A:6-102 UniProt: 6-102                                                                 ----- PROSITE
           Transcript 2 (1) Exon 2.1a  PDB: A:1-46 UniProt: 1-46          ---------------------Exon 2.4b  PDB: A:68-107 UniProt: 68-116 Transcript 2 (1)
           Transcript 2 (2) ---------------------------------------------Exon 2.3a  PDB: A:46-6---------------------------------------- Transcript 2 (2)
                 1ka7 A   1 MDAVAVYHGKISRETGEKLLLATGLDGSYLLRDSESVPGVYCLCVLYHGYIYTYRVSQTETGSWSAETAPGVHKRYFRKIKNLISAFQKPDQGIVIPLQYPVEKKSS 107
                                    10        20        30        40        50        60        70        80        90       100

Chain B from PDB  Type:PROTEIN  Length:12
 aligned with SLAF1_HUMAN | Q13291 from UniProtKB/Swiss-Prot  Length:335

    Alignment length:12
                                   284  
          SLAF1_HUMAN   275 KKSLTIYAQVQK 286
               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 1 Exon 1.5     Transcript 1
                 1ka7 B 275 RKSLTIYAQVQK 286
                                   284

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 '\|'

NMR Structure

Classes(

)

Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: SH2-like (260)

Superfamily: SH2 domain (260)

Family: SH2 domain (225)

Protein domain: The Xlp protein Sap (6)

Human (Homo sapiens) [TaxId: 9606] (6)

d1ka7a_

NMR Structure

Classes(

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Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: SHC Adaptor Protein (206)

Homologous Superfamily: SHC Adaptor Protein (206)

Human (Homo sapiens) (147)

1ka7A00

A:1-107

NMR Structure

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: SH2] (119)

Family: SH2 (119)

Homo sapiens (Human) (79)

SH2-1ka7A01

A:6-87

NMR Structure(hide GO term definitions)

Chain A (SH21A_HUMAN | O60880)

molecular function
	GO:0005070	SH3/SH2 adaptor activity	Interacting selectively and non-covalently and simultaneously with one or more signal transduction molecules, usually acting as a scaffold to bring these molecules into close proximity either using their own SH2/SH3 domains (e.g. Grb2) or those of their target molecules (e.g. SAM68).
	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).
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:0007267	cell-cell signaling	Any process that mediates the transfer of information from one cell to another. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell. Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions.
	GO:0006968	cellular defense response	A defense response that is mediated by cells.
	GO:0006959	humoral immune response	An immune response mediated through a body fluid.
	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:0045954	positive regulation of natural killer cell mediated cytotoxicity	Any process that activates or increases the frequency, rate or extent of natural killer cell mediated cytotoxicity.
	GO:0009967	positive regulation of signal transduction	Any process that activates or increases the frequency, rate or extent of signal transduction.
	GO:0050776	regulation of immune response	Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
cellular component
	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.

Chain B (SLAF1_HUMAN | Q13291)

molecular function
	GO:0003823	antigen binding	Interacting selectively and non-covalently with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen.
	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:0004872	receptor activity	Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
	GO:0004888	transmembrane signaling receptor activity	Combining with an extracellular or intracellular signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity or state as part of signal transduction.
	GO:0001618	virus receptor activity	Combining with a virus component and mediating entry of the virus into the cell.
biological process
	GO:0035744	T-helper 1 cell cytokine production	Any process that contributes to cytokine production by a T-helper 1 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: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: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:0046649	lymphocyte activation	A change in morphology and behavior of a lymphocyte resulting from exposure to a specific antigen, mitogen, cytokine, chemokine, cellular ligand, or soluble factor.
	GO:0002277	myeloid dendritic cell activation involved in immune response	The change in morphology and behavior of a myeloid dendritic cell resulting from exposure to a cytokine, chemokine, cellular ligand, or soluble factor, leading to the initiation or perpetuation of an immune response.
	GO:0001779	natural killer cell differentiation	The process in which a relatively unspecialized cell acquires the specialized features of a natural killer cell.
	GO:0001787	natural killer cell proliferation	The expansion of a natural killer cell population by cell division.
	GO:2000349	negative regulation of CD40 signaling pathway	Any process that stops, prevents or reduces the frequency, rate or extent of signaling via the CD40 signaling pathway.
	GO:0002725	negative regulation of T cell cytokine production	Any process that stops, prevents, or reduces the frequency, rate, or extent of T cell cytokine production.
	GO:1902714	negative regulation of interferon-gamma secretion	Any process that stops, prevents or reduces the frequency, rate or extent of interferon-gamma secretion.
	GO:0032695	negative regulation of interleukin-12 production	Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-12 production.
	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:0032720	negative regulation of tumor necrosis factor production	Any process that stops, prevents, or reduces the frequency, rate, or extent of tumor necrosis factor production.
	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:0070374	positive regulation of ERK1 and ERK2 cascade	Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade.
	GO:0046330	positive regulation of JNK cascade	Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the JNK cascade.
	GO:0042104	positive regulation of activated T cell proliferation	Any process that activates or increases the rate or extent of activated T cell proliferation.
	GO:0008284	positive regulation of cell proliferation	Any process that activates or increases the rate or extent of cell proliferation.
	GO:1902715	positive regulation of interferon-gamma secretion	Any process that activates or increases the frequency, rate or extent of interferon-gamma secretion.
	GO:0050790	regulation of catalytic activity	Any process that modulates the activity of an enzyme.
	GO:0031338	regulation of vesicle fusion	Any process that modulates the frequency, rate or extent of vesicle fusion.
	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:0046718	viral entry into host cell	The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
	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:0009986	cell surface	The external part of the cell wall and/or plasma membrane.
	GO:0009897	external side of plasma membrane	The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
	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: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: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:0045335	phagocytic vesicle	A membrane-bounded intracellular vesicle that arises from the ingestion of particulate material by phagocytosis.
	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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	1ka7
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UniProtKB/Swiss-Prot
	SH21A_HUMAN \| O60880	:	1d1z 1d4t 1d4w 1ka6 1m27
	SLAF1_HUMAN \| Q13291	:	1d4t 1d4w 1i3z 1ka6 1m27 2dzf 2ie9 2ifl 2ig5

1ka6	SAP/SH2D1A BOUND TO PEPTIDE N-PY

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (20, 20)

PROSITE Motifs (1, 1)

Exons (4, 4)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (1, 1)

Gene Ontology (48, 52)

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