1X3A - JenaLib

Title :   SOLUTION STRUCTURE OF THE BSD DOMAIN OF HUMAN SYNAPSE ASSOCIATED PROTEIN 1

Authors :   M. Yoneyama, N. Tochio, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   02 May 05 (Deposition) - 02 Nov 05 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Synapse Associated Protein 1, Bsd Domain, Homolog Of The Drosophila Sap47, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Yoneyama, N. Tochio, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama
Solution Structure Of The Bsd Domain Of Human Synapse Associated Protein 1
To Be Published
PubMed: search
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 20)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (4, 4)

NMR Structure (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000380155	1a	ENSE00001483985	X:16737755-16738022	268	SYAP1_HUMAN	1-59	59	0	-	-
1.2	ENST00000380155	2	ENSE00001150620	X:16753350-16753468	119	SYAP1_HUMAN	59-98	40	1	A:2-7 (gaps)	30
1.3a	ENST00000380155	3a	ENSE00001150613	X:16754289-16754355	67	SYAP1_HUMAN	99-121	23	0	-	-
1.4	ENST00000380155	4	ENSE00001150608	X:16759839-16759912	74	SYAP1_HUMAN	121-145	25	1	A:8-23	16
1.5	ENST00000380155	5	ENSE00001150603	X:16761824-16761963	140	SYAP1_HUMAN	146-192	47	1	A:24-70	47
1.6	ENST00000380155	6	ENSE00001150594	X:16773068-16773216	149	SYAP1_HUMAN	192-242	51	1	A:70-100 (gaps)	42
1.7	ENST00000380155	7	ENSE00001150590	X:16774786-16774844	59	SYAP1_HUMAN	242-261	20	0	-	-
1.8	ENST00000380155	8	ENSE00001150585	X:16775285-16775432	148	SYAP1_HUMAN	262-311	50	0	-	-
1.9	ENST00000380155	9	ENSE00001483909	X:16778355-16783459	5105	SYAP1_HUMAN	311-352	42	0	-	-

Sequences/Alignments

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:100
 aligned with SYAP1_HUMAN | Q96A49 from UniProtKB/Swiss-Prot  Length:352

    Alignment length:176
                                    67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227      
          SYAP1_HUMAN    58 GNYLFNFASAATKKITESVAETAQTIKKSVEEGKIDGIIDKTIIGDFQKEQKKFVEEQHTKKSEAAVPPWVDTNDEETIQQQILALSADKRNFLRDPPAGVQFNFDFDQMYPVALVMLQEDELLSKMRFALVPKLVKEEVFWRNYFYRVSLIKQSAQLTALAAQQQAAGKEEKSNG 233
               SCOP domains ------------------------------------------------------------------------d1x3aa1 A:8-94 Synapse associated protein 1, SYAP1                                     ----------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------BSD-1x3aA01 A:33-94                                           ----------------- Pfam domains
         Sec.struct. author .------.....------------------------.-----------------------------------...hhhhhhhhhhhhh.hhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.--------..---... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------BSD  PDB: A:36-88 UniProt: 158-210                   ----------------------- PROSITE
           Transcript 1 (1) 1.---------------------------------------Exon 1.3a  PDB: -      ------------------------Exon 1.5  PDB: A:24-70 UniProt: 146-192        ----------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -Exon 1.2  PDB: A:2-7 (gaps) [INCOMPLETE]----------------------Exon 1.4  PDB: A:8-23    ----------------------------------------------Exon 1.6  PDB: A:70-100 (gaps)             Transcript 1 (2)
                 1x3a A   1 G------SSGSS------------------------G-----------------------------------TNDEETIQQQILALSADKRNFLRDPPAGVQFNFDFDQMYPVALVMLQEDELLSKMRFALVPKLVKEEVFWRNYFYRVSLIKQSAQLTS--------GP---SSG 100
                            |      | 4 |       -         -      |  -         -         -         -  |     15        25        35        45        55        65        75        85        95        97   |  
                            |      2   6                        7                                   8                                                                                     95       96|  98  
                            1                                                                                                                                                                       97

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)

CATH Domains (0, 0)

Pfam Domains (1, 1)

Gene Ontology (6, 6)

NMR Structure(hide GO term definitions)

Chain A (SYAP1_HUMAN | Q96A49)

molecular function
	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).
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: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:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	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.

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	Cis Peptide Bonds
		Val A:67 - Pro A:68	[ RasMol ]

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