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Title :   THE SOLUTION STRUCTURE OF THE VHS DOMAIN OF HUMAN SIGNAL TRANSDUCING ADAPTOR MOLECULE 2

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

Date :   15 May 05 (Deposition) - 15 Nov 05 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Vhs Domain, Ubiquitin Binding, Stam2, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Tochio, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama
The Solution Structure Of The Vhs Domain Of Human Signal Transducing Adaptor Molecule 2
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - SIGNAL TRANSDUCING ADAPTOR MOLECULE 2
	Chains	:	A
	Engineered	:	YES
	Expression System Plasmid	:	P040607-06
	Expression System Vector Type	:	PLASMID
	Fragment	:	VHS DOMAIN
	Gene	:	STAM2
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	CELL-FREE PROTEIN SYNTHESIS


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1X5B)

(no "Site" information available for 1X5B)

(no "SS Bond" information available for 1X5B)

(no "Cis Peptide Bond" information available for 1X5B)

(no "SAP(SNP)/Variant" information available for 1X5B)

NMR Structure (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	VHS	PS50179	VHS domain profile.	STAM2_HUMAN	16-144	1	A:23-151

NMR Structure (6, 6)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000263904	1a	ENSE00001351655	chr2:153032506-153032117	390	STAM2_HUMAN	1-14	14	1	A:8-21	14
1.2a	ENST00000263904	2a	ENSE00001070314	chr2:153006743-153006659	85	STAM2_HUMAN	14-42	29	1	A:21-49	29
1.3	ENST00000263904	3	ENSE00000964279	chr2:153004814-153004739	76	STAM2_HUMAN	42-67	26	1	A:49-74	26
1.4	ENST00000263904	4	ENSE00000778033	chr2:153004636-153004538	99	STAM2_HUMAN	68-100	33	1	A:75-107	33
1.5	ENST00000263904	5	ENSE00000840594	chr2:153003822-153003676	147	STAM2_HUMAN	101-149	49	1	A:108-156	49
1.6	ENST00000263904	6	ENSE00000778050	chr2:153001471-153001402	70	STAM2_HUMAN	150-173	24	1	A:157-163 (gaps)	13
1.8c	ENST00000263904	8c	ENSE00001070312	chr2:153000527-153000341	187	STAM2_HUMAN	173-235	63	0	-	-
1.9	ENST00000263904	9	ENSE00001070310	chr2:152992117-152992023	95	STAM2_HUMAN	235-267	33	0	-	-
1.10	ENST00000263904	10	ENSE00000778064	chr2:152989998-152989916	83	STAM2_HUMAN	267-294	28	0	-	-
1.11	ENST00000263904	11	ENSE00000778067	chr2:152989774-152989687	88	STAM2_HUMAN	295-324	30	0	-	-
1.12a	ENST00000263904	12a	ENSE00000840600	chr2:152988682-152988628	55	STAM2_HUMAN	324-342	19	0	-	-
1.13a	ENST00000263904	13a	ENSE00000840601	chr2:152982893-152982740	154	STAM2_HUMAN	342-393	52	0	-	-
1.14b	ENST00000263904	14b	ENSE00000778080	chr2:152980449-152980280	170	STAM2_HUMAN	394-450	57	0	-	-
1.15b	ENST00000263904	15b	ENSE00001296024	chr2:152977316-152973315	4002	STAM2_HUMAN	450-525	76	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)
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Chain A from PDB  Type:PROTEIN  Length:163
 aligned with STAM2_HUMAN | O75886 from UniProtKB/Swiss-Prot  Length:525

    Alignment length:169
                                   1                                                                                                                                                                 
                                   | 3        13        23        33        43        53        63        73        83        93       103       113       123       133       143       153         
          STAM2_HUMAN     - -------MPLFTANPFEQDVEKATNEYNTTEDWSLIMDICDKVGSTPNGAKDCLKAIMKRVNHKVPHVALQALTLLGACVANCGKIFHLEVCSRDFATEVRAVIKNKAHPKVCEKLKSLMVEWSEEFQKDPQFSLISATIKSMKEEGITFPPAGSQTVSAAAKNGTSSN 162
               SCOP domains d1x5ba_ A: automated matches                                                                                                                                              SCOP domains
               CATH domains -------------1x5bA01 A:14-148  [code=1.25.40.90, no name defined]                                                                                   --------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhh.......hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh.............------..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------VHS  PDB: A:23-151 UniProt: 16-144                                                                                               ------------------ PROSITE
           Transcript 1 (1) -------Exon 1.1a     ---------------------------Exon 1.3  PDB: A:49-74    Exon 1.4  PDB: A:75-107          Exon 1.5  PDB: A:108-156 UniProt: 101-149        Exon 1.6      Transcript 1 (1)
           Transcript 1 (2) --------------------Exon 1.2a  PDB: A:21-49      ------------------------------------------------------------------------------------------------------------------------ Transcript 1 (2)
                 1x5b A   1 GSSGSSGMPLFTANPFEQDVEKATNEYNTTEDWSLIMDICDKVGSTPNGAKDCLKAIMKRVNHKVPHVALQALTLLGACVANCGKIFHLEVCSRDFATEVRAVIKNKAHPKVCEKLKSLMVEWSEEFQKDPQFSLISATIKSMKEEGITFPPAGSQTS------GPSSG 163
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       | -    |    
                                                                                                                                                                                       158    159

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(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

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Class: All alpha proteins (14657)

Fold: alpha-alpha superhelix (690)

Superfamily: ENTH/VHS domain (36)

Family: automated matches (8)

Protein domain: automated matches (8)

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

d1x5ba_

NMR Structure

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Alpha Horseshoe (399)

Topology: Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat (320)

Homologous Superfamily: [code=1.25.40.90, no name defined] (33)

Human (Homo sapiens) (20)

1x5bA01

A:14-148

(no "Pfam Domain" information available for 1X5B)

NMR Structure(hide GO term definitions)

Chain A (STAM2_HUMAN | O75886)

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).
biological process
	GO:0006914	autophagy	The process in which cells digest parts of their own cytoplasm; allows for both recycling of macromolecular constituents under conditions of cellular stress and remodeling the intracellular structure for cell differentiation.
	GO:0016197	endosomal transport	The directed movement of substances into, out of, or mediated by an endosome, a membrane-bounded organelle that carries materials newly ingested by endocytosis. It passes many of the materials to lysosomes for degradation.
	GO:0006886	intracellular protein transport	The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell.
	GO:0036258	multivesicular body assembly	The aggregation, arrangement and bonding together of a set of components to form a multivesicular body, a type of late endosome in which regions of the limiting endosomal membrane invaginate to form internal vesicles; membrane proteins that enter the internal vesicles are sequestered from the cytoplasm.
	GO:0042059	negative regulation of epidermal growth factor receptor signaling pathway	Any process that stops, prevents, or reduces the frequency, rate or extent of epidermal growth factor receptor signaling pathway activity.
	GO:0015031	protein transport	The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0033565	ESCRT-0 complex	A protein complex required for the recycling of Golgi proteins, formation of lumenal membranes and sorting of ubiquitinated proteins into those membranes. This complex includes Vps1p and Hse1p in yeast and the Hrs and STAM proteins in mammals.
	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:0031901	early endosome membrane	The lipid bilayer surrounding an early endosome.
	GO:0005768	endosome	A vacuole to which materials ingested by endocytosis are delivered.
	GO:0043231	intracellular membrane-bounded organelle	Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.

NMR Structure
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