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NMR Structure - model 1 (Jmol Viewer)

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Description

Title :   SOLUTION STRUCTURE OF THE SH3 DOMAIN OF HUMAN OSTEOCLAST STIMULATING FACTOR 1 (OSTF1)

Authors :   Y. O. Kamatari, T. Tomizawa, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   25 Apr 05 (Deposition) - 25 Oct 05 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Sh3 Domain, Human Osteoclast Stimulating Factor 1, Ostf1, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. O. Kamatari, T. Tomizawa, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama
Solution Structure Of The Sh3 Domain Of Human Osteoclast Stimulating Factor 1 (Ostf1)
To Be Published
PubMed: search
(for further references see the PDB file header)

Compounds

Molecule 1 - OSTEOCLAST STIMULATING FACTOR 1
	Chains	:	A
	Engineered	:	YES
	Expression System Plasmid	:	P040329-95
	Expression System Vector Type	:	PLASMID
	Fragment	:	SH3 DOMAIN
	Gene	:	OSTF1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	CELL-FREE PROTEIN SYNTHESIS
	Synonym	:	OSTF1

Structural Features

Chains, Units


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1X2K)

Sites (0, 0)

(no "Site" information available for 1X2K)

SS Bonds (0, 0)

(no "SS Bond" information available for 1X2K)

Cis Peptide Bonds (0, 0)

(no "Cis Peptide Bond" information available for 1X2K)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

NMR Structure (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_048309	N	48	S	OSTF1_HUMAN	Polymorphism	2295862	A	N	41	S

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

PROSITE Motifs (2, 2)

NMR Structure (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SH3	PS50002	Src homology 3 (SH3) domain profile.	OSTF1_HUMAN	12-71	1	A:7-62
2	ANK_REP_REGION	PS50297	Ankyrin repeat region circular profile.	OSTF1_HUMAN	72-171	1	A:68-68

Exons (6, 6)

NMR Structure (6, 6)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000346234	1	ENSE00001428405	chr9:77703459-77703642	184	OSTF1_HUMAN	1-12	12	1	A:1-7	7
1.2	ENST00000346234	2	ENSE00001023928	chr9:77732420-77732466	47	OSTF1_HUMAN	12-27	16	1	A:7-20 (gaps)	16
1.3	ENST00000346234	3	ENSE00001198586	chr9:77742485-77742535	51	OSTF1_HUMAN	28-44	17	1	A:21-37	17
1.4	ENST00000346234	4	ENSE00000707172	chr9:77745494-77745557	64	OSTF1_HUMAN	45-66	22	1	A:38-59	22
1.5	ENST00000346234	5	ENSE00000803850	chr9:77746686-77746739	54	OSTF1_HUMAN	66-84	19	1	A:59-68 (gaps)	19
1.6	ENST00000346234	6	ENSE00000707175	chr9:77748210-77748317	108	OSTF1_HUMAN	84-120	37	1	A:68-68	1
1.7	ENST00000346234	7	ENSE00000803852	chr9:77749262-77749311	50	OSTF1_HUMAN	120-136	17	0	-	-
1.8	ENST00000346234	8	ENSE00000803853	chr9:77752454-77752532	79	OSTF1_HUMAN	137-163	27	0	-	-
1.9	ENST00000346234	9	ENSE00000803854	chr9:77755750-77755848	99	OSTF1_HUMAN	163-196	34	0	-	-
1.10	ENST00000346234	10	ENSE00001198580	chr9:77761599-77762181	583	OSTF1_HUMAN	196-214	19	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
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Chain A from PDB  Type:PROTEIN  Length:68
 aligned with OSTF1_HUMAN | Q92882 from UniProtKB/Swiss-Prot  Length:214

    Alignment length:79
                                    15        25        35        45        55        65        75         
           OSTF1_HUMAN    6 PKPVKPGQVKVFRALYTFEPRTPDELYFEEGDIIYITDMSDTNWWKGTSKGRTGLIPSNYVAEQAESIDNPLHEAAKRG 84
               SCOP domains d1x2ka_   A: automated matches                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------------------------------------Ank_2-1x2kA01      --------------- Pfam domains (1)
           Pfam domains (2) ------------SH3_1-1x2kA02 A:11-56                         --------------------- Pfam domains (2)
         Sec.struct. author .......--eeeee..................eeeeee.....eeeee....eeeee...eee...---------.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------S------------------------------------ SAPs(SNPs)
                    PROSITE ------SH3  PDB: A:7-62 UniProt: 12-71                             ANK_REP_REGIO PROSITE
           Transcript 1 (1) 1.1    ---------------Exon 1.3         Exon 1.4  PDB: A:38-59-----------------1 Transcript 1 (1)
           Transcript 1 (2) ------Exon 1.2        --------------------------------------Exon 1.5            Transcript 1 (2)
                  1x2k A  1 GSSGSSG--KVFRALYTFEPRTPDELYFEEGDIIYITDMSDTNWWKGTSKGRTGLIPSNYVAEQSG---------PSSG 68
                                  |  8        18        28        38        48        58     |   -     |   
                                  7  8                                                      64        65

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

NMR Structure

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: SH3-like barrel (1035)

Superfamily: SH3-domain (369)

Family: automated matches (114)

Protein domain: automated matches (114)

Human (Homo sapiens) [TaxId: 9606] (74)

d1x2ka_

CATH Domains (0, 0)

(no "CATH Domain" information available for 1X2K)

Pfam Domains (2, 2)

NMR Structure

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Ank (35)

Family: Ank_2 (14)

Homo sapiens (Human) (8)

Ank_2-1x2kA01

A:44-62

Clan: SH3 (175)

Family: SH3_1 (141)

Homo sapiens (Human) (69)

SH3_1-1x2kA02

A:11-56

Gene Ontology (7, 7)

NMR Structure(hide GO term definitions)

Chain A (OSTF1_HUMAN | Q92882)

molecular function
	GO:0017124	SH3 domain binding	Interacting selectively and non-covalently with a SH3 domain (Src homology 3) of a protein, small protein modules containing approximately 50 amino acid residues found in a great variety of intracellular or membrane-associated proteins.
	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:0001503	ossification	The formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance.
	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.
cellular component
	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: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.

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Related Entries

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UniProtKB/Swiss-Prot
	OSTF1_HUMAN \| Q92882	:	1zlm 3ehq 3ehr

Related Entries Specified in the PDB File

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