1ZLM - JenaLib

Asym./Biol. Unit - manually

Asym./Biol. Unit

collapse

expand

Asym./Biol. Unit - manually (Jmol Viewer)

Asym./Biol. Unit (Jmol Viewer)

Description

Title :   CRYSTAL STRUCTURE OF THE SH3 DOMAIN OF HUMAN OSTEOCLAST STIMULATING FACTOR

Authors :   L. Chen, Y. Wang, D. Wells, D. Toh, H. Harold, J. Zhou, E. Digiammarino, E. J. Meehan

Date :   06 May 05 (Deposition) - 16 May 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.07

Chains :   Asym./Biol. Unit : A

Keywords :   Beta Barrel, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Chen, Y. Wang, D. Wells, D. Toh, H. Harold, J. Zhou, E. Digiammarino, E. J. Meehan
Structure Of The Sh3 Domain Of Human Osteoclast-Stimulating Factor At Atomic Resolution.
Acta Crystallogr. , Sect. F V. 62 844 2006
PubMed-ID: 16946461 | Reference-DOI: 10.1107/S1744309106030004
(for further references see the PDB file header)

Compounds

Molecule 1 - OSTEOCLAST STIMULATING FACTOR 1
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET28-OSF-SH3
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	SH3 DOMAIN
	Gene	:	OSTF1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Structural Features

Chains, Units

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (0, 0)

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

Sites (0, 0)

(no "Site" information available for 1ZLM)

SS Bonds (0, 0)

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

Cis Peptide Bonds (0, 0)

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

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

Asymmetric/Biological Unit (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	48	S

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

PROSITE Motifs (1, 1)

Asymmetric/Biological Unit (1, 1)

	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:12-69

Exons (5, 5)

Asymmetric/Biological Unit (5, 5)

	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:12-12	1
1.2	ENST00000346234	2	ENSE00001023928	chr9:77732420-77732466	47	OSTF1_HUMAN	12-27	16	1	A:12-27	16
1.3	ENST00000346234	3	ENSE00001198586	chr9:77742485-77742535	51	OSTF1_HUMAN	28-44	17	1	A:28-44	17
1.4	ENST00000346234	4	ENSE00000707172	chr9:77745494-77745557	64	OSTF1_HUMAN	45-66	22	1	A:45-66	22
1.5	ENST00000346234	5	ENSE00000803850	chr9:77746686-77746739	54	OSTF1_HUMAN	66-84	19	1	A:66-69	4
1.6	ENST00000346234	6	ENSE00000707175	chr9:77748210-77748317	108	OSTF1_HUMAN	84-120	37	0	-	-
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

Asymmetric/Biological Unit

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:58
 aligned with OSTF1_HUMAN | Q92882 from UniProtKB/Swiss-Prot  Length:214

    Alignment length:58
                                    21        31        41        51        61        
           OSTF1_HUMAN   12 GQVKVFRALYTFEPRTPDELYFEEGDIIYITDMSDTNWWKGTSKGRTGLIPSNYVAEQ 69
               SCOP domains d1zlma_ A: automated matches                               SCOP domains
               CATH domains 1zlmA00 A:12-69 SH3 Domains                                CATH domains
           Pfam domains (1) ---------------------------------------Ank_2-1zlmA01       Pfam domains (1)
           Pfam domains (2) ------SH3_1-1zlmA02 A:18-63                         ------ Pfam domains (2)
         Sec.struct. author ...eeeee..................eeeeee.....eeeeee..eeeeee...eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------S--------------------- SAPs(SNPs)
                    PROSITE SH3  PDB: A:12-69 UniProt: 12-71                           PROSITE
           Transcript 1 (1) 1---------------Exon 1.3         Exon 1.4  PDB: A:45-66--- Transcript 1 (1)
           Transcript 1 (2) Exon 1.2        --------------------------------------1.5  Transcript 1 (2)
                  1zlm A 12 GQVKVFRALYTFEPRTPDELYFEEGDIIYITDMSDTNWWKGTSKGRTGLIPSNYVAEQ 69
                                    21        31        41        51        61

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)

Asymmetric/Biological Unit

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)

d1zlma_

CATH Domains (1, 1)

Asymmetric/Biological Unit

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)

1zlmA00

A:12-69

Pfam Domains (2, 2)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Ank (35)

Family: Ank_2 (14)

Homo sapiens (Human) (8)

Ank_2-1zlmA01

A:51-69

Clan: SH3 (175)

Family: SH3_1 (141)

Homo sapiens (Human) (69)

SH3_1-1zlmA02

A:18-63

Gene Ontology (7, 7)

Asymmetric/Biological Unit(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.

Visualization

Interactive Views

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1zlm)

	Sites
(no "Sites" information available for 1zlm)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1zlm)

Still Images

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	1zlm
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	OSTF1_HUMAN \| Q92882
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Analysis Tools

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	OSTF1_HUMAN \| Q92882
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
	OSTF1_HUMAN \| Q92882	:	1x2k 3ehq 3ehr

Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1ZLM)