3EHR - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HUMAN OSTEOCLAST STIMULATING FACTOR

Authors :   S. Tong, H. Zhou, Y. Gao, Z. Zhu, X. Zhang, M. Teng, L. Niu

Date :   14 Sep 08 (Deposition) - 04 Aug 09 (Release) - 04 Aug 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Beta Barrel, Helix-Turn-Helix, Sh3, Ankyrin Repeat, Signaling Protein, Ank Repeat, Cytoplasm, Phosphoprotein, Polymorphism, Sh3 Domain (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Tong, H. Zhou, Y. Gao, Z. Zhu, X. Zhang, M. Teng, L. Niu
Crystal Structure Of Human Osteoclast Stimulating Factor
Proteins V. 75 245 2009
PubMed-ID: 19137598 | Reference-DOI: 10.1002/PROT.22333
(for further references see the PDB file header)

Molecule 1 - OSTEOCLAST-STIMULATING FACTOR 1
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET22B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	OSTF1
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 6)

No.	Name	Count	Type	Full Name
1	MSE	6	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (1, 3)

No.	Name	Count	Type	Full Name
1	MSE	3	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (1, 3)

No.	Name	Count	Type	Full Name
1	MSE	3	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 3EHR)

(no "SS Bond" information available for 3EHR)

(no "Cis Peptide Bond" information available for 3EHR)

Asymmetric Unit (2, 4)

								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/B	N	48	S
2	UniProt	VAR_026573	L	159	F	OSTF1_HUMAN	Polymorphism	17850197	A/B	L	159	F

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

Biological Unit 1 (2, 2)

								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
2	UniProt	VAR_026573	L	159	F	OSTF1_HUMAN	Polymorphism	17850197	A	L	159	F

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

Biological Unit 2 (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_048309	N	48	S	OSTF1_HUMAN	Polymorphism	2295862	B	N	48	S
2	UniProt	VAR_026573	L	159	F	OSTF1_HUMAN	Polymorphism	17850197	B	L	159	F

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

Asymmetric Unit (3, 5)

	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	B:12-71
2	ANK_REP_REGION	PS50297	Ankyrin repeat region circular profile.	OSTF1_HUMAN	72-171	2	A:72-171 B:72-171
3	ANK_REPEAT	PS50088	Ankyrin repeat profile.	OSTF1_HUMAN	139-171	2	A:139-171 B:139-171

Biological Unit 1 (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	0	-
2	ANK_REP_REGION	PS50297	Ankyrin repeat region circular profile.	OSTF1_HUMAN	72-171	1	A:72-171 -
3	ANK_REPEAT	PS50088	Ankyrin repeat profile.	OSTF1_HUMAN	139-171	1	A:139-171 -

Biological Unit 2 (3, 3)

	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	B:12-71
2	ANK_REP_REGION	PS50297	Ankyrin repeat region circular profile.	OSTF1_HUMAN	72-171	1	- B:72-171
3	ANK_REPEAT	PS50088	Ankyrin repeat profile.	OSTF1_HUMAN	139-171	1	- B:139-171

Asymmetric Unit (9, 17)

	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	- B:12-12	- 1
1.2	ENST00000346234	2	ENSE00001023928	chr9:77732420-77732466	47	OSTF1_HUMAN	12-27	16	2	A:13-27 B:12-27	15 16
1.3	ENST00000346234	3	ENSE00001198586	chr9:77742485-77742535	51	OSTF1_HUMAN	28-44	17	2	A:28-44 B:28-44	17 17
1.4	ENST00000346234	4	ENSE00000707172	chr9:77745494-77745557	64	OSTF1_HUMAN	45-66	22	2	A:45-66 B:45-66	22 22
1.5	ENST00000346234	5	ENSE00000803850	chr9:77746686-77746739	54	OSTF1_HUMAN	66-84	19	2	A:66-84 B:66-84	19 19
1.6	ENST00000346234	6	ENSE00000707175	chr9:77748210-77748317	108	OSTF1_HUMAN	84-120	37	2	A:84-120 B:84-120	37 37
1.7	ENST00000346234	7	ENSE00000803852	chr9:77749262-77749311	50	OSTF1_HUMAN	120-136	17	2	A:120-136 B:120-136	17 17
1.8	ENST00000346234	8	ENSE00000803853	chr9:77752454-77752532	79	OSTF1_HUMAN	137-163	27	2	A:137-163 B:137-163	27 27
1.9	ENST00000346234	9	ENSE00000803854	chr9:77755750-77755848	99	OSTF1_HUMAN	163-196	34	2	A:163-190 B:163-190	28 28
1.10	ENST00000346234	10	ENSE00001198580	chr9:77761599-77762181	583	OSTF1_HUMAN	196-214	19	0	-	-

Asymmetric 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:178
 aligned with OSTF1_HUMAN | Q92882 from UniProtKB/Swiss-Prot  Length:214

    Alignment length:178
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182        
          OSTF1_HUMAN    13 QVKVFRALYTFEPRTPDELYFEEGDIIYITDMSDTNWWKGTSKGRTGLIPSNYVAEQAESIDNPLHEAAKRGNLSWLRECLDNRVGVNGLDKAGSTALYWACHGGHKDIVEMLFTQPNIELNQQNKLGDTALHAAAWKGYADIVQLLLAKGARTDLRNIEKKLAFDMATNAACASLLK 190
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3ehrA01 A:13-74 SH3 Domains                                   3ehrA02 A:75-190  [code=1.25.40.20, no name defined]                                                                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..................eeeeee.....eeeeee..eeeeeehhhhhhheeee.hhhhhhhhhhhhhhhhhhhhh............hhhhhhhhh.hhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhh...........hhhhhh.hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -----------------------------------S--------------------------------------------------------------------------------------------------------------F------------------------------- SAPs(SNPs)
                PROSITE (1) SH3  PDB: - UniProt: 12-71                                 ANK_REP_REGION  PDB: A:72-171 UniProt: 72-171                                                       ------------------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------ANK_REPEAT  PDB: A:139-171       ------------------- PROSITE (2)
           Transcript 1 (1) ---------------Exon 1.3         Exon 1.4  PDB: A:45-66-----------------Exon 1.6  PDB: A:84-120              ----------------Exon 1.8  PDB: A:137-163   --------------------------- Transcript 1 (1)
           Transcript 1 (2) Exon 1.2       --------------------------------------Exon 1.5           -----------------------------------Exon 1.7         --------------------------Exon 1.9  PDB: A:163-190     Transcript 1 (2)
                 3ehr A  13 QVKVFRALYTFEPRTPDELYIEEGDIIYITDmSDTNWWKGTSKGRTGLIPSNYVAEQAESIDNPLHEAAKRGNLSWLRECLDNRVGVNGLDKAGSTALYWACHGGHKDIVEmLFTQPNIELNQQNKLGDTALHAAAWKGYADIVQLLLAKGARTDLRNIEKKLAFDmATNAACASLLK 190
                                    22        32        42 |      52        62        72        82        92       102       112       122 |     132       142       152       162       172      |182        
                                                          44-MSE                                                                         124-MSE                                                179-MSE

Chain B from PDB  Type:PROTEIN  Length:179
 aligned with OSTF1_HUMAN | Q92882 from UniProtKB/Swiss-Prot  Length:214

    Alignment length:179
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181         
          OSTF1_HUMAN    12 GQVKVFRALYTFEPRTPDELYFEEGDIIYITDMSDTNWWKGTSKGRTGLIPSNYVAEQAESIDNPLHEAAKRGNLSWLRECLDNRVGVNGLDKAGSTALYWACHGGHKDIVEMLFTQPNIELNQQNKLGDTALHAAAWKGYADIVQLLLAKGARTDLRNIEKKLAFDMATNAACASLLK 190
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3ehrB01 B:12-74 SH3 Domains                                    3ehrB02 B:75-190  [code=1.25.40.20, no name defined]                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..................eeeeee.....eeeeee..eeeeeehhhhhhheeee.hhhhhhhhhhhhhhhhhhhhh............hhhhhhhhh.hhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhh...........hhhhhh.hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------S--------------------------------------------------------------------------------------------------------------F------------------------------- SAPs(SNPs)
                PROSITE (1) SH3  PDB: B:12-71 UniProt: 12-71                            ANK_REP_REGION  PDB: B:72-171 UniProt: 72-171                                                       ------------------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------ANK_REPEAT  PDB: B:139-171       ------------------- PROSITE (2)
           Transcript 1 (1) 1---------------Exon 1.3         Exon 1.4  PDB: B:45-66-----------------Exon 1.6  PDB: B:84-120              ----------------Exon 1.8  PDB: B:137-163   --------------------------- Transcript 1 (1)
           Transcript 1 (2) Exon 1.2        --------------------------------------Exon 1.5           -----------------------------------Exon 1.7         --------------------------Exon 1.9  PDB: B:163-190     Transcript 1 (2)
                 3ehr B  12 GQVKVFRALYTFEPRTPDELYIEEGDIIYITDmSDTNWWKGTSKGRTGLIPSNYVAEQAESIDNPLHEAAKRGNLSWLRECLDNRVGVNGLDKAGSTALYWACHGGHKDIVEmLFTQPNIELNQQNKLGDTALHAAAWKGYADIVQLLLAKGARTDLRNIEKKLAFDmATNAACASLLK 190
                                    21        31        41  |     51        61        71        81        91       101       111       121  |    131       141       151       161       171       181         
                                                           44-MSE                                                                         124-MSE                                                179-MSE

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 '\|'

(no "SCOP Domain" information available for 3EHR)

Asymmetric Unit

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=1.25.40.20, no name defined] (65)

Human (Homo sapiens) (31)

1a	3ehrA02	A:75-190
1b	3ehrB02	B:75-190

Class: Mainly Beta (13760)

Architecture: Roll (1513)

Topology: SH3 type barrels. (648)

Homologous Superfamily: SH3 Domains (267)

Human (Homo sapiens) (133)

2a	3ehrB01	B:12-74
2b	3ehrA01	A:13-74

(no "Pfam Domain" information available for 3EHR)

Asymmetric Unit(hide GO term definitions)

Chain A,B (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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	OSTF1_HUMAN \| Q92882	:	1x2k 1zlm 3ehq

Description

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Ligands, Modified Residues, Ions (1, 6)

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