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Asym./Biol. Unit (Jmol Viewer)

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Title :   STRUCTURE OF A NOVEL EXTRACELLULAR CA2+-BINDING MODULE IN BM-40(SLASH)SPARC(SLASH)OSTEONECTIN

Authors :   E. Hohenester, P. Maurer, C. Hohenadl, R. Timpl, J. N. Jansonius, J. Engel

Date :   21 Aug 95 (Deposition) - 08 Mar 96 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym./Biol. Unit : A

Keywords :   Extracellular Matrix Protein, Calcium-Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Hohenester, P. Maurer, C. Hohenadl, R. Timpl, J. N. Jansonius, J. Engel
Structure Of A Novel Extracellular Ca(2+)-Binding Module In Bm-40.
Nat. Struct. Biol. V. 3 67 1996
PubMed-ID: 8548457 | Reference-DOI: 10.1038/NSB0196-67
(for further references see the PDB file header)

Molecule 1 - SPARC
	Chains	:	A
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Atcc Number	:	1573
	Expression System Cell Line	:	HUMAN EMBRYONIC KIDNEY CELLS (293, ATCC CRL 1573)
	Expression System Common	:	HUMAN
	Expression System Gene	:	HUMAN BM-40
	Expression System Plasmid	:	BLUESCRIPT, PCIS
	Expression System Taxid	:	9606
	Fragment	:	CARBOXY-TERMINAL DOMAIN (RESIDUES 136 - 286)
	Gene	:	HUMAN BM-40
	Organ	:	KIDNEY
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	CRYSTALLIZED FROM 0.7 M K, NA-TARTRATE, PH 7.5 + 2 MM CACL2
	Synonym	:	BM-40, OSTEONECTIN

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 3)

No.	Name	Count	Type	Full Name
1	CA	3	Ligand/Ion	CALCIUM ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:222 , PRO A:225 , ASP A:227 , TYR A:229 , GLU A:234 , HOH A:408	BINDING SITE FOR RESIDUE CA A 301
2	AC2	SOFTWARE	ASP A:257 , ASP A:259 , ASP A:261 , TYR A:263 , GLU A:268 , HOH A:405	BINDING SITE FOR RESIDUE CA A 302
3	AC3	SOFTWARE	PRO A:241 , ILE A:243 , GLU A:246 , HOH A:416 , HOH A:488	BINDING SITE FOR RESIDUE CA A 303
4	EF1	AUTHOR	ASP A:222 , PRO A:225 , ASP A:227 , TYR A:229 , GLU A:234	EF-HAND 1 TO WHICH CA+2(301) IS BOUND; CA+2 LIGANDS ARE LISTED
5	EF2	AUTHOR	ASP A:257 , ASP A:259 , ASP A:261 , TYR A:263 , GLU A:268	EF-HAND 2 TO WHICH CA+2(302) IS BOUND
6	MET	AUTHOR	ALA A:240 , LEU A:242 , MET A:245	BINDING SITE FOR THIRD, UNIDENTIFIED METAL ION MODELED AS CALCIUM CA+2(303)

Asymmetric/Biological Unit

No.	Residues
1	A:138	-	A:248
2	A:256	-	A:272

Asymmetric/Biological Unit

No.	Residues
1	His A:224	-	Pro A:225

Asymmetric/Biological Unit (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_075142	R	166	H	SPRC_HUMAN	Disease (OI17)	---	A	R	149	H
2	UniProt	VAR_075143	E	263	K	SPRC_HUMAN	Disease (OI17)	---	A	E	246	K

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

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	OSTEONECTIN_2	PS00613	Osteonectin domain signature 2.	SPRC_HUMAN	163-173	1	A:146-156
2	EF_HAND_1	PS00018	EF-hand calcium-binding domain.	SPRC_HUMAN	274-286	1	A:257-269

Asymmetric/Biological Unit (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000231061	1a	ENSE00001218290	chr5:151066726-151066426	301	SPRC_HUMAN	-	0	0	-	-
1.3	ENST00000231061	3	ENSE00002171871	chr5:151055762-151055693	70	SPRC_HUMAN	1-19	19	0	-	-
1.4	ENST00000231061	4	ENSE00000767880	chr5:151054235-151054173	63	SPRC_HUMAN	20-40	21	0	-	-
1.5b	ENST00000231061	5b	ENSE00000767879	chr5:151052777-151052690	88	SPRC_HUMAN	41-70	30	0	-	-
1.6b	ENST00000231061	6b	ENSE00000841273	chr5:151051255-151051134	122	SPRC_HUMAN	70-110	41	0	-	-
1.7	ENST00000231061	7	ENSE00000841272	chr5:151049345-151049225	121	SPRC_HUMAN	111-151	41	0	-	-
1.8c	ENST00000231061	8c	ENSE00000841271	chr5:151047161-151047028	134	SPRC_HUMAN	151-195	45	1	A:136-178	43
1.9b	ENST00000231061	9b	ENSE00000841270	chr5:151046070-151045922	149	SPRC_HUMAN	196-245	50	1	A:179-228	50
1.10	ENST00000231061	10	ENSE00000841269	chr5:151043796-151043648	149	SPRC_HUMAN	245-295	51	1	A:228-278	51
1.11b	ENST00000231061	11b	ENSE00001023043	chr5:151043160-151040657	2504	SPRC_HUMAN	295-303	9	1	A:278-286	9

Asymmetric/Biological Unit

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	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:151
 aligned with SPRC_HUMAN | P09486 from UniProtKB/Swiss-Prot  Length:303

    Alignment length:151
                                   162       172       182       192       202       212       222       232       242       252       262       272       282       292       302 
           SPRC_HUMAN   153 PPCLDSELTEFPLRMRDWLKNVLVTLYERDEDNNLLTEKQKLRVKKIHENEKRLEAGDHPVELLARDFEKNYNMYIFPVHWQFGQLDQHPIDGYLSHTELAPLRAPLIPMEHCTTRFFETCDLDNDKYIALDEWAGCFGIKQKDIDKDLVI 303
               SCOP domains d1sraa_ A: C-terminal (EC) domain of BM-40/SPARC/osteonectin                                                                                            SCOP domains
               CATH domains 1sraA00 A:136-286 EF-hand                                                                                                                               CATH domains
               Pfam domains SPARC_Ca_bdg-1sraA01 A:136-272                                                                                                           -------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhh............hhhhhhhhhh.hhhhhhhhhhhhhhh.......ee.....hhhh......hhhhhhhhhhh.......eehhhhhhhh...hhh..hhh.. Sec.struct. author
                 SAPs(SNPs) -------------H------------------------------------------------------------------------------------------------K---------------------------------------- SAPs(SNPs)
                    PROSITE ----------OSTEONECTIN----------------------------------------------------------------------------------------------------EF_HAND_1    ----------------- PROSITE
           Transcript 1 (1) Exon 1.8c  PDB: A:136-178 UniProt: 151-195 -------------------------------------------------Exon 1.10  PDB: A:228-278 UniProt: 245-295         -------- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------Exon 1.9b  PDB: A:179-228 UniProt: 196-245        -------------------------------------------------1.11b     Transcript 1 (2)
                 1sra A 136 PPCLDSELTEFPLRMRDWLKNVLVTLYERDEDNNLLTEKQKLRVKKIHENEKRLEAGDHPVELLARDFEKNYNMYIFPVHWQFGQLDQHPIDGYLSHTELAPLRAPLIPMEHCTTRFFETCDLDNDKYIALDEWAGCFGIKQKDIDKDLVI 286
                                   145       155       165       175       185       195       205       215       225       235       245       255       265       275       285

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 '\|'

Asymmetric/Biological Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: All alpha proteins (14657)

Fold: EF Hand-like (739)

Superfamily: EF-hand (657)

Family: Osteonectin (3)

Protein domain: C-terminal (EC) domain of BM-40/SPARC/osteonectin (3)

Human (Homo sapiens) [TaxId: 9606] (3)

d1sraa_

Asymmetric/Biological Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Recoverin; domain 1 (474)

Homologous Superfamily: EF-hand (412)

Human (Homo sapiens) (106)

1sraA00

A:136-286

Asymmetric/Biological Unit

Clans(

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Families(

)

Organisms( (-)

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Clan: EF_hand (270)

Family: SPARC_Ca_bdg (3)

Homo sapiens (Human) (3)

SPARC_Ca_bdg-1sraA01

A:136-272

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (SPRC_HUMAN | P09486)

molecular function
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0005518	collagen binding	Interacting selectively and non-covalently with collagen, a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals. Collagen is highly enriched in glycine (some regions are 33% glycine) and proline, occurring predominantly as 3-hydroxyproline (about 20%).
	GO:0050840	extracellular matrix binding	Interacting selectively and non-covalently with a component of the extracellular matrix.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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:0060348	bone development	The process whose specific outcome is the progression of bone over time, from its formation to the mature structure. Bone is the hard skeletal connective tissue consisting of both mineral and cellular components.
	GO:0071363	cellular response to growth factor stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a growth factor stimulus.
	GO:0030198	extracellular matrix organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix.
	GO:0007507	heart development	The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
	GO:0048839	inner ear development	The process whose specific outcome is the progression of the inner ear over time, from its formation to the mature structure.
	GO:0030324	lung development	The process whose specific outcome is the progression of the lung over time, from its formation to the mature structure. In all air-breathing vertebrates the lungs are developed from the ventral wall of the oesophagus as a pouch which divides into two sacs. In amphibians and many reptiles the lungs retain very nearly this primitive sac-like character, but in the higher forms the connection with the esophagus becomes elongated into the windpipe and the inner walls of the sacs become more and more divided, until, in the mammals, the air spaces become minutely divided into tubes ending in small air cells, in the walls of which the blood circulates in a fine network of capillaries. In mammals the lungs are more or less divided into lobes, and each lung occupies a separate cavity in the thorax.
	GO:0016525	negative regulation of angiogenesis	Any process that stops, prevents, or reduces the frequency, rate or extent of angiogenesis.
	GO:0001937	negative regulation of endothelial cell proliferation	Any process that stops, prevents, or reduces the rate or extent of endothelial cell proliferation.
	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:0002576	platelet degranulation	The regulated exocytosis of secretory granules containing preformed mediators such as histamine and serotonin by a platelet.
	GO:0010595	positive regulation of endothelial cell migration	Any process that increases the rate, frequency, or extent of the orderly movement of an endothelial cell into the extracellular matrix to form an endothelium.
	GO:0006898	receptor-mediated endocytosis	An endocytosis process in which cell surface receptors ensure specificity of transport. A specific receptor on the cell surface binds tightly to the extracellular macromolecule (the ligand) that it recognizes; the plasma-membrane region containing the receptor-ligand complex then undergoes endocytosis, forming a transport vesicle containing the receptor-ligand complex and excluding most other plasma-membrane proteins. Receptor-mediated endocytosis generally occurs via clathrin-coated pits and vesicles.
	GO:0022604	regulation of cell morphogenesis	Any process that modulates the frequency, rate or extent of cell morphogenesis. Cell morphogenesis is the developmental process in which the shape of a cell is generated and organized.
	GO:0042127	regulation of cell proliferation	Any process that modulates the frequency, rate or extent of cell proliferation.
	GO:0033591	response to L-ascorbic acid	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an L-ascorbic acid (vitamin C) stimulus.
	GO:0051591	response to cAMP	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate) stimulus.
	GO:0046686	response to cadmium ion	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cadmium (Cd) ion stimulus.
	GO:0051592	response to calcium ion	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a calcium ion stimulus.
	GO:0034097	response to cytokine	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cytokine stimulus.
	GO:0045471	response to ethanol	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ethanol stimulus.
	GO:0051384	response to glucocorticoid	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glucocorticoid stimulus. Glucocorticoids are hormonal C21 corticosteroids synthesized from cholesterol with the ability to bind with the cortisol receptor and trigger similar effects. Glucocorticoids act primarily on carbohydrate and protein metabolism, and have anti-inflammatory effects.
	GO:0009629	response to gravity	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a gravitational stimulus.
	GO:0010288	response to lead ion	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lead ion stimulus.
	GO:0032496	response to lipopolysaccharide	Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
	GO:0043434	response to peptide hormone	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a peptide hormone stimulus. A peptide hormone is any of a class of peptides that are secreted into the blood stream and have endocrine functions in living animals.
	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.
	GO:0042060	wound healing	The series of events that restore integrity to a damaged tissue, following an injury.
cellular component
	GO:0005604	basement membrane	A thin layer of dense material found in various animal tissues interposed between the cells and the adjacent connective tissue. It consists of the basal lamina plus an associated layer of reticulin fibers.
	GO:0009986	cell surface	The external part of the cell wall and/or plasma membrane.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0071682	endocytic vesicle lumen	The volume enclosed by the membrane of an endocytic vesicle.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
	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.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
	GO:0016363	nuclear matrix	The dense fibrillar network lying on the inner side of the nuclear membrane.
	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.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
	GO:0031091	platelet alpha granule	A secretory organelle found in blood platelets, which is unique in that it exhibits further compartmentalization and acquires its protein content via two distinct mechanisms: (1) biosynthesis predominantly at the megakaryocyte (MK) level (with some vestigial platelet synthesis) (e.g. platelet factor 4) and (2) endocytosis and pinocytosis at both the MK and circulating platelet levels (e.g. fibrinogen (Fg) and IgG).
	GO:0031093	platelet alpha granule lumen	The volume enclosed by the membrane of the platelet alpha granule.
	GO:0031092	platelet alpha granule membrane	The lipid bilayer surrounding the platelet alpha granule.
	GO:0005578	proteinaceous extracellular matrix	A layer consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that forms a sheet underlying or overlying cells such as endothelial and epithelial cells. The proteins are secreted by cells in the vicinity. An example of this component is found in Mus musculus.

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		His A:224 - Pro A:225	[ RasMol ]

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	SPRC_HUMAN \| P09486	:	1bmo 1nub 2v53

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