3Q13 - JenaLib

Title :   THE STRUCTURE OF THE CA2+-BINDING, GLYCOSYLATED F-SPONDIN DOMAIN OF F-SPONDIN, A C2-DOMAIN VARIANT FROM EXTRACELLULAR MATRIX

Authors :   K. Tan, J. Lawler

Date :   16 Dec 10 (Deposition) - 29 Jun 11 (Release) - 29 Jun 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

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

Keywords :   F-Spondin, Fs-Domain, Membrane Targeting, Axon Guidance, C2-Domain Derivative, Glycosylated, Extracellular Matrix, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Tan, J. Lawler
The Structure Of The Ca2+-Binding, Glycosylated F-Spondin Domain Of F-Spondin - A C2-Domain Variant In An Extracellular Matrix Protein.
Bmc Struct. Biol. V. 11 22 2011
PubMed-ID: 21569239 | Reference-DOI: 10.1186/1472-6807-11-22

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 8)

Asymmetric Unit (5, 8)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	BMA	1	Ligand/Ion	BETA-D-MANNOSE
3	CA	1	Ligand/Ion	CALCIUM ION
4	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
5	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 1 (4, 7)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	BMA	1	Ligand/Ion	BETA-D-MANNOSE
3	CA	-1	Ligand/Ion	CALCIUM ION
4	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
5	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 2 (4, 14)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	BMA	2	Ligand/Ion	BETA-D-MANNOSE
3	CA	-1	Ligand/Ion	CALCIUM ION
4	NAG	4	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
5	SO4	6	Ligand/Ion	SULFATE ION

Sites (8, 8)

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:212 , ASN A:214 , GLN A:399 , NAG A:502	BINDING SITE FOR RESIDUE NAG A 501
2	AC2	SOFTWARE	TYR A:212 , ARG A:402 , NAG A:501 , BMA A:503 , HOH A:957 , HOH A:994 , HOH A:995 , HOH A:1021	BINDING SITE FOR RESIDUE NAG A 502
3	AC3	SOFTWARE	ARG A:402 , NAG A:502 , HOH A:957 , HOH A:994	BINDING SITE FOR RESIDUE BMA A 503
4	AC4	SOFTWARE	ASP A:325 , ASP A:354 , ASP A:358 , HOH A:942 , HOH A:943 , HOH A:946	BINDING SITE FOR RESIDUE CA A 601
5	AC5	SOFTWARE	ILE A:196 , LEU A:197 , ASP A:198 , CYS A:199 , LYS A:241 , ARG A:309 , HIS A:312 , HOH A:873	BINDING SITE FOR RESIDUE SO4 A 621
6	AC6	SOFTWARE	TYR A:224 , PRO A:225 , ARG A:226 , ARG A:227 , GLU A:364 , HOH A:826	BINDING SITE FOR RESIDUE SO4 A 622
7	AC7	SOFTWARE	ARG A:226 , ARG A:227	BINDING SITE FOR RESIDUE SO4 A 623
8	AC8	SOFTWARE	ARG A:273 , THR A:281 , VAL A:282 , HOH A:1005	BINDING SITE FOR RESIDUE ACT A 641

SS Bonds (3, 3)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

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:236
 aligned with SPON1_HUMAN | Q9HCB6 from UniProtKB/Swiss-Prot  Length:807

    Alignment length:236
                                   201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421      
          SPON1_HUMAN   192 TDKPILDCCACGTAKYRLTFYGNWSEKTHPKDYPRRANHWSAIIGGSHSKNYVLWEYGGYASEGVKQVAELGSPVKMEEEIRQQSDEVLTVIKAKAQWPAWQPLNVRAAPSAEFSVDRTRHLMSFLTMMGPSPDWNVGLSAEDLCTKECGWVQKVVQDLIPWDAGTDSGVTYESPNKPTIPQEKIRPLTSLDHPQSPFYDPEGGSITQVARVVIERIARKGEQCNIVPDNVDDIVA 427
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------Spond_N-3q13A01 A:204-399                                                                                                                                                                           ---------------------------- Pfam domains
         Sec.struct. author ............eeeeeeeeee................ee..eeeeee.............hhhhhhhhhhh.hhhhhhhhhhhhh.eeeeeee................eeeeeee....eeeeeeeee....eeeeeeeee..........eeeeee..ee......................ee......................eeeeeeeeeee.............ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---SPONDIN  PDB: A:195-388 UniProt: 195-388                                                                                                                                                          --------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3q13 A 192 TDKPILDCCACGTAKYRLTFYGNWSEKTHPKDYPRRANHWSAIIGGSHSKNYVLWEYGGYASEGVKQVAELGSPVKMEEEIRQQSDEVLTVIKAKAQWPAWQPLNVRAAPSAEFSVDRTRHLMSFLTMMGPSPDWNVGLSAEDLCTKECGWVQKVVQDLIPWDAGTDSGVTYESPNKPTIPQEKIRPLTSLDHPQSPFYDPEGGSITQVARVVIERIARKGEQCNIVPDNVDDIVA 427
                                   201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421

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 (0, 0)

CATH Domains (0, 0)

Pfam Domains (1, 1)

Gene Ontology (9, 9)

Asymmetric Unit(hide GO term definitions)

Chain A (SPON1_HUMAN | Q9HCB6)

molecular function
	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:0007155	cell adhesion	The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
	GO:0036066	protein O-linked fucosylation	The process of transferring a fucosyl group to a serine or threonine residues in a protein acceptor molecule, to form an O-linked protein-sugar linkage.
cellular component
	GO:0005788	endoplasmic reticulum lumen	The volume enclosed by the membranes of the endoplasmic reticulum.
	GO:0031012	extracellular matrix	A structure lying external to one or more cells, which provides structural support for cells or tissues.
	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: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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	Ligands, Modified Residues, Ions
		ACT	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
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	Cis Peptide Bonds
		Gly A:321 - Pro A:322	[ RasMol ]
		Ile A:371 - Pro A:372	[ RasMol ]
		Trp A:289 - Pro A:290	[ RasMol ]

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