1YUU - JenaLib

NMR Structure - model 1 (Jmol Viewer)

NMR Structure - model 1, sites (Jmol Viewer)

NMR Structure - all models (Jmol Viewer)

Title :   SOLUTION STRUCTURE OF CALCIUM-S100A13

Authors :   F. Arnesano, L. Banci, I. Bertini, A. Fantoni, L. Tenori, M. S. Viezzoli, Structural Proteomics In Europe (Spine)

Date :   14 Feb 05 (Deposition) - 18 Oct 05 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A,B  (25x)

Keywords :   S100A13, Ef Hand Calcium-Binding Proteins, Copper(Ii), Nmr Structure, Structural Genomics, Structural Proteomics In Europe, Spine, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. Arnesano, L. Banci, I. Bertini, A. Fantoni, L. Tenori, M. S. Viezzoli
Structural Interplay Between Calcium(Ii) And Copper(Ii) Binding To S100A13 Protein
Angew. Chem. Int. Ed. Engl. V. 44 6341 2005
PubMed-ID: 16145699 | Reference-DOI: 10.1002/ANIE.200500540
(for further references see the PDB file header)

Molecule 1 - S100 CALCIUM-BINDING PROTEIN A13
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET21S100
	Expression System Strain	:	BL21GOLD(DE3)
	Expression System Taxid	:	562
	Expression System Vector	:	PET21A
	Expression System Vector Type	:	PLASMID
	Gene	:	S100A13
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606


NMR Structure (25x)	:

Summary Information (see also Sequences/Alignments below)

NMR Structure (1, 4)

No.	Name	Count	Type	Full Name
1	CA	4	Ligand/Ion	CALCIUM ION

NMR Structure (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:24 , GLU A:27 , GLY A:28 , ARG A:29 , SER A:32 , GLU A:37	BINDING SITE FOR RESIDUE CA A 197
2	AC2	SOFTWARE	ASP A:64 , ASN A:66 , ASP A:68 , GLU A:70 , GLU A:75	BINDING SITE FOR RESIDUE CA A 198
3	AC3	SOFTWARE	ALA B:24 , GLY B:28 , ARG B:29 , SER B:32 , GLU B:37	BINDING SITE FOR RESIDUE CA B 199
4	AC4	SOFTWARE	ASP B:64 , ASP B:68 , GLU B:70 , GLU B:75	BINDING SITE FOR RESIDUE CA B 200

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

NMR Structure

No.	Model	Residues
1	1	Asp A:92	-	Leu A:93
2	1, 5, 18, 23	Glu B:27	-	Gly B:28
3	2	Val B:35	-	Asn B:36
4	4	Leu B:46	-	Pro B:47
5	5	Glu B:10	-	Glu B:11
6	9	Arg A:96	-	Lys A:97
7	12	Lys A:89	-	Lys A:90
8	12	Lys A:90	-	Lys A:91
9	12, 18	Ala B:2	-	Ala B:3
10	13	Lys A:97	-	Lys A:98
11	22	Gly B:28	-	Arg B:29

(no "SAP(SNP)/Variant" information available for 1YUU)

(no "PROSITE Motif" information available for 1YUU)

NMR Structure (2, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.9f	ENST00000392623	9f	ENSE00001512519	chr1:153599744-153599615	130	S10AD_HUMAN	-	0	0	-	-
1.9j	ENST00000392623	9j	ENSE00002186841	chr1:153599009-153598796	214	S10AD_HUMAN	1-51	51	2	A:1-51 B:1-51	51 51
1.10b	ENST00000392623	10b	ENSE00001364911	chr1:153591514-153591280	235	S10AD_HUMAN	52-98	47	2	A:52-98 B:52-98	47 47

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
	(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:98
 aligned with S10AD_HUMAN | Q99584 from UniProtKB/Swiss-Prot  Length:98

    Alignment length:98
                                    10        20        30        40        50        60        70        80        90        
           S10AD_HUMAN    1 MAAEPLTELEESIETVVTTFFTFARQEGRKDSLSVNEFKELVTQQLPHLLKDVGSLDEKMKSLDVNQDSELKFNEYWRLIGELAKEIRKKKDLKIRKK 98
               SCOP domains d1yuua_ A: automated matches                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhhh.....eehhhhhhhhhhhh.........hhhhhhhhhh......eehhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.9j  PDB: A:1-51 UniProt: 1-51               Exon 1.10b  PDB: A:52-98 UniProt: 52-98         Transcript 1
                  1yuu A  1 MAAEPLTELEESIETVVTTFFTFARQEGRKDSLSVNEFKELVTQQLPHLLKDVGSLDEKMKSLDVNQDSELKFNEYWRLIGELAKEIRKKKDLKIRKK 98
                                    10        20        30        40        50        60        70        80        90

Chain B from PDB  Type:PROTEIN  Length:98
 aligned with S10AD_HUMAN | Q99584 from UniProtKB/Swiss-Prot  Length:98

    Alignment length:98
                                    10        20        30        40        50        60        70        80        90        
           S10AD_HUMAN    1 MAAEPLTELEESIETVVTTFFTFARQEGRKDSLSVNEFKELVTQQLPHLLKDVGSLDEKMKSLDVNQDSELKFNEYWRLIGELAKEIRKKKDLKIRKK 98
               SCOP domains d1yuub_ B: automated matches                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------S_100-1yuuB01 B:9-52                        ---------------------------------------------- Pfam domains (1)
           Pfam domains (2) --------S_100-1yuuB02 B:9-52                        ---------------------------------------------- Pfam domains (2)
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhh...........hhhhhhhhh.........hhhhhhhhhh...........hhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.9j  PDB: B:1-51 UniProt: 1-51               Exon 1.10b  PDB: B:52-98 UniProt: 52-98         Transcript 1
                  1yuu B  1 MAAEPLTELEESIETVVTTFFTFARQEGRKDSLSVNEFKELVTQQLPHLLKDVGSLDEKMKSLDVNQDSELKFNEYWRLIGELAKEIRKKKDLKIRKK 98
                                    10        20        30        40        50        60        70        80        90

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 '\|'

NMR Structure

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: EF Hand-like (739)

Superfamily: EF-hand (657)

Family: automated matches (65)

Protein domain: automated matches (65)

Human (Homo sapiens) [TaxId: 9606] (35)

1a	d1yuua_	A:
1b	d1yuub_	B:

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

NMR Structure

Clans(

)

Families(

)

Organisms( (-)

)

Clan: EF_hand (270)

Family: S_100 (63)

Homo sapiens (Human) (41)

1a	S_100-1yuuB01	B:9-52
1b	S_100-1yuuB02	B:9-52

NMR Structure(hide GO term definitions)

Chain A,B (S10AD_HUMAN | Q99584)

molecular function
	GO:0050786	RAGE receptor binding	Interacting selectively and non-covalently with the RAGE receptor, the receptor for advanced glycation end-products.
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0005507	copper ion binding	Interacting selectively and non-covalently with copper (Cu) ions.
	GO:0017134	fibroblast growth factor binding	Interacting selectively and non-covalently with a fibroblast growth factor.
	GO:0008289	lipid binding	Interacting selectively and non-covalently with a lipid.
	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).
	GO:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0050663	cytokine secretion	The regulated release of cytokines from a cell. Cytokines are any of a group of proteins that function to control the survival, growth and differentiation of tissues and cells, and which have autocrine and paracrine activity.
	GO:0050703	interleukin-1 alpha secretion	The regulated release of interleukin-1 alpha from a cell.
	GO:0043303	mast cell degranulation	The regulated exocytosis of secretory granules containing preformed mediators such as histamine, serotonin, and neutral proteases by a mast cell.
	GO:0043123	positive regulation of I-kappaB kinase/NF-kappaB signaling	Any process that activates or increases the frequency, rate or extent of I-kappaB kinase/NF-kappaB signaling.
	GO:0008284	positive regulation of cell proliferation	Any process that activates or increases the rate or extent of cell proliferation.
	GO:0015031	protein transport	The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0008360	regulation of cell shape	Any process that modulates the surface configuration of a cell.
	GO:0046688	response to copper 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 copper ion stimulus.
	GO:0051602	response to electrical stimulus	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 electrical stimulus.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	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: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:0042629	mast cell granule	Coarse, bluish-black staining cytoplasmic granules, bounded by a plasma membrane and found in mast cells and basophils. Contents include histamine, heparin, chondroitin sulfates, chymase and tryptase.
	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:0048471	perinuclear region of cytoplasm	Cytoplasm situated near, or occurring around, the nucleus.

NMR Structure
	Complete Structure
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	Cis Peptide Bonds
		Ala B:2 - Ala B:3	[ RasMol ]
		Arg A:96 - Lys A:97	[ RasMol ]
		Asp A:92 - Leu A:93	[ RasMol ]
		Glu B:10 - Glu B:11	[ RasMol ]
		Glu B:27 - Gly B:28	[ RasMol ]
		Gly B:28 - Arg B:29	[ RasMol ]
		Leu B:46 - Pro B:47	[ RasMol ]
		Lys A:89 - Lys A:90	[ RasMol ]
		Lys A:90 - Lys A:91	[ RasMol ]
		Lys A:97 - Lys A:98	[ RasMol ]
		Val B:35 - Asn B:36	[ RasMol ]

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	1yuu
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UniProtKB/Swiss-Prot
	S10AD_HUMAN \| Q99584	:	1yur 1yus 1yut 2egd 2h2k 2k8m 2ki4 2ki6 2kot 2l5x 2le9

1yur	SOLUTION STRUCTURE OF APO-S100A13 (MINIMIZED MEAN STRUCTURE)
1yus	SOLUTION STRUCTURE OF APO-S100A13
1yut	SOLUTION STRUCTURE OF CALCIUM-S100A13 (MINIMIZED MEAN STRUCTURE) RELATED ID: CIRMMP11 RELATED DB: TARGETDB

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (11, 15)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (2, 4)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (1, 2)

Gene Ontology (27, 27)

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