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Title :   X-RAY STRUCTURE OF BOVINE SBI523,CA(2+)-S100B

Authors :   T. H. Charpentier, D. J. Weber, E. A. Toth

Date :   09 Mar 09 (Deposition) - 09 Jun 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Ef Hand, Alpha Helical, Metal-Binding, Nucleus, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. H. Charpentier, P. T. Wilder, M. A. Liriano, K. M. Varney, S. Zhong, A. Coop, E. Pozharski, A. D. Mackerell, E. A. Toth, D. J. Weber
Small Molecules Bound To Unique Sites In The Target Protein Binding Cleft Of Calcium-Bound S100B As Characterized By Nuclear Magnetic Resonance And X-Ray Crystallography.
Biochemistry V. 48 6202 2009
PubMed-ID: 19469484 | Reference-DOI: 10.1021/BI9005754

Molecule 1 - PROTEIN S100-B
	Chains	:	X
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET11B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	S100B
	Organism Common	:	BOVINE,COW,DOMESTIC CATTLE,DOMESTIC COW
	Organism Scientific	:	BOS TAURUS
	Organism Taxid	:	9913
	Synonym	:	S100 CALCIUM-BINDING PROTEIN B, S-100 PROTEIN SUBUNIT BETA, S-100 PROTEIN BETA CHAIN

		1
Asymmetric Unit	:	X
Biological Unit 1 (2x)	:	X

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 3)

No.	Name	Count	Type	Full Name
1	53A	1	Ligand/Ion	ETHYL 5-{[(1R)-1-(ETHOXYCARBONYL)-2-OXOPROPYL]SULFANYL}-1,2-DIHYDRO[1,2,3]TRIAZOLO[1,5-A]QUINAZOLINE-3-CARBOXYLATE
2	CA	2	Ligand/Ion	CALCIUM ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	53A	2	Ligand/Ion	ETHYL 5-{[(1R)-1-(ETHOXYCARBONYL)-2-OXOPROPYL]SULFANYL}-1,2-DIHYDRO[1,2,3]TRIAZOLO[1,5-A]QUINAZOLINE-3-CARBOXYLATE
2	CA	-1	Ligand/Ion	CALCIUM ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER X:18 , GLU X:21 , ASP X:23 , LYS X:26 , GLU X:31 , HOH X:117	BINDING SITE FOR RESIDUE CA X 92
2	AC2	SOFTWARE	ASP X:61 , ASP X:63 , ASP X:65 , GLU X:67 , GLU X:72 , HOH X:113	BINDING SITE FOR RESIDUE CA X 93
3	AC3	SOFTWARE	SER X:41 , HIS X:42 , PHE X:43 , LEU X:44 , GLU X:45 , HOH X:132 , HOH X:133	BINDING SITE FOR RESIDUE 53A X 94

(no "SS Bond" information available for 3GK4)

(no "Cis Peptide Bond" information available for 3GK4)

(no "SAP(SNP)/Variant" information available for 3GK4)

Asymmetric Unit (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EF_HAND_2	PS50222	EF-hand calcium-binding domain profile.	S100B_BOVIN	49-84	1	X:48-83
2	S100_CABP	PS00303	S-100/ICaBP type calcium binding protein signature.	S100B_BOVIN	57-78	1	X:56-77
3	EF_HAND_1	PS00018	EF-hand calcium-binding domain.	S100B_BOVIN	62-74	1	X:61-73

Biological Unit 1 (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EF_HAND_2	PS50222	EF-hand calcium-binding domain profile.	S100B_BOVIN	49-84	2	X:48-83
2	S100_CABP	PS00303	S-100/ICaBP type calcium binding protein signature.	S100B_BOVIN	57-78	2	X:56-77
3	EF_HAND_1	PS00018	EF-hand calcium-binding domain.	S100B_BOVIN	62-74	2	X:61-73

Asymmetric Unit (2, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENSBTAT00000006275	1	ENSBTAE00000256656	chr1:149249251-149249199	53	S100B_BOVIN	-	0	0	-	-
1.2	ENSBTAT00000006275	2	ENSBTAE00000256655	chr1:149246090-149245953	138	S100B_BOVIN	1-46	46	1	X:0-45	46
1.3	ENSBTAT00000006275	3	ENSBTAE00000050031	chr1:149243137-149241849	1289	S100B_BOVIN	47-92	46	1	X:46-89	44

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
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Chain X from PDB  Type:PROTEIN  Length:90
 aligned with S100B_BOVIN | P02638 from UniProtKB/Swiss-Prot  Length:92

    Alignment length:90
                                    10        20        30        40        50        60        70        80        90
           S100B_BOVIN    1 MSELEKAVVALIDVFHQYSGREGDKHKLKKSELKELINNELSHFLEEIKEQEVVDKVMETLDSDGDGECDFQEFMAFVAMITTACHEFFE 90
               SCOP domains d3gk4x_ X: Calcyclin (S100)                                                                SCOP domains
               CATH domains 3gk4X00 X:0-89 EF-hand                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhh........hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ------------------------------------------------EF_HAND_2  PDB: X:48-83             ------ PROSITE (1)
                PROSITE (2) --------------------------------------------------------S100_CABP  PDB: X:56-7------------ PROSITE (2)
                PROSITE (3) -------------------------------------------------------------EF_HAND_1    ---------------- PROSITE (3)
               Transcript 1 Exon 1.2  PDB: X:0-45 UniProt: 1-46           Exon 1.3  PDB: X:46-89 UniProt: 47-92        Transcript 1
                  3gk4 X  0 MSELEKAVVALIDVFHQYSGREGDKHKLKKSELKELINNELSHFLEEIKEQEVVDKVMETLDSDGDGECDFQEFMAFVAMITTACHEFFE 89
                                     9        19        29        39        49        59        69        79        89

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 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: S100 proteins (101)

Protein domain: Calcyclin (S100) (69)

Cow (Bos taurus), s100b [TaxId: 9913] (16)

d3gk4x_

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Recoverin; domain 1 (474)

Homologous Superfamily: EF-hand (412)

Bovine,cow,domestic cattle,domestic cow (Bos taurus) (4)

3gk4X00

X:0-89

(no "Pfam Domain" information available for 3GK4)

Asymmetric Unit(hide GO term definitions)

Chain X (S100B_BOVIN | P02638)

molecular function
	GO:0050786	RAGE receptor binding	Interacting selectively and non-covalently with the RAGE receptor, the receptor for advanced glycation end-products.
	GO:0044548	S100 protein binding	Interacting selectively and non-covalently with a S100 protein. S100 is a small calcium and zinc binding protein produced in astrocytes that is implicated in Alzheimer's disease, Down Syndrome and ALS.
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0048306	calcium-dependent 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), in the presence of calcium.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0019210	kinase inhibitor activity	Stops, prevents or reduces the activity of a kinase, an enzyme which catalyzes of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	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:0048156	tau protein binding	Interacting selectively and non-covalently with tau protein. tau is a microtubule-associated protein, implicated in Alzheimer's disease, Down Syndrome and ALS.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0048143	astrocyte activation	A change in morphology and behavior of an astrocyte resulting from exposure to a cytokine, chemokine, cellular ligand, or soluble factor.
	GO:0007409	axonogenesis	De novo generation of a long process of a neuron, that carries efferent (outgoing) action potentials from the cell body towards target cells. Refers to the morphogenesis or creation of shape or form of the developing axon.
	GO:0007611	learning or memory	The acquisition and processing of information and/or the storage and retrieval of this information over time.
	GO:0007613	memory	The activities involved in the mental information processing system that receives (registers), modifies, stores, and retrieves informational stimuli. The main stages involved in the formation and retrieval of memory are encoding (processing of received information by acquisition), storage (building a permanent record of received information as a result of consolidation) and retrieval (calling back the stored information and use it in a suitable way to execute a given task).
	GO:0071638	negative regulation of monocyte chemotactic protein-1 production	Any process that stops, prevents, or reduces the frequency, rate, or extent of production of monocyte chemotactic protein-1.
	GO:0042326	negative regulation of phosphorylation	Any process that stops, prevents or decreases the rate of addition of phosphate groups to a molecule.
	GO:0016310	phosphorylation	The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
	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:0045917	positive regulation of complement activation	Any process that activates or increases the frequency, rate or extent of complement activation.
	GO:0048168	regulation of neuronal synaptic plasticity	A process that modulates neuronal synaptic plasticity, the ability of neuronal synapses to change as circumstances require. They may alter function, such as increasing or decreasing their sensitivity, or they may increase or decrease in actual numbers.
	GO:0006417	regulation of translation	Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0043231	intracellular membrane-bounded organelle	Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
	GO:0043025	neuronal cell body	The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
	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.
	GO:0001726	ruffle	Projection at the leading edge of a crawling cell; the protrusions are supported by a microfilament meshwork.

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1dt7	SOLUTION STRUCTURE OF THE C-TERMINAL NEGATIVE REGULATORY DOMAIN OF P53 IN A COMPLEX WITH CA2+-BOUND S100B(BB)
1mho	THE 2.0 A STRUCTURE OF HOLO S100B FROM BOVINE BRAIN
3cr2	X-RAY STRUCTURE OF BOVINE ZN(2+),CA(2+)-S100B
3cr4	X-RAY STRUCTURE OF BOVINE PNT,CA(2+)-S100B
3cr5	X-RAY STRUCTURE OF BOVINE PNT-ZN(2+),CA(2+)-S100B
3gk1
3gk2

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