1K9K - JenaLib

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Title :   CRYSTAL STRUCTURE OF CALCIUM BOUND HUMAN S100A6

Authors :   L. R. Otterbein, R. Dominguez

Date :   29 Oct 01 (Deposition) - 10 Apr 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.76

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

Keywords :   S100A6, Calcyclin, Calcium Regulatory Protein, Calcium Bound, Cacy, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. R. Otterbein, J. Kordowska, C. Witte-Hoffmann, C. L. Wang, R. Dominguez
Crystal Structures Of S100A6 In The Ca(2+)-Free And Ca(2+)-Bound States: The Calcium Sensor Mechanism Of S100 Proteins Revealed At Atomic Resolution.
Structure V. 10 557 2002
PubMed-ID: 11937060 | Reference-DOI: 10.1016/S0969-2126(02)00740-2
(for further references see the PDB file header)

Molecule 1 - S100A6
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PAED4
	Expression System Strain	:	BL21 (DE3) PLYS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	S100A6
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	CALCYCLIN, CACY

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 6)

No.	Name	Count	Type	Full Name
1	BME	2	Ligand/Ion	BETA-MERCAPTOETHANOL
2	CA	4	Ligand/Ion	CALCIUM ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	BME	2	Ligand/Ion	BETA-MERCAPTOETHANOL
2	CA	-1	Ligand/Ion	CALCIUM ION

Biological Unit 2 (1, 4)

No.	Name	Count	Type	Full Name
1	BME	4	Ligand/Ion	BETA-MERCAPTOETHANOL
2	CA	-1	Ligand/Ion	CALCIUM ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:20 , GLU A:23 , ASP A:25 , THR A:28 , GLU A:33 , HOH A:409	BINDING SITE FOR RESIDUE CA A 300
2	AC2	SOFTWARE	ASP A:61 , ASN A:63 , ASP A:65 , GLU A:67 , GLU A:72 , HOH A:401	BINDING SITE FOR RESIDUE CA A 400
3	AC3	SOFTWARE	SER B:20 , GLU B:23 , ASP B:25 , THR B:28 , GLU B:33 , HOH B:402	BINDING SITE FOR RESIDUE CA B 300
4	AC4	SOFTWARE	ASP B:61 , ASN B:63 , ASP B:65 , GLU B:67 , GLU B:72 , HOH B:416	BINDING SITE FOR RESIDUE CA B 400
5	AC5	SOFTWARE	CYS A:3 , HOH A:452 , LYS B:40	BINDING SITE FOR RESIDUE BME A 100
6	AC6	SOFTWARE	LYS A:40 , CYS B:3	BINDING SITE FOR RESIDUE BME B 200

(no "SS Bond" information available for 1K9K)

(no "Cis Peptide Bond" information available for 1K9K)

Asymmetric Unit (4, 8)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_011982	H	27	R	S10A6_HUMAN	Polymorphism	11974	A/B	H	27	R
2	UniProt	VAR_011983	N	69	S	S10A6_HUMAN	Polymorphism	1802581	A/B	N	69	S
3	UniProt	VAR_011984	I	83	T	S10A6_HUMAN	Polymorphism	1802582	A/B	I	83	T
4	UniProt	VAR_029281	G	90	D	S10A6_HUMAN	Polymorphism	2228293	A/B	G	90	D

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

Biological Unit 1 (4, 8)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_011982	H	27	R	S10A6_HUMAN	Polymorphism	11974	A/B	H	27	R
2	UniProt	VAR_011983	N	69	S	S10A6_HUMAN	Polymorphism	1802581	A/B	N	69	S
3	UniProt	VAR_011984	I	83	T	S10A6_HUMAN	Polymorphism	1802582	A/B	I	83	T
4	UniProt	VAR_029281	G	90	D	S10A6_HUMAN	Polymorphism	2228293	A/B	G	90	D

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

Biological Unit 2 (4, 16)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_011982	H	27	R	S10A6_HUMAN	Polymorphism	11974	A/B	H	27	R
2	UniProt	VAR_011983	N	69	S	S10A6_HUMAN	Polymorphism	1802581	A/B	N	69	S
3	UniProt	VAR_011984	I	83	T	S10A6_HUMAN	Polymorphism	1802582	A/B	I	83	T
4	UniProt	VAR_029281	G	90	D	S10A6_HUMAN	Polymorphism	2228293	A/B	G	90	D

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

Asymmetric Unit (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EF_HAND_2	PS50222	EF-hand calcium-binding domain profile.	S10A6_HUMAN	48-83	2	A:48-83 B:48-83
2	S100_CABP	PS00303	S-100/ICaBP type calcium binding protein signature.	S10A6_HUMAN	56-77	2	A:56-77 B:56-77
3	EF_HAND_1	PS00018	EF-hand calcium-binding domain.	S10A6_HUMAN	61-73	2	A:61-73 B: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.	S10A6_HUMAN	48-83	2	A:48-83 B:48-83
2	S100_CABP	PS00303	S-100/ICaBP type calcium binding protein signature.	S10A6_HUMAN	56-77	2	A:56-77 B:56-77
3	EF_HAND_1	PS00018	EF-hand calcium-binding domain.	S10A6_HUMAN	61-73	2	A:61-73 B:61-73

Biological Unit 2 (3, 12)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EF_HAND_2	PS50222	EF-hand calcium-binding domain profile.	S10A6_HUMAN	48-83	4	A:48-83 B:48-83
2	S100_CABP	PS00303	S-100/ICaBP type calcium binding protein signature.	S10A6_HUMAN	56-77	4	A:56-77 B:56-77
3	EF_HAND_1	PS00018	EF-hand calcium-binding domain.	S10A6_HUMAN	61-73	4	A:61-73 B:61-73

Asymmetric Unit (2, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000368720	1a	ENSE00001447842	chr1:153508720-153508584	137	S10A6_HUMAN	-	0	0	-	-
1.1e	ENST00000368720	1e	ENSE00001447841	chr1:153508409-153508264	146	S10A6_HUMAN	-	0	0	-	-
1.2c	ENST00000368720	2c	ENSE00002178082	chr1:153507835-153507678	158	S10A6_HUMAN	1-46	46	2	A:2-46 B:2-46	45 45
1.3b	ENST00000368720	3b	ENSE00001447839	chr1:153507306-153507075	232	S10A6_HUMAN	47-90	44	2	A:47-90 B:47-90	44 44

Asymmetric 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:89
 aligned with S10A6_HUMAN | P06703 from UniProtKB/Swiss-Prot  Length:90

    Alignment length:89
                                    11        21        31        41        51        61        71        81         
           S10A6_HUMAN    2 ACPLDQAIGLLVAIFHKYSGREGDKHTLSKKELKELIQKELTIGSKLQDAEIARLMEDLDRNKDQEVNFQEYVTFLGALALIYNEALKG 90
               SCOP domains d1k9ka_ A: Calcyclin (S100)                                                               SCOP domains
               CATH domains 1k9kA00 A:2-90 EF-hand                                                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh......eehhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh......eehhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------R-----------------------------------------S-------------T------D SAPs(SNPs)
                PROSITE (1) ----------------------------------------------EF_HAND_2  PDB: A:48-83             ------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------S100_CABP  PDB: A:56-7------------- PROSITE (2)
                PROSITE (3) -----------------------------------------------------------EF_HAND_1    ----------------- PROSITE (3)
               Transcript 1 Exon 1.2c  PDB: A:2-46 UniProt: 1-46         Exon 1.3b  PDB: A:47-90 UniProt: 47-90       Transcript 1
                  1k9k A  2 ACPLDQAIGLLVAIFHKYSGREGDKHTLSKKELKELIQKELTIGSKLQDAEIARLMEDLDRNKDQEVNFQEYVTFLGALALIYNEALKG 90
                                    11        21        31        41        51        61        71        81

Chain B from PDB  Type:PROTEIN  Length:89
 aligned with S10A6_HUMAN | P06703 from UniProtKB/Swiss-Prot  Length:90

    Alignment length:89
                                    11        21        31        41        51        61        71        81         
           S10A6_HUMAN    2 ACPLDQAIGLLVAIFHKYSGREGDKHTLSKKELKELIQKELTIGSKLQDAEIARLMEDLDRNKDQEVNFQEYVTFLGALALIYNEALKG 90
               SCOP domains d1k9kb_ B: Calcyclin (S100)                                                               SCOP domains
               CATH domains 1k9kB00 B:2-90 EF-hand                                                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------R-----------------------------------------S-------------T------D SAPs(SNPs)
                PROSITE (1) ----------------------------------------------EF_HAND_2  PDB: B:48-83             ------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------S100_CABP  PDB: B:56-7------------- PROSITE (2)
                PROSITE (3) -----------------------------------------------------------EF_HAND_1    ----------------- PROSITE (3)
               Transcript 1 Exon 1.2c  PDB: B:2-46 UniProt: 1-46         Exon 1.3b  PDB: B:47-90 UniProt: 47-90       Transcript 1
                  1k9k B  2 ACPLDQAIGLLVAIFHKYSGREGDKHTLSKKELKELIQKELTIGSKLQDAEIARLMEDLDRNKDQEVNFQEYVTFLGALALIYNEALKG 90
                                    11        21        31        41        51        61        71        81

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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)

Human (Homo sapiens), s100a6 [TaxId: 9606] (4)

1a	d1k9ka_	A:
1b	d1k9kb_	B:

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)

Human (Homo sapiens) (106)

1a	1k9kA00	A:2-90
1b	1k9kB00	B:2-90

(no "Pfam Domain" information available for 1K9K)

Asymmetric Unit(hide GO term definitions)

Chain A,B (S10A6_HUMAN | P06703)

molecular function
	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:0015075	ion transmembrane transporter activity	Enables the transfer of an ion from one side of a membrane to the other.
	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:0005523	tropomyosin binding	Interacting selectively and non-covalently with tropomyosin, a protein associated with actin filaments both in cytoplasm and, in association with troponin, in the thin filament of striated muscle.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	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:0034220	ion transmembrane transport	A process in which an ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
	GO:0048146	positive regulation of fibroblast proliferation	Any process that activates or increases the frequency, rate or extent of multiplication or reproduction of fibroblast cells.
	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: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:0031234	extrinsic component of cytoplasmic side of plasma membrane	The component of a plasma membrane consisting of gene products and protein complexes that are loosely bound to its cytoplasmic surface, but not integrated into the hydrophobic region.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005635	nuclear envelope	The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space).
	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: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:0001726	ruffle	Projection at the leading edge of a crawling cell; the protrusions are supported by a microfilament meshwork.

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	S10A6_HUMAN \| P06703	:	1k8u 1k96 1k9p 2m1k 4ybh

1k8u	CRYSTAL STRUCTURE OF CALCIUM FREE HUMAN S100A6 MUTANT CYS3MET (SE DERIVATIVE)
1k96	CRYSTAL STRUCTURE OF CALCIUM BOUND HUMAN S100A6
1k9p	CRYSTAL STRUCTURE OF CALCIUM FREE HUMAN S100A6 WILD TYPE

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