2CT9 - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   THE CRYSTAL STRUCTURE OF CALCINEURIN B HOMOLOGOUS PROEIN 1 (CHP1)

Authors :   Y. Naoe, K. Arita, H. Hashimoto, H. Kanazawa, M. Sato, T. Shimizu

Date :   23 May 05 (Deposition) - 05 Jul 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: A,B  (1x)

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

Reference :   Y. Naoe, K. Arita, H. Hashimoto, H. Kanazawa, M. Sato, T. Shimizu
Structural Characterization Of Calcineurin B Homologous Protein 1
J. Biol. Chem. V. 280 32372 2005
PubMed-ID: 15987692 | Reference-DOI: 10.1074/JBC.M503390200

Molecule 1 - CALCIUM-BINDING PROTEIN P22
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET21B
	Expression System Strain	:	BL21(DE3)RIL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Common	:	NORWAY RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116
	Synonym	:	CALCINEURIN B HOMOLOGOUS PROTEIN 1, CALCIUM-BINDING PROTEIN CHP, CALCINEURIN HOMOLOGOUS PROTEIN

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

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

Biological Unit 1 (0, 0)

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

Biological Unit 2 (0, 0)

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

Biological Unit 3 (0, 0)

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

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:123 , ASP A:125 , ASP A:127 , LYS A:129 , GLU A:134 , HOH A:325	BINDING SITE FOR RESIDUE CA A 301
2	AC2	SOFTWARE	ASP A:164 , ASP A:166 , ASP A:168 , ALA A:170 , GLU A:175 , HOH A:343	BINDING SITE FOR RESIDUE CA A 302
3	AC3	SOFTWARE	ASP B:123 , ASP B:125 , ASP B:127 , LYS B:129 , GLU B:134 , HOH B:375	BINDING SITE FOR RESIDUE CA B 303
4	AC4	SOFTWARE	ASP B:164 , ASP B:166 , ASP B:168 , ALA B:170 , GLU B:175 , HOH B:344	BINDING SITE FOR RESIDUE CA B 304

(no "SS Bond" information available for 2CT9)

(no "Cis Peptide Bond" information available for 2CT9)

(no "SAP(SNP)/Variant" information available for 2CT9)

Asymmetric Unit (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EF_HAND_2	PS50222	EF-hand calcium-binding domain profile.	CHP1_RAT	26-61 110-145 151-186	6	A:26-61 B:26-61 A:110-145 B:110-145 A:151-186 B:151-186
2	EF_HAND_1	PS00018	EF-hand calcium-binding domain.	CHP1_RAT	123-135	2	A:123-135 B:123-135

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EF_HAND_2	PS50222	EF-hand calcium-binding domain profile.	CHP1_RAT	26-61 110-145 151-186	3	A:26-61 - A:110-145 - A:151-186 -
2	EF_HAND_1	PS00018	EF-hand calcium-binding domain.	CHP1_RAT	123-135	1	A:123-135 -

Biological Unit 2 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EF_HAND_2	PS50222	EF-hand calcium-binding domain profile.	CHP1_RAT	26-61 110-145 151-186	3	- B:26-61 - B:110-145 - B:151-186
2	EF_HAND_1	PS00018	EF-hand calcium-binding domain.	CHP1_RAT	123-135	1	- B:123-135

Biological Unit 3 (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EF_HAND_2	PS50222	EF-hand calcium-binding domain profile.	CHP1_RAT	26-61 110-145 151-186	6	A:26-61 B:26-61 A:110-145 B:110-145 A:151-186 B:151-186
2	EF_HAND_1	PS00018	EF-hand calcium-binding domain.	CHP1_RAT	123-135	2	A:123-135 B:123-135

Asymmetric Unit (7, 14)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENSRNOT00000056405	1	ENSRNOE00000331081	chr3:106066389-106066590	202	CHP1_RAT	1-23	23	2	A:8-23 B:3-23	16 21
1.2	ENSRNOT00000056405	2	ENSRNOE00000044975	chr3:106077844-106077916	73	CHP1_RAT	23-47	25	2	A:23-47 B:23-47	25 25
1.3	ENSRNOT00000056405	3	ENSRNOE00000045069	chr3:106083190-106083270	81	CHP1_RAT	47-74	28	2	A:47-74 B:47-74	28 28
1.4	ENSRNOT00000056405	4	ENSRNOE00000045174	chr3:106087793-106087920	128	CHP1_RAT	74-117	44	2	A:74-117 (gaps) B:74-117 (gaps)	44 44
1.5	ENSRNOT00000056405	5	ENSRNOE00000045275	chr3:106096017-106096078	62	CHP1_RAT	117-137	21	2	A:117-137 B:117-137	21 21
1.6	ENSRNOT00000056405	6	ENSRNOE00000045396	chr3:106099224-106099346	123	CHP1_RAT	138-178	41	2	A:138-178 B:138-178	41 41
1.7	ENSRNOT00000056405	7	ENSRNOE00000380968	chr3:106099792-106101626	1835	CHP1_RAT	179-195	17	2	A:179-195 B:179-195	17 17

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:185
 aligned with CHP1_RAT | P61023 from UniProtKB/Swiss-Prot  Length:195

    Alignment length:196
                                                                                                                                                                                                                     195        
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       | -      
             CHP1_RAT     8 LLRDEELEEIKKETGFSHSQITRLYSRFTSLDKGENGTLSREDFQRIPELAINPLGDRIINAFFSEGEDQVNFRGFMRTLAHFRPIEDNEKSKDVNGPEPLNSRSNKLHFAFRLYDLDKDDKISRDELLQVLRMMVGVNISDEQLGSIADRTIQEADQDGDSAISFTEFVKVLEKVDVEQKMSIRFLH--------   -
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2ct9A00 A:8-203 EF-hand                                                                                                                                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.....ee.hhhhhhhhhhhh..hhhhhhhh........eehhhhhhhhhh.....-----------....hhhhhhhhhhhhhh.....eehhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh......eehhhhhhh....hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------EF_HAND_2  PDB: A:26-61             ------------------------------------------------EF_HAND_2  PDB: A:110-145           -----EF_HAND_2  PDB: A:151-186           ----------------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------EF_HAND_1    -------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.1        -----------------------Exon 1.3  PDB: A:47-74      ------------------------------------------Exon 1.5             Exon 1.6  PDB: A:138-178 UniProt: 138-178Exon 1.7         -------- Transcript 1 (1)
           Transcript 1 (2) ---------------Exon 1.2  PDB: A:23-47   --------------------------Exon 1.4  PDB: A:74-117 (gaps)              -------------------------------------------------------------------------------------- Transcript 1 (2)
                 2ct9 A   8 LLRDEELEEIKKETGFSHSQITRLYSRFTSLDKGENGTLSREDFQRIPELAINPLGDRIINAFFSEGEDQVNFRGFMRTLAHFRPIE-----------EPLNSRSNKLHFAFRLYDLDKDDKISRDELLQVLRMMVGVNISDEQLGSIADRTIQEADQDGDSAISFTEFVKVLEKVDVEQKMSIRFLHKLAAALEH 203
                                    17        27        37        47        57        67        77        87      |  -       107       117       127       137       147       157       167       177       187       197      
                                                                                                                 94         106

Chain B from PDB  Type:PROTEIN  Length:198
 aligned with CHP1_RAT | P61023 from UniProtKB/Swiss-Prot  Length:195

    Alignment length:201
                                                                                                                                                                                                                          195        
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192  |      - 
             CHP1_RAT     3 SRASTLLRDEELEEIKKETGFSHSQITRLYSRFTSLDKGENGTLSREDFQRIPELAINPLGDRIINAFFSEGEDQVNFRGFMRTLAHFRPIEDNEKSKDVNGPEPLNSRSNKLHFAFRLYDLDKDDKISRDELLQVLRMMVGVNISDEQLGSIADRTIQEADQDGDSAISFTEFVKVLEKVDVEQKMSIRFLH--------   -
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2ct9B00 B:3-203 EF-hand                                                                                                                                                                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh......eehhhhhhhhhhhh..hhhhhhhhh......eehhhhhhhhhhhhhhhhhh.---.........hhhhhhhhhhhhhh.....eehhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh......eehhhhhhhh...hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------------EF_HAND_2  PDB: B:26-61             ------------------------------------------------EF_HAND_2  PDB: B:110-145           -----EF_HAND_2  PDB: B:151-186           ----------------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------EF_HAND_1    -------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.1  PDB: B:3-23-----------------------Exon 1.3  PDB: B:47-74      ------------------------------------------Exon 1.5             Exon 1.6  PDB: B:138-178 UniProt: 138-178Exon 1.7         -------- Transcript 1 (1)
           Transcript 1 (2) --------------------Exon 1.2  PDB: B:23-47   --------------------------Exon 1.4  PDB: B:74-117 (gaps)              -------------------------------------------------------------------------------------- Transcript 1 (2)
                 2ct9 B   3 SRASTLLRDEELEEIKKETGFSHSQITRLYSRFTSLDKGENGTLSREDFQRIPELAINPLGDRIINAFFSEGEDQVNFRGFMRTLAHFRPIEDNE---DVNGPEPLNSRSNKLHFAFRLYDLDKDDKISRDELLQVLRMMVGVNISDEQLGSIADRTIQEADQDGDSAISFTEFVKVLEKVDVEQKMSIRFLHKLAAALEH 203
                                    12        22        32        42        52        62        72        82        92    |  102       112       122       132       142       152       162       172       182       192       202 
                                                                                                                         97 101

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 '\|'

(no "SCOP Domain" information available for 2CT9)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Recoverin; domain 1 (474)

Homologous Superfamily: EF-hand (412)

Norway rat (Rattus norvegicus) (37)

1a	2ct9A00	A:8-203
1b	2ct9B00	B:3-203

(no "Pfam Domain" information available for 2CT9)

Asymmetric Unit(hide GO term definitions)

Chain A,B (CHP1_RAT | P61023)

molecular function
	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:0019900	kinase binding	Interacting selectively and non-covalently with a kinase, any enzyme that catalyzes the transfer of a phosphate group.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008017	microtubule binding	Interacting selectively and non-covalently with microtubules, filaments composed of tubulin monomers.
	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:0004860	protein kinase inhibitor activity	Stops, prevents or reduces the activity of a protein kinase, an enzyme which phosphorylates a protein.
	GO:0005215	transporter activity	Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.
biological process
	GO:0017156	calcium ion regulated exocytosis	The release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle by fusion of the vesicle with the plasma membrane of a cell, induced by a rise in cytosolic calcium-ion levels.
	GO:0019722	calcium-mediated signaling	Any intracellular signal transduction in which the signal is passed on within the cell via calcium ions.
	GO:0071468	cellular response to acidic pH	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 pH stimulus with pH < 7. pH is a measure of the acidity or basicity of an aqueous solution.
	GO:0031122	cytoplasmic microtubule organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of structures formed of microtubules and associated proteins in the cytoplasm of a cell.
	GO:0022406	membrane docking	The initial attachment of a membrane or protein to a target membrane. Docking requires only that the proteins come close enough to interact and adhere.
	GO:0061025	membrane fusion	The membrane organization process that joins two lipid bilayers to form a single membrane.
	GO:0061024	membrane organization	A process which results in the assembly, arrangement of constituent parts, or disassembly of a membrane. A membrane is a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins.
	GO:0001578	microtubule bundle formation	A process that results in a parallel arrangement of microtubules.
	GO:0032088	negative regulation of NF-kappaB transcription factor activity	Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of the transcription factor NF-kappaB.
	GO:0070885	negative regulation of calcineurin-NFAT signaling cascade	Any process that stops, prevents, or reduces the frequency, rate or extent of the calcineurin-NFAT signaling cascade.
	GO:0010923	negative regulation of phosphatase activity	Any process that decreases the rate or frequency of phosphatase activity. Phosphatases catalyze the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
	GO:0031953	negative regulation of protein autophosphorylation	Any process that stops, prevents or decreases the rate of the phosphorylation by a protein of one or more of its own residues.
	GO:0042308	negative regulation of protein import into nucleus	Any process that stops, prevents, or reduces the frequency, rate or extent of the movement of proteins from the cytoplasm into the nucleus.
	GO:0006469	negative regulation of protein kinase activity	Any process that stops, prevents, or reduces the frequency, rate or extent of protein kinase activity.
	GO:0001933	negative regulation of protein phosphorylation	Any process that stops, prevents or reduces the rate of addition of phosphate groups to amino acids within a protein.
	GO:0031397	negative regulation of protein ubiquitination	Any process that stops, prevents, or reduces the frequency, rate or extent of the addition of ubiquitin groups to a protein.
	GO:0060050	positive regulation of protein glycosylation	Any process that activates or increases the frequency, rate or extent of the glycosylation of one or more amino acid residues within a protein. Protein glycosylation is the addition of a carbohydrate or carbohydrate derivative unit to a protein amino acid, e.g. the addition of glycan chains to proteins.
	GO:0090314	positive regulation of protein targeting to membrane	Any process that increases the frequency, rate or extent of the process of directing proteins towards a membrane, usually using signals contained within the protein.
	GO:0051222	positive regulation of protein transport	Any process that activates or increases the frequency, rate or extent of the directed movement of a protein into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0032417	positive regulation of sodium:proton antiporter activity	Any process that activates or increases the activity of a sodium:hydrogen antiporter, which catalyzes the reaction: Na+(out) + H+(in) = Na+(in) + H+(out).
	GO:0006611	protein export from nucleus	The directed movement of a protein from the nucleus into the cytoplasm.
	GO:0051259	protein oligomerization	The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of component monomers; protein oligomers may be composed of different or identical monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
	GO:0050821	protein stabilization	Any process involved in maintaining the structure and integrity of a protein and preventing it from degradation or aggregation.
	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:0051453	regulation of intracellular pH	Any process that modulates the internal pH of a cell, measured by the concentration of the hydrogen ion.
	GO:1901214	regulation of neuron death	Any process that modulates the frequency, rate or extent of neuron death.
	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:0000139	Golgi membrane	The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005856	cytoskeleton	Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
	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:0012505	endomembrane system	A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles.
	GO:0005783	endoplasmic reticulum	The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
	GO:0005793	endoplasmic reticulum-Golgi intermediate compartment	A complex system of membrane-bounded compartments located between endoplasmic reticulum (ER) and the Golgi complex, with a distinctive membrane protein composition; involved in ER-to-Golgi and Golgi-to-ER transport.
	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:0005925	focal adhesion	Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0015630	microtubule cytoskeleton	The part of the cytoskeleton (the internal framework of a cell) composed of microtubules and associated proteins.
	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:0030133	transport vesicle	Any of the vesicles of the constitutive secretory pathway, which carry cargo from the endoplasmic reticulum to the Golgi, between Golgi cisternae, from the Golgi to the ER (retrograde transport) or to destinations within or outside the cell.

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