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Title :   CRYSTAL STRUCTURE OF CALMODULIN IN COMPLEX WITH A RYANODINE RECEPTOR PEPTIDE

Authors :   A. A. Maximciuc, Y. Shamoo, K. R. Mackenzie

Date :   19 Oct 05 (Deposition) - 31 Oct 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym./Biol. Unit : A,B

Keywords :   Ef-Hand, Type-2 Turn, Calcium Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. A. Maximciuc, J. A. Putkey, Y. Shamoo, K. R. Mackenzie
Complex Of Calmodulin With A Ryanodine Receptor Target Reveals A Novel, Flexible Binding Mode.
Structure V. 14 1547 2006
PubMed-ID: 17027503 | Reference-DOI: 10.1016/J.STR.2006.08.011
(for further references see the PDB file header)

Molecule 1 - CALMODULIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	CALM
	Organism Common	:	CHICKEN
	Organism Scientific	:	GALLUS GALLUS
	Organism Taxid	:	9031
	Synonym	:	CAM

Molecule 2 - RYANODINE RECEPTOR 1
	Chains	:	B
	Engineered	:	YES
	Fragment	:	RESIDUES 3614-3643
	Other Details	:	SYNTHETIC PEPTIDE BASED ON THE SEQUENCE OF RABBIT RYANODINE RECEPTOR 1
	Synonym	:	SKELETAL MUSCLE-TYPE RYANODINE RECEPTOR, RYR1, RYR-1, SKELETAL MUSCLE CALCIUM RELEASE CHANNEL
	Synthetic	:	YES

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 4)

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

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:20 , ASP A:22 , ASP A:24 , THR A:26 , GLU A:31 , HOH A:171	BINDING SITE FOR RESIDUE CA A 149
2	AC2	SOFTWARE	ASP A:56 , ASP A:58 , ASN A:60 , THR A:62 , GLU A:67	BINDING SITE FOR RESIDUE CA A 150
3	AC3	SOFTWARE	ASP A:93 , ASP A:95 , ASN A:97 , TYR A:99 , GLU A:104 , HOH A:160	BINDING SITE FOR RESIDUE CA A 151
4	AC4	SOFTWARE	ASP A:129 , ASP A:131 , ASP A:133 , GLN A:135 , GLU A:140 , HOH A:154	BINDING SITE FOR RESIDUE CA A 152

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

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

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

Asymmetric/Biological 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.	CALM_CHICK	8-43 44-79 81-116 117-149	4	A:7-42 A:43-78 A:80-115 A:116-145
2	EF_HAND_1	PS00018	EF-hand calcium-binding domain.	CALM_CHICK	21-33 57-69 94-106 130-142	4	A:20-32 A:56-68 A:93-105 A:129-141

(no "Exon" information available for 2BCX)

Asymmetric/Biological 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:142
 aligned with CALM_CHICK | P62149 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:142
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144  
          CALM_CHICK      5 LTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMM  146
               SCOP domains d2bcxa_ A: Calmodulin                                                                                                                          SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh.......eehhhhhhhhhhhh....hhhhhhhhhhh........eehhhhhhhhhhhhh.....hhhhhhhhhhh.....eehhhhhhhhhhhh....hhhhhhhhhhhhh......eehhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---EF_HAND_2  PDB: A:7-42 UniProt: 8-43EF_HAND_2  PDB: A:43-78             -EF_HAND_2  PDB: A:80-115            EF_HAND_2  PDB: A:116-145      PROSITE (1)
                PROSITE (2) ----------------EF_HAND_1    -----------------------EF_HAND_1    ------------------------EF_HAND_1    -----------------------EF_HAND_1    ---- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2bcx A    4 LTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMM  145
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143

Chain B from PDB  Type:PROTEIN  Length:27
 aligned with RYR1_RABIT | P11716 from UniProtKB/Swiss-Prot  Length:5037

    Alignment length:27
                                  3623      3633       
          RYR1_RABIT   3614 KSKKAVWHKLLSKQRRRAVVACFRMTP 3640
               SCOP domains --------------------------- SCOP domains
               CATH domains --------------------------- CATH domains
               Pfam domains --------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------- SAPs(SNPs)
                    PROSITE --------------------------- PROSITE
                 Transcript --------------------------- Transcript
                2bcx B 3614 KSKKAVWHKLLSKQRRRAVVACFRMTP 3640
                                  3623      3633

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: EF Hand-like (739)

Superfamily: EF-hand (657)

Family: Calmodulin-like (356)

Protein domain: Calmodulin (152)

Chicken (Gallus gallus) [TaxId: 9031] (9)

d2bcxa_

(no "CATH Domain" information available for 2BCX)

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (CALM_CHICK | P62149)

molecular function
	GO:0031997	N-terminal myristoylation domain binding	Interacting selectively and non-covalently with the N-terminus of a protein that has the potential to be, or has been, modified by N-terminal myristoylation. Binding affinity is typically altered by myristoylation; for example, N-terminal myristoylation of HIV Nef increases its affinity for calmodulin.
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0044325	ion channel binding	Interacting selectively and non-covalently with one or more specific sites on an ion channel, a protein complex that spans a membrane and forms a water-filled channel across the phospholipid bilayer allowing selective ion transport down its electrochemical gradient.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0017022	myosin binding	Interacting selectively and non-covalently with any part of a myosin complex; myosins are any of a superfamily of molecular motor proteins that bind to actin and use the energy of ATP hydrolysis to generate force and movement along actin filaments.
	GO:0043274	phospholipase binding	Interacting selectively and non-covalently with any phospholipase, enzymes that catalyze of the hydrolysis of a glycerophospholipid.
	GO:0019904	protein domain specific binding	Interacting selectively and non-covalently with a specific domain of a protein.
	GO:0019901	protein kinase binding	Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
	GO:0072542	protein phosphatase activator activity	Increases the activity of a protein phosphatase, an enzyme which catalyzes of the removal of a phosphate group from a protein substrate molecule.
	GO:0031996	thioesterase binding	Interacting selectively and non-covalently with any thioesterase enzyme.
	GO:0031432	titin binding	Interacting selectively and non-covalently with titin, any of a family of giant proteins found in striated and smooth muscle. In striated muscle, single titin molecules span half the sarcomere, with their N- and C-termini in the Z-disc and M-line, respectively.
biological process
	GO:0005513	detection of calcium ion	The series of events in which a calcium ion stimulus is received by a cell and converted into a molecular signal.
	GO:0030801	positive regulation of cyclic nucleotide metabolic process	Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving cyclic nucleotides.
	GO:0051343	positive regulation of cyclic-nucleotide phosphodiesterase activity	Any process that activates or increases the frequency, rate or extent of cyclic nucleotide phosphodiesterase activity, the catalysis of the reaction: nucleotide 3',5'-cyclic phosphate + H2O = nucleotide 5'-phosphate.
	GO:0032516	positive regulation of phosphoprotein phosphatase activity	Any process that activates or increases the activity of a phosphoprotein phosphatase.
	GO:0035307	positive regulation of protein dephosphorylation	Any process that activates or increases the frequency, rate or extent of removal of phosphate groups from a protein.
	GO:0060316	positive regulation of ryanodine-sensitive calcium-release channel activity	Any process that increases the activity of a ryanodine-sensitive calcium-release channel. The ryanodine-sensitive calcium-release channel catalyzes the transmembrane transfer of a calcium ion by a channel that opens when a ryanodine class ligand has been bound by the channel complex or one of its constituent parts.
	GO:0055117	regulation of cardiac muscle contraction	Any process that modulates the frequency, rate or extent of cardiac muscle contraction.
	GO:0032465	regulation of cytokinesis	Any process that modulates the frequency, rate or extent of the division of the cytoplasm of a cell and its separation into two daughter cells.
	GO:0002027	regulation of heart rate	Any process that modulates the frequency or rate of heart contraction.
	GO:0010880	regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum	Any process that modulates the rate, frequency or extent of release of sequestered calcium ion into cytosol by the sarcoplasmic reticulum, the process in which the release of sequestered calcium ion by sarcoplasmic reticulum into cytosol occurs via calcium release channels.
	GO:0051592	response to calcium 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 calcium ion stimulus.
	GO:0021762	substantia nigra development	The progression of the substantia nigra over time from its initial formation until its mature state. The substantia nigra is the layer of gray substance that separates the posterior parts of the cerebral peduncles (tegmentum mesencephali) from the anterior parts; it normally includes a posterior compact part with many pigmented cells (pars compacta) and an anterior reticular part whose cells contain little pigment (pars reticularis).
cellular component
	GO:0034704	calcium channel complex	An ion channel complex through which calcium ions pass.
	GO:0005813	centrosome	A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle.
	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: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:0030017	sarcomere	The repeating unit of a myofibril in a muscle cell, composed of an array of overlapping thick and thin filaments between two adjacent Z discs.
	GO:0005876	spindle microtubule	Any microtubule that is part of a mitotic or meiotic spindle; anchored at one spindle pole.
	GO:0000922	spindle pole	Either of the ends of a spindle, where spindle microtubules are organized; usually contains a microtubule organizing center and accessory molecules, spindle microtubules and astral microtubules.
	GO:0031982	vesicle	Any small, fluid-filled, spherical organelle enclosed by membrane.

Chain B (RYR1_RABIT | P11716)

molecular function
	GO:0005262	calcium channel activity	Enables the facilitated diffusion of a calcium ion (by an energy-independent process) involving passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism.
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0015278	calcium-release channel activity	Enables the transmembrane transfer of a calcium ion from intracellular stores by a channel that opens when a specific intracellular ligand has been bound by the channel complex or one of its constituent parts.
	GO:0005516	calmodulin binding	Interacting selectively and non-covalently with calmodulin, a calcium-binding protein with many roles, both in the calcium-bound and calcium-free states.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0005216	ion channel activity	Enables the facilitated diffusion of an ion (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism. May be either selective (it enables passage of a specific ion only) or non-selective (it enables passage of two or more ions of same charge but different size).
	GO:0044325	ion channel binding	Interacting selectively and non-covalently with one or more specific sites on an ion channel, a protein complex that spans a membrane and forms a water-filled channel across the phospholipid bilayer allowing selective ion transport down its electrochemical gradient.
	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:0005219	ryanodine-sensitive calcium-release channel activity	Enables the transmembrane transfer of a calcium ion by a channel that opens when a ryanodine class ligand has been bound by the channel complex or one of its constituent parts.
	GO:0015643	toxic substance binding	Interacting selectively and non-covalently with a toxic substance, a poisonous substance that causes damage to biological systems.
	GO:0005245	voltage-gated calcium channel activity	Enables the transmembrane transfer of a calcium ion by a voltage-gated channel. A voltage-gated channel is a channel whose open state is dependent on the voltage across the membrane in which it is embedded.
biological process
	GO:0070588	calcium ion transmembrane transport	A process in which a calcium ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
	GO:0006816	calcium ion transport	The directed movement of calcium (Ca) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0006874	cellular calcium ion homeostasis	Any process involved in the maintenance of an internal steady state of calcium ions at the level of a cell.
	GO:0071313	cellular response to caffeine	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 caffeine stimulus. Caffeine is an alkaloid found in numerous plant species, where it acts as a natural pesticide that paralyzes and kills certain insects feeding upon them.
	GO:0006811	ion transport	The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0007275	multicellular organism development	The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
	GO:0006936	muscle contraction	A process in which force is generated within muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis.
	GO:0043931	ossification involved in bone maturation	The formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone, involved in the progression of the skeleton from its formation to its mature state.
	GO:0003151	outflow tract morphogenesis	The process in which the anatomical structures of the outflow tract are generated and organized. The outflow tract is the portion of the heart through which blood flows into the arteries.
	GO:0014808	release of sequestered calcium ion into cytosol by sarcoplasmic reticulum	The process in which the release of sequestered calcium ion by sarcoplasmic reticulum into cytosol occurs via calcium release channels.
	GO:0048741	skeletal muscle fiber development	The process whose specific outcome is the progression of the skeletal muscle fiber over time, from its formation to the mature structure. Muscle fibers are formed by the maturation of myotubes. They can be classed as slow, intermediate/fast or fast.
	GO:0043588	skin development	The process whose specific outcome is the progression of the skin over time, from its formation to the mature structure. The skin is the external membranous integument of an animal. In vertebrates the skin generally consists of two layers, an outer nonsensitive and nonvascular epidermis (cuticle or skarfskin) composed of cells which are constantly growing and multiplying in the deeper, and being thrown off in the superficial layers, as well as an inner vascular dermis (cutis, corium or true skin) composed mostly of connective tissue.
	GO:0055085	transmembrane transport	The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other
	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:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0016529	sarcoplasmic reticulum	A fine reticular network of membrane-limited elements that pervades the sarcoplasm of a muscle cell; continuous over large portions of the cell and with the nuclear envelope; that part of the endoplasmic reticulum specialized for calcium release, uptake and storage.
	GO:0033017	sarcoplasmic reticulum membrane	The lipid bilayer surrounding the sarcoplasmic reticulum.
	GO:0014802	terminal cisterna	The portion of sarcoplasmic reticulum devoted to calcium ion storage and calcium ion release.

Asymmetric/Biological Unit
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