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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE LIGAND BINDING SUPPRESSOR DOMAIN OF TYPE 3 INOSITOL 1,4,5-TRISPHOSPHATE RECEPTOR

Authors :   J. Chan, N. Ishiyama, M. Ikura

Date :   08 Sep 09 (Deposition) - 15 Sep 10 (Release) - 15 Sep 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Beta-Trefoil, Calcium Channel, Calcium Transport, Endoplasmic Reticulum, Ion Transport, Ionic Channel, Membrane, Phosphoprotein, Receptor, Transmembrane, Transport, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Chan, H. Yamazaki, N. Ishiyama, T. K. Mal, T. Michikawa, K. Mikoshiba, M. Ikura
A 1. 9 Angstrom Crystal Structure Of The Suppressor Domain O Type 3 Inositol 1, 4, 5-Trisphosphate Receptor
To Be Published
PubMed: search

Molecule 1 - INOSITOL 1,4,5-TRISPHOSPHATE RECEPTOR TYPE 3
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-2T
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 1-224
	Gene	:	ITPR3
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	TYPE 3 INOSITOL 1,4,5-TRISPHOSPHATE RECEPTOR, TYPE 3 INSP3 RECEPTOR, IP3 RECEPTOR ISOFORM 3, INSP3R3

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

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3JRR)

(no "Site" information available for 3JRR)

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

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

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

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MIR	PS50919	MIR domain profile.	ITPR3_MOUSE	113-173 174-224 232-288 295-372 378-434	4	A:113-173 B:113-173 A:174-224 B:174-224 - - -

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MIR	PS50919	MIR domain profile.	ITPR3_MOUSE	113-173 174-224 232-288 295-372 378-434	2	A:113-173 - A:174-224 - - - -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MIR	PS50919	MIR domain profile.	ITPR3_MOUSE	113-173 174-224 232-288 295-372 378-434	2	- B:113-173 - B:174-224 - - -

(no "Exon" information available for 3JRR)

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:216
 aligned with ITPR3_MOUSE | P70227 from UniProtKB/Swiss-Prot  Length:2670

    Alignment length:223
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221   
          ITPR3_MOUSE     2 NEMSSFLHIGDIVSLYAEGSVNGFISTLGLVDDRCVVEPAAGDLDNPPKKFRDCLFKVCPMNRYSAQKQYWKAKQTKQDKEKIADVVLLQKLQHAAQMEQKQNDTENKKVHGDVVKYGSVIQLLHMKSNKYLTVNKRLPALLEKNAMRVTLDATGNEGSWLFIQPFWKLRSNGDNVVVGDKVILNPVNAGQPLHASNYELSDNAGCKEVNSVNCNTSWKINLF 224
               SCOP domains d3jrra_ A: automated matches                                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeeee...eeeeee.......eee.hhhh.......hhhhh.eeee....hhhhhhhhhhh-------hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........eeeeee....eeeeeeeeee.......eeeeee...hhhh.eeeee...............eeeeee......eeeeeeee..eeeeeeeee.....eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------MIR  PDB: A:113-173 UniProt: 113-173                         MIR  PDB: A:174-224 UniProt: 174-224                PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jrr A   2 NEMSSFLHIGDIVSLYAEGSVNGFISTLGLVDDRCVVEPAAGDLDNPPKKFRDCLFKVCPMNRYSAQKQYWKAK-------KIADVVLLQKLQHAAQMEQKQNDTENKKVHGDVVKYGSVIQLLHMKSNKYLTVNKRLPALLEKNAMRVTLDATGNEGSWLFIQPFWKLRSNGDNVVVGDKVILNPVNAGQPLHASNYELSDNAGCKEVNSVNCNTSWKINLF 224
                                    11        21        31        41        51        61        71   |     - |      91       101       111       121       131       141       151       161       171       181       191       201       211       221   
                                                                                                    75      83

Chain B from PDB  Type:PROTEIN  Length:219
 aligned with ITPR3_MOUSE | P70227 from UniProtKB/Swiss-Prot  Length:2670

    Alignment length:221
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223 
          ITPR3_MOUSE     4 MSSFLHIGDIVSLYAEGSVNGFISTLGLVDDRCVVEPAAGDLDNPPKKFRDCLFKVCPMNRYSAQKQYWKAKQTKQDKEKIADVVLLQKLQHAAQMEQKQNDTENKKVHGDVVKYGSVIQLLHMKSNKYLTVNKRLPALLEKNAMRVTLDATGNEGSWLFIQPFWKLRSNGDNVVVGDKVILNPVNAGQPLHASNYELSDNAGCKEVNSVNCNTSWKINLF 224
               SCOP domains d3jrrb_ B: automated matches                                                                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Ins145_P3_rec-3jrrB01 B:4-224                                                                                                                                                                                                 Pfam domains (1)
           Pfam domains (2) Ins145_P3_rec-3jrrB02 B:4-224                                                                                                                                                                                                 Pfam domains (2)
         Sec.struct. author .........eeeeeee...eeeeee.......eee............hhhhh.eeee....hhhhhhhhhhhhh.--..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........eeeeee....eeeeeeeeee.......eeeeee...hhhh.eeeee...............eeeeee......eeeeeeee..eeeeeeeee.....eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------MIR  PDB: B:113-173 UniProt: 113-173                         MIR  PDB: B:174-224 UniProt: 174-224                PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jrr B   4 MSSFLHIGDIVSLYAEGSVNGFISTLGLVDDRCVVEPAAGDLDNPPKKFRDCLFKVCPMNRYSAQKQYWKAKQTK--KEKIADVVLLQKLQHAAQMEQKQNDTENKKVHGDVVKYGSVIQLLHMKSNKYLTVNKRLPALLEKNAMRVTLDATGNEGSWLFIQPFWKLRSNGDNVVVGDKVILNPVNAGQPLHASNYELSDNAGCKEVNSVNCNTSWKINLF 224
                                    13        23        33        43        53        63        73    |  |83        93       103       113       123       133       143       153       163       173       183       193       203       213       223 
                                                                                                     78 81

Legend:		→ Mismatch	(orange background)
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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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: beta-Trefoil (385)

Superfamily: MIR domain (15)

Family: Ryanodine receptor N-terminal-like (12)

Protein domain: automated matches (9)

Mouse (Mus musculus) [TaxId: 10090] (9)

1a	d3jrra_	A:
1b	d3jrrb_	B:

(no "CATH Domain" information available for 3JRR)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Trefoil (131)

Family: Ins145_P3_rec (3)

Mus musculus (Mouse) (2)

1a	Ins145_P3_rec-3jrrB01	B:4-224
1b	Ins145_P3_rec-3jrrB02	B:4-224

Asymmetric Unit(hide GO term definitions)

Chain A,B (ITPR3_MOUSE | P70227)

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:0043533	inositol 1,3,4,5 tetrakisphosphate binding	Interacting selectively and non-covalently with inositol 1,3,4,5 tetrakisphosphate.
	GO:0070679	inositol 1,4,5 trisphosphate binding	Interacting selectively and non-covalently with inositol 1,4,5 trisphosphate.
	GO:0005220	inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity	Enables the transmembrane transfer of a calcium ion by a channel that opens when inositol 1,4,5-trisphosphate (IP3) has been bound by the channel complex or one of its constituent parts.
	GO:0000822	inositol hexakisphosphate binding	Interacting selectively and non-covalently with inositol hexakisphosphate.
	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:0035091	phosphatidylinositol binding	Interacting selectively and non-covalently with any inositol-containing glycerophospholipid, i.e. phosphatidylinositol (PtdIns) and its phosphorylated derivatives.
	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).
biological process
	GO:0007186	G-protein coupled receptor signaling pathway	A series of molecular signals that proceeds with an activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction, or for basal GPCR signaling the pathway begins with the receptor activating its G protein in the absence of an agonist, and ends with regulation of a downstream cellular process, e.g. transcription. The pathway can start from the plasma membrane, Golgi or nuclear membrane (PMID:24568158 and PMID:16902576).
	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:0060402	calcium ion transport into cytosol	The directed movement of calcium ions (Ca2+) into the cytosol.
	GO:0071320	cellular response to cAMP	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 cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate) stimulus.
	GO:0048016	inositol phosphate-mediated signaling	Any intracellular signal transduction in which the signal is passed on within the cell via an inositol phosphate. Includes production of the inositol phosphate, and downstream effectors that further transmit the signal within the cell. Inositol phosphates are a group of mono- to poly-phosphorylated inositols, and include inositol monophosphate (IP), inositol trisphosphate (IP3), inositol pentakisphosphate (IP5) and inositol hexaphosphate (IP6).
	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:0060291	long-term synaptic potentiation	A process that modulates synaptic plasticity such that synapses are changed resulting in the increase in the rate, or frequency of synaptic transmission at the synapse.
	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:0007204	positive regulation of cytosolic calcium ion concentration	Any process that increases the concentration of calcium ions in the cytosol.
	GO:0051291	protein heterooligomerization	The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of component monomers that are not all identical. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
	GO:0051260	protein homooligomerization	The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of identical component monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
	GO:0051209	release of sequestered calcium ion into cytosol	The process in which calcium ions sequestered in the endoplasmic reticulum, Golgi apparatus or mitochondria are released into the cytosolic compartment.
	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:0050913	sensory perception of bitter taste	The series of events required to receive a bitter taste stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process.
	GO:0050916	sensory perception of sweet taste	The series of events required to receive a sweet taste stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process.
	GO:0050917	sensory perception of umami taste	The series of events required to receive an umami taste stimulus, convert it to a molecular signal, and recognize and characterize the signal. Umami taste is the savory taste of meats and other foods that are rich in glutamates. This is a neurological process.
	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: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:0030425	dendrite	A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body.
	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:0005789	endoplasmic reticulum membrane	The lipid bilayer surrounding the endoplasmic reticulum.
	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:0005887	integral component of plasma membrane	The component of the plasma 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:0043209	myelin sheath	An electrically insulating fatty layer that surrounds the axons of many neurons. It is an outgrowth of glial cells: Schwann cells supply the myelin for peripheral neurons while oligodendrocytes supply it to those of the central nervous system.
	GO:0043025	neuronal cell body	The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
	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:0005640	nuclear outer membrane	The outer, i.e. cytoplasm-facing, lipid bilayer of the nuclear envelope; continuous with the endoplasmic reticulum of the cell and sometimes studded with ribosomes.
	GO:0005730	nucleolus	A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	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:0043235	receptor complex	Any protein complex that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.

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	3jrr
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