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(-) Description

Title :  CRYSTAL STRUCTURE OF THE INOSITOL 1,4,5-TRISPHOSPHATE RECEPTOR BINDING CORE IN COMPLEX WITH IP3
 
Authors :  I. Bosanac, J. R. Alattia, T. K. Mal, J. Chan, S. Talarico, F. K. Tong, K. I. Tong, F. Yoshikawa, T. Furuichi, M. Iwai, T. Michikawa, K. Mikoshiba, M. Ikura
Date :  31 Oct 02  (Deposition) - 25 Dec 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Ip3 Receptor, Ip3-Binding Core, Calcium Channel, Protein- Ligand Complex, B-Trefoil Fold, Armadillo-Like Fold, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  I. Bosanac, J. R. Alattia, T. K. Mal, J. Chan, S. Talarico, F. K. Tong, K. I. Tong, F. Yoshikawa, T. Furuichi, M. Iwai, T. Michikawa, K. Mikoshiba, M. Ikura
Structure Of The Inositol 1, 4, 5-Trisphosphate Receptor Binding Core In Complex With Its Ligand.
Nature V. 420 696 2002
PubMed-ID: 12442173  |  Reference-DOI: 10.1038/NATURE01268
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - INOSITOL 1,4,5-TRISPHOSPHATE RECEPTOR TYPE 1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX-2T
    Expression System StrainBL21-CODONPLUS(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentIP3-BINDING CORE
    GeneITPR1 OR INSP3R
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymTYPE 1 INOSITOL 1,4,5- TRISPHOSPHATE RECEPTOR, TYPE 1 INSP3 RECEPTOR, IP3 RECEPTOR ISOFORM 1, INSP3R1, INOSITOL 1,4,5-TRISPHOSPHATE-BINDING PROTEIN P400, PURKINJE CELL PROTEIN 1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1I3P1Ligand/IonD-MYO-INOSITOL-1,4,5-TRIPHOSPHATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:265 , THR A:267 , GLY A:268 , ARG A:269 , LYS A:508 , ARG A:511 , TYR A:567 , ARG A:568 , LYS A:569 , HOH A:1126 , HOH A:1128 , HOH A:1139 , HOH A:1146 , HOH A:1148 , HOH A:1157 , HOH A:1193 , HOH A:1198 , HOH A:1222BINDING SITE FOR RESIDUE I3P A 1000

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1N4K)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1N4K)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1N4K)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MIRPS50919 MIR domain profile.ITPR1_MOUSE112-166
173-223
231-287
294-373
379-435
  2-
-
-
A:302-372
A:387-435

(-) Exons   (0, 0)

(no "Exon" information available for 1N4K)

(-) Sequences/Alignments

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:292
 aligned with ITPR1_MOUSE | P11881 from UniProtKB/Swiss-Prot  Length:2749

    Alignment length:367
                                   245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       
          ITPR1_MOUSE   236 GGDVVRLFHAEQEKFLTCDEHRKKQHVFLRTTGRQSATSATSSKALWEVEVVQHDPCRGGAGYWNSLFRFKHLATGHYLAAEVDPDFEEECLEFQPSVDPDQDASRSRLRNAQEKMVYSLVSVPEGNDISSIFELDPTTLRGGDSLVPRNSYVRLRHLCTNTWVHSTNIPIDKEEEKPVMLKIGTSPLKEDKEAFAIVPVSPAEVRDLDFANDASKVLGSIAGKLEKGTITQNERRSVTKLLEDLVYFVTGGTNSGQDVLEVVFSKPNRERQKLMREQNILKQIFKLLQAPFTDCGDGPMLRLEELGDQRHAPFRHICRLCYRVLRHSQQDYRKNQEYIAKQFGFMQKQIGYDVLAEDTITALLHNN 602
               SCOP domains d1n4ka2 A:236-435 IP3 receptor type 1 binding core, d             omain 1                                                                                                                               d1n4ka1 A:436-602 IP3 receptor type 1 binding core, domain 2                                                                                                            SCOP domains
               CATH domains 1n4kA01 A:236-434  [code=2.80.10.50, no name defined]                                                                                                                                                  1n4kA02 A:435-599 IP3 receptor type 1 binding core, domain 2                                                                                                         --- CATH domains
               Pfam domains MIR-1n4kA01 A:236-433                                                                                                                                                                                 --------------------------------------RYDR_ITPR-1n4kA02 A:472-602                                                                                                         Pfam domains
         Sec.struct. author ...eeeeee....eeeeeee....eeeeee.....hhhhh.hhhh.eeeee..-------------.eeeee.....eeeeee.-------------------------------..eeeeee....hhhh.eeee.--------------..eeee....eeeeeeeee.........eeeeeee........eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh........hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh-----------------hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE MIR  PDB: - UniProt: 231-287                        ------MIR  PDB: A:302-372 UniProt: 294-373                                            -----MIR  PDB: A:387-435 UniProt: 379-435                     ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1n4k A 236 GGDVVRLFHAEQEKFLTCDEHRKKQHVFLRTTGRQSATSATSSKALWEVEVVQ-------------LFRFKHLATGHYLAAEVD-------------------------------MVYSLVSVPEGNDISSIFELDP--------------YVRLRHLCTNTWVHSTNIPIDKEEEKPVMLKIGTSPLKEDKEAFAIVPVSPAEVRDLDFANDASKVLGSIAGKLEKGTITQNERRSVTKLLEDLVYFVTGGTNSGQDVLEVVFSKPNRERQKLMREQNILKQIFKLLQAPFT-----------------HAPFRHICRLCYRVLRHSQQDYRKNQEYIAKQFGFMQKQIGYDVLAEDTITALLHNN 602
                                   245       255       265       275       285  |      -      |305       315   |     -         -         -     | 355       365      |  -         - |     395       405       415       425       435       445       455       465       475       485       495       505       515       525  |      -         -|      555       565       575       585       595       
                                                                              288           302              319                             351                  372            387                                                                                                                                          528               546                                                        

   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 '|'

 Classification and Annotation

(-) SCOP Domains  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: Trefoil (131)

(-) Gene Ontology  (36, 36)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (ITPR1_MOUSE | P11881)
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:0019855    calcium channel inhibitor activity    Stops, prevents, or reduces the activity of a calcium channel.
    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: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: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:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    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:0032469    endoplasmic reticulum calcium ion homeostasis    Any process involved in the maintenance of an internal steady state of calcium ions within the endoplasmic reticulum of a cell or between the endoplasmic reticulum and its surroundings.
    GO:0042045    epithelial fluid transport    The directed movement of fluid across epithelia.
    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:0070059    intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress    A series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway is induced in response to a stimulus indicating endoplasmic reticulum (ER) stress, and ends when the execution phase of apoptosis is triggered. ER stress usually results from the accumulation of unfolded or misfolded proteins in the ER lumen.
    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:0050849    negative regulation of calcium-mediated signaling    Any process that stops, prevents, or reduces the frequency, rate or extent of calcium-mediated signaling.
    GO:0009791    post-embryonic development    The process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. See embryonic development.
    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:0001666    response to hypoxia    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 stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
    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.
    GO:0050882    voluntary musculoskeletal movement    The movement of an organism or part of an organism using mechanoreceptors, the nervous system, striated muscle and/or the skeletal system that can be controlled at will.
cellular component
    GO:0005955    calcineurin complex    A heterodimeric calcium ion and calmodulin dependent protein phosphatase composed of catalytic and regulatory subunits; the regulatory subunit is very similar in sequence to calmodulin.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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: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:0005637    nuclear inner membrane    The inner, i.e. lumen-facing, lipid bilayer of the nuclear envelope.
    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:0031088    platelet dense granule membrane    The lipid bilayer surrounding the platelet dense granule.
    GO:0031094    platelet dense tubular network    A network of membrane-bounded compartments found in blood platelets, where they regulate platelet activation by sequestering or releasing calcium. The dense tubular network exists as thin elongated membranes in resting platelets, and undergoes a major ultrastructural change, to a rounded vesicular form, upon addition of thrombin.
    GO:0014069    postsynaptic density of dendrite    An electron dense network of proteins within and adjacent to the postsynaptic membrane of the dendrite of asymetric synapses. Its major components include neurotransmitter receptors and the proteins that spatially and functionally organize them such as anchoring and scaffolding molecules, signaling enzymes and cytoskeletal components.
    GO:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.
    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.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        ITPR1_MOUSE | P118811xzz 5gug 5x9z 5xa0 5xa1

(-) Related Entries Specified in the PDB File

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