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(-) Description

Title :  CRYSTAL STRUCTURE OF MOUSE RYANODINE RECEPTOR 2 N-TERMINAL DOMAIN (1-217) DISEASE MUTANT A77V
 
Authors :  F. Van Petegem, P. A. Lobo
Date :  09 Aug 09  (Deposition) - 17 Nov 09  (Release) - 01 Dec 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.21
Chains :  Asym./Biol. Unit :  A
Keywords :  Ryanodine Receptor, Calcium Release Channel, Ion Channel, Arrhythmia, Arvd2, Arvc2, Cpvt, Tachycardia, Disease Mutation, Ion Transport, Ionic Channel, Transmembrane, Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. A. Lobo, F. Van Petegem
Crystal Structures Of The N-Terminal Domains Of Cardiac And Skeletal Muscle Ryanodine Receptors: Insights Into Disease Mutations.
Structure V. 17 1505 2009
PubMed-ID: 19913485  |  Reference-DOI: 10.1016/J.STR.2009.08.016
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CARDIAC CA2+ RELEASE CHANNEL
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28HMT
    Expression System Strain: ROSETTA DE3 PLACI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL DOMAIN
    Gene: RYR2
    Mutation: YES
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 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
1SO41Ligand/IonSULFATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:197 , ASN A:198 , SER A:199 , SER A:200 , HIS A:202 , HOH A:234BINDING SITE FOR RESIDUE SO4 A 218

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3IM7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3IM7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3IM7)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MIRPS50919 MIR domain profile.RYR2_MOUSE110-165
172-217
225-280
286-343
351-408		  2A:110-165
A:172-217
-
-
-

(-) Exons   (0, 0)

(no "Exon" information available for 3IM7)

(-) 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:174
 aligned with RYR2_MOUSE | E9Q401 from UniProtKB/Swiss-Prot  Length:4966

    Alignment length:206
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211      
           RYR2_MOUSE    12 QFLRTDDEVVLQCTATIHKEQQKLCLAAEGFGNRLCFLESTSNSKNVPPDLSICTFVLEQSLSVRALQEMLANTVEKSEGQVDVEKWKFMMKTAQGGGHRTLLYGHAILLRHSYSGMYLCCLSTSRSSTDKLAFDVGLQEDTTGEACWWTIHPASKQRSEGEKVRVGDDLILVSVSSERYLHLSYGNSSWHVDAAFQQTLWSVAPI 217
               SCOP domains d3im7a_ A: automated matches                                                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeee..eeeeeeee.........eeee..----...hhhhh.eeeeeeehhhhhhhhhhh...----------------------........eeeeee.....eeee....------..eeeeee........eeeeee...............eeeeee.....eeeeee....eeeeee.....eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------MIR  PDB: A:110-165 UniProt: 110-165                    ------MIR  PDB: A:172-217 UniProt: 172-217           PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3im7 A  12 QFLRTDDEVVLQCTATIHKEQQKLCLAAEGFGNRLCFLESTS----VPPDLSICTFVLEQSLSVRVLQEMLANTVE----------------------HRTLLYGHAILLRHSYSGMYLCCLSTS------LAFDVGLQEDTTGEACWWTIHPASKQRSEGEKVRVGDDLILVSVSSERYLHLSYGNSSWHVDAAFQQTLWSVAPI 217
                                    21        31        41        51 |    | 61        71        81     |   -         -       111       121       131    |    - |     151       161       171       181       191       201       211      
                                                                    53   58                           87                    110                       136    143
   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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3IM7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3IM7)

(-) Gene Ontology  (69, 69)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RYR2_MOUSE | E9Q401)
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:0048763    calcium-induced calcium release activity    Enables transmembrane transfer of calcium ions from an intracellular store to the cytosol on induction by increased calcium concentration.
    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:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    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:0097159    organic cyclic compound binding    Interacting selectively and non-covalently with an organic cyclic compound, any molecular entity that contains carbon arranged in a cyclic molecular structure.
    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:0034236    protein kinase A catalytic subunit binding    Interacting selectively and non-covalently with one or both of the catalytic subunits of protein kinase A.
    GO:0034237    protein kinase A regulatory subunit binding    Interacting selectively and non-covalently with one or both of the regulatory subunits of protein kinase A.
    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:0043621    protein self-association    Interacting selectively and non-covalently with a domain within the same polypeptide.
    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:0043924    suramin binding    Interacting selectively and non-covalently with suramin, a naphthalenesulfonic acid compound which is used in the treatment of diseases caused by trypanosomes and worms.
biological process
    GO:0030509    BMP signaling pathway    A series of molecular signals initiated by the binding of a member of the BMP (bone morphogenetic protein) family to a receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0086029    Purkinje myocyte to ventricular cardiac muscle cell signaling    Any process that mediates the transfer of information from a Purkinje myocyte to a ventricular cardiac muscle cell.
    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:0019722    calcium-mediated signaling    Any intracellular signal transduction in which the signal is passed on within the cell via calcium ions.
    GO:0035584    calcium-mediated signaling using intracellular calcium source    A series of molecular signals in which a cell uses calcium ions released from an intracellular store to convert a signal into a response.
    GO:0060070    canonical Wnt signaling pathway    The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes. In this pathway, the activated receptor signals via downstream effectors that result in the inhibition of beta-catenin phosphorylation, thereby preventing degradation of beta-catenin. Stabilized beta-catenin can then accumulate and travel to the nucleus to trigger changes in transcription of target genes.
    GO:0060048    cardiac muscle contraction    Muscle contraction of cardiac muscle tissue.
    GO:0003300    cardiac muscle hypertrophy    The enlargement or overgrowth of all or part of the heart muscle due to an increase in size of cardiac muscle cells without cell division.
    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:0071872    cellular response to epinephrine stimulus    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 an epinephrine stimulus. Epinephrine is a catecholamine that has the formula C9H13NO3; it is secreted by the adrenal medulla to act as a hormone, and released by certain neurons to act as a neurotransmitter active in the central nervous system.
    GO:0060401    cytosolic calcium ion transport    The directed movement of calcium ions (Ca2+) into, out of or within the cytosol.
    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:0003143    embryonic heart tube morphogenesis    The process in which the anatomical structures of the embryonic heart tube are generated and organized. The embryonic heart tube is an epithelial tube that will give rise to the mature heart.
    GO:0072599    establishment of protein localization to endoplasmic reticulum    The directed movement of a protein to a specific location in the endoplasmic reticulum.
    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:0003220    left ventricular cardiac muscle tissue morphogenesis    The process in which the anatomical structures of left cardiac ventricle muscle are generated and organized.
    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:1901896    positive regulation of calcium-transporting ATPase activity    Any process that activates or increases the frequency, rate or extent of calcium-transporting ATPase activity.
    GO:0010460    positive regulation of heart rate    Any process that activates or increases the frequency or rate of heart contraction.
    GO:0051284    positive regulation of sequestering of calcium ion    Any process that activates or increases the frequency, rate or extent of the binding or confining calcium ions such that they are separated from other components of a biological system.
    GO:0098735    positive regulation of the force of heart contraction    Any process that increases the force of heart muscle contraction.
    GO:0098904    regulation of AV node cell action potential    Any process that modulates the frequency, rate or extent of action potential creation, propagation or termination in an atrioventricular node myocyte. This typically occurs via modulation of the activity or expression of voltage-gated ion channels.
    GO:0098907    regulation of SA node cell action potential    Any process that modulates the frequency, rate or extent of action potential creation, propagation or termination in an SA node cardiac myocyte. This typically occurs via modulation of the activity or expression of voltage-gated ion channels.
    GO:0098910    regulation of atrial cardiac muscle cell action potential    Any process that modulates the frequency, rate or extent of action potential creation, propagation or termination in an atrial cardiac muscle cell contributing to the regulation of its contraction. This typically occurs via modulation of the activity or expression of voltage-gated ion channels.
    GO:0055117    regulation of cardiac muscle contraction    Any process that modulates the frequency, rate or extent of cardiac muscle contraction.
    GO:0010882    regulation of cardiac muscle contraction by calcium ion signaling    Any process that modulates the frequency, rate or extent of cardiac muscle contraction by changing the calcium ion signals that trigger contraction.
    GO:0010881    regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion    Any process that modulates the frequency, rate or extent of cardiac muscle contraction via the regulation of the release of sequestered calcium ion by sarcoplasmic reticulum into cytosol. The sarcoplasmic reticulum is the endoplasmic reticulum of striated muscle, specialised for the sequestration of calcium ions that are released upon receipt of a signal relayed by the T tubules from the neuromuscular junction.
    GO:0002027    regulation of heart rate    Any process that modulates the frequency or rate of heart contraction.
    GO:0098911    regulation of ventricular cardiac muscle cell action potential    Any process that modulates the frequency, rate or extent of action potential creation, propagation or termination in a ventricular cardiac muscle cell contributing to the regulation of its contraction. This typically occurs via modulation of the activity or expression of voltage-gated ion channels.
    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: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:0031000    response to caffeine    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 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: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:0014850    response to muscle activity    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 muscle activity stimulus.
    GO:0035994    response to muscle stretch    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 myofibril being extended beyond its slack length.
    GO:0051775    response to redox state    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 redox state. Redox state refers to the balance of oxidized versus reduced forms of electron donors and acceptors in an organelle, cell or organ; plastoquinone, glutathione (GSH/GSSG), and nicotinamide nucleotides (NAD+/NADH and NADP+/NADPH) are among the most important.
    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:0097050    type B pancreatic cell apoptotic process    Any apoptotic process in a type B pancreatic cell, a cell located towards center of the islets of Langerhans that secretes insulin.
    GO:0086005    ventricular cardiac muscle cell action potential    An action potential that occurs in a ventricular cardiac muscle cell.
cellular component
    GO:0030018    Z disc    Platelike region of a muscle sarcomere to which the plus ends of actin filaments are attached.
    GO:0034704    calcium channel complex    An ion channel complex through which calcium ions pass.
    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: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: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: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: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:0005790    smooth endoplasmic reticulum    The smooth endoplasmic reticulum (smooth ER or SER) has no ribosomes attached to it. The smooth ER is the recipient of the proteins synthesized in the rough ER. Those proteins to be exported are passed to the Golgi complex, the resident proteins are returned to the rough ER and the lysosomal proteins after phosphorylation of their mannose residues are passed to the lysosomes. Glycosylation of the glycoproteins also continues. The smooth ER is the site of synthesis of lipids, including the phospholipids. The membranes of the smooth ER also contain enzymes that catalyze a series of reactions to detoxify both lipid-soluble drugs and harmful products of metabolism. Large quantities of certain compounds such as phenobarbital cause an increase in the amount of the smooth ER.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RYR2_MOUSE | E9Q401: 2mc2 3im5 3im6 3qr5 4etv 4kei 4kej 4kek 4l4h 4l4i 4p9i 4p9l 5c33

(-) Related Entries Specified in the PDB File

3ila CORRESPONDING DOMAIN IN RYANODINE RECEPTOR 1
3im5 CORRESPONDING WILD TYPE DOMAIN
3im6 CORRESPONDING DOMAIN MUTANT V186M