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(-) Description

Title :  CRYSTAL STRUCTURE OF DISTAL N-TERMINAL BETA-TREFOIL DOMAIN OF RYANODINE RECEPTOR TYPE 1
 
Authors :  F. J. Amador, S. Liu, N. Ishiyama, M. J. Plevin, A. Wilson, D. H. Maclennan, M. Ikura
Date :  10 Jun 09  (Deposition) - 28 Jul 09  (Release) - 18 Aug 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Beta-Trefoil, Calcium, Calcium Channel, Calcium Transport, Glycoprotein, Ion Transport, Ionic Channel, Membrane, Phosphoprotein, Receptor, S-Nitrosylation, Transmembrane, Transport, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  F. J. Amador, S. Liu, N. Ishiyama, M. J. Plevin, A. Wilson, D. H. Maclennan, M. Ikura
Crystal Structure Of Type I Ryanodine Receptor Amino-Terminal Beta-Trefoil Domain Reveals A Disease-Associated Mutation "Hot Spot" Loop
Proc. Natl. Acad. Sci. Usa V. 106 11040 2009
PubMed-ID: 19541610  |  Reference-DOI: 10.1073/PNAS.0905186106
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RYANODINE RECEPTOR 1
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET232A
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentSEQUENCE DATABASE RESIDUES 1-210
    GeneRYR1
    Organism CommonRABBIT
    Organism ScientificORYCTOLAGUS CUNICULUS
    Organism Taxid9986
    SynonymRYR-1, RYR1, SKELETAL MUSCLE-TYPE RYANODINE RECEPTOR, SKELETAL MUSCLE CALCIUM RELEASE CHANNEL

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

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

(-) Sites  (0, 0)

(no "Site" information available for 3HSM)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MIRPS50919 MIR domain profile.RYR1_RABIT98-153
 
160-205
 
211-265
271-334
336-394
  4A:98-153
B:98-153
A:160-205
B:160-205
-
-
-
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MIRPS50919 MIR domain profile.RYR1_RABIT98-153
 
160-205
 
211-265
271-334
336-394
  2A:98-153
-
A:160-205
-
-
-
-
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MIRPS50919 MIR domain profile.RYR1_RABIT98-153
 
160-205
 
211-265
271-334
336-394
  2-
B:98-153
-
B:160-205
-
-
-

(-) Exons   (0, 0)

(no "Exon" information available for 3HSM)

(-) Sequences/Alignments

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:164
 aligned with RYR1_RABIT | P11716 from UniProtKB/Swiss-Prot  Length:5037

    Alignment length:195
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200     
           RYR1_RABIT    11 VQFLRTDDEVVLQCSATVLKEQLKLCLAAEGFGNRLCFLEPTSNAQNVPPDLAICCFTLEQSLSVRALQEMLANTVEAGVESSQGGGHRTLLYGHAILLRHAHSRMYLSCLTTSRSMTDKLAFDVGLQEDATGEACWWTMHPASKQRSEGEKVRVGDDLILVSVSSERYLHLSTASGELQVDASFMQTLWNMNPI 205
               SCOP domains d3hsma_ A: N-termi    nal domain of ryanod        ine receptor type 1                                                                                                                               SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeee....----.eeeee.........eeeee--------hhhhhheeeeeeehhhhhhhhhhh.-----------.........eeeeee.....eeee.....----...eeeeee.........eeeee................eeeee.....eeeee.----.eeeee......eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------MIR  PDB: A:98-153 UniProt: 98-153                      ------MIR  PDB: A:160-205 UniProt: 160-205           PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hsm A  11 VQFLRTDDEVVLQCSATV----LKLCLAAEGFGNRLCFLEPT--------DLAICCFTLEQSLSVRALQEMLANT-----------GHRTLLYGHAILLRHAHSRMYLSCLTTSR----KLAFDVGLQEDATGEACWWTMHPASKQRSEGEKVRVGDDLILVSVSSERYLHLST----LQVDASFMQTLWNMNPI 205
                                    20       | -  |     40        50 |       -|       70        80    |    -      |100       110       120    |  130       140       150       160       170       180   |   190       200     
                                            28   33                 52       61                      85          97                         125  130                                                   184  189                

Chain B from PDB  Type:PROTEIN  Length:159
 aligned with RYR1_RABIT | P11716 from UniProtKB/Swiss-Prot  Length:5037

    Alignment length:195
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200     
           RYR1_RABIT    11 VQFLRTDDEVVLQCSATVLKEQLKLCLAAEGFGNRLCFLEPTSNAQNVPPDLAICCFTLEQSLSVRALQEMLANTVEAGVESSQGGGHRTLLYGHAILLRHAHSRMYLSCLTTSRSMTDKLAFDVGLQEDATGEACWWTMHPASKQRSEGEKVRVGDDLILVSVSSERYLHLSTASGELQVDASFMQTLWNMNPI 205
               SCOP domains d3hsmb_ B: N-te       rminal domain of rya       nodine receptor type 1                                                                                                                             SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeee.-------..eeee.........eeee.-------.......eeeeeeeehhhhhhhh..-------------.......eeeeeee.....eeee....-----...eeeeee....hhhh.eeeee................eeeee.....eeeee.----.eeeee.....eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------MIR  PDB: B:98-153 UniProt: 98-153                      ------MIR  PDB: B:160-205 UniProt: 160-205           PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hsm B  11 VQFLRTDDEVVLQCS-------LKLCLAAEGFGNRLCFLEPT-------PDLAICCFTLEQSLSVRALQEMLAN-------------HRTLLYGHAILLRHAHSRMYLSCLTTS-----KLAFDVGLQEDATGEACWWTMHPASKQRSEGEKVRVGDDLILVSVSSERYLHLST----LQVDASFMQTLWNMNPI 205
                                    20    |    -  |     40        50 |      60        70        80   |     -       100       110       120   |   130       140       150       160       170       180   |   190       200     
                                         25      33                 52      60                      84            98                       124   130                                                   184  189                

   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, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (30, 30)

Asymmetric Unit(hide GO term definitions)
Chain A,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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RYR1_RABIT | P117162bcx 2xoa 3ila 3j8h 3rqr 4ert 4esu 4ett 4etu 4i0y 4i1e 4i2s 4i37 4i3n 4i6i 4i7i 4i8m 4i96 4p9j 4uwa 4uwe 5c30 5gky 5gkz 5gl0 5gl1 5j8v 5t15 5t9m 5t9n 5t9r 5t9s 5t9v 5ta3 5tal 5tam 5tan 5tap 5taq 5tas 5tat 5tau 5tav 5taw 5tax 5tay 5taz 5tb0 5tb1 5tb2 5tb3 5tb4

(-) Related Entries Specified in the PDB File

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