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(-) Description

Title :  SOLUTION STRUCTURE OF CA2+-S100A1-RYRP12
 
Authors :  N. T. Wright, K. M. Varney, D. J. Weber
Date :  01 Apr 08  (Deposition) - 29 Jul 08  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B,C,D  (20x)
Keywords :  S100, Ef Hand, Ryanodine Receptor, Calcium Binding, Alternative Splicing, Calcium Channel, Calcium Transport, Glycoprotein, Ion Transport, Ionic Channel, Membrane, Polymorphism, Transmembrane, Transport, Cytoplasm, Metal- Binding, Zinc, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. T. Wright, B. L. Prosser, K. M. Varney, D. B. Zimmer, M. F. Schneider, D. J. Weber
S100A1 And Calmodulin Compete For The Same Binding Site On Ryanodine Receptor.
J. Biol. Chem. V. 283 26676 2008
PubMed-ID: 18650434  |  Reference-DOI: 10.1074/JBC.M804432200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RYANODINE RECEPTOR 1 PEPTIDE
    Chains: C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET14B
    Expression System Strain: HMS(DE3)
    Expression System Vector Type: PLASMID
    Gene: RYR1
    Organism Common: RAT
    Organism Scientific: RATTUS NORVEGICUS
 
Molecule 2 - PROTEIN S100-A1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET14B
    Expression System Strain: HMS(DE3)
    Expression System Vector Type: PLASMID
    Gene: S100A1
    Organism Common: RAT
    Organism Scientific: RATTUS NORVEGICUS
    Synonym: S100 CALCIUM-BINDING PROTEIN A1, S-100 PROTEIN ALPHA SUBUNIT, S-100 PROTEIN ALPHA CHAIN

 Structural Features

(-) Chains, Units

  
NMR Structure (20x): 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

NMR Structure (1, 4)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION

(-) Sites  (4, 4)

NMR Structure (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:19 , GLY A:23 , ASP A:24 , LEU A:28BINDING SITE FOR RESIDUE CA A 94
2AC2SOFTWAREHIS B:18 , SER B:19 , GLY B:20 , GLY B:23 , ASP B:24BINDING SITE FOR RESIDUE CA B 94
3AC3SOFTWARELEU A:61 , ASN A:64 , ASP A:66 , ASP A:70BINDING SITE FOR RESIDUE CA A 95
4AC4SOFTWARELEU B:61 , ASP B:62 , ASN B:64 , ASP B:66 , GLU B:68 , ASP B:70BINDING SITE FOR RESIDUE CA B 95

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2K2F)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2K2F)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2K2F)

(-) PROSITE Motifs  (3, 6)

NMR Structure (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EF_HAND_2PS50222 EF-hand calcium-binding domain profile.S10A1_RAT50-85
 		  2A:49-84
B:49-84
2S100_CABPPS00303 S-100/ICaBP type calcium binding protein signature.S10A1_RAT58-79
 		  2A:57-78
B:57-78
3EF_HAND_1PS00018 EF-hand calcium-binding domain.S10A1_RAT63-75
 		  2A:62-74
B:62-74

(-) Exons   (2, 4)

NMR Structure (2, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSRNOT000000170001ENSRNOE00000119000chr2:182787370-182787230141S10A1_RAT1-47472A:1-46
B:1-46		46
46
1.2ENSRNOT000000170002ENSRNOE00000119682chr2:182784961-182784818144S10A1_RAT48-94472A:47-93
B:47-93		47
47

(-) Sequences/Alignments

NMR Structure
   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:93
 aligned with S10A1_RAT | P35467 from UniProtKB/Swiss-Prot  Length:94

    Alignment length:93
                                    11        21        31        41        51        61        71        81        91   
           S10A1_RAT      2 GSELETAMETLINVFHAHSGKEGDKYKLSKKELKDLLQTELSSFLDVQKDADAVDKIMKELDENGDGEVDFQEFVVLVAALTVACNNFFWENS   94
               SCOP domains d2k2fa_ A: Calcyclin (S100)                                                                   SCOP domains
               CATH domains 2k2fA00 A:1-93 EF-hand                                                                        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh.......eehhhhhhhhhhh.........hhhhhhhhhhhhh.....eehhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------------------------------EF_HAND_2  PDB: A:49-84             --------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------S100_CABP  PDB: A:57-7--------------- PROSITE (2)
                PROSITE (3) -------------------------------------------------------------EF_HAND_1    ------------------- PROSITE (3)
               Transcript 1 Exon 1.1  PDB: A:1-46 UniProt: 1-47           Exon 1.2  PDB: A:47-93 UniProt: 48-94           Transcript 1
                2k2f A    1 GSELETAMETLINVFHAHSGKEGDKYKLSKKELKDLLQTELSSFLDVQKDADAVDKIMKELDENGDGEVDFQEFVVLVAALTVACNNFFWENS   93
                                    10        20        30        40        50        60        70        80        90   


Chain B from PDB  Type:PROTEIN  Length:93
 aligned with S10A1_RAT | P35467 from UniProtKB/Swiss-Prot  Length:94

    Alignment length:93
                                    11        21        31        41        51        61        71        81        91   
           S10A1_RAT      2 GSELETAMETLINVFHAHSGKEGDKYKLSKKELKDLLQTELSSFLDVQKDADAVDKIMKELDENGDGEVDFQEFVVLVAALTVACNNFFWENS   94
               SCOP domains d2k2fb_ B: Calcyclin (S100)                                                                   SCOP domains
               CATH domains 2k2fB00 B:1-93 EF-hand                                                                        CATH domains
           Pfam domains (1) ---S_100-2k2fB01 B:4-47                        -----efhand-2k2fB03 B:53-81       ------------ Pfam domains (1)
           Pfam domains (2) ---S_100-2k2fB02 B:4-47                        -----efhand-2k2fB04 B:53-81       ------------ Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh.......eehhhhhhhhhhh.........hhhhhhhhhhhhh.....eehhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------------------------------EF_HAND_2  PDB: B:49-84             --------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------S100_CABP  PDB: B:57-7--------------- PROSITE (2)
                PROSITE (3) -------------------------------------------------------------EF_HAND_1    ------------------- PROSITE (3)
               Transcript 1 Exon 1.1  PDB: B:1-46 UniProt: 1-47           Exon 1.2  PDB: B:47-93 UniProt: 48-94           Transcript 1
                2k2f B    1 GSELETAMETLINVFHAHSGKEGDKYKLSKKELKDLLQTELSSFLDVQKDADAVDKIMKELDENGDGEVDFQEFVVLVAALTVACNNFFWENS   93
                                    10        20        30        40        50        60        70        80        90   


Chain C from PDB  Type:PROTEIN  Length:12
 aligned with RYR2_RAT | B0LPN4 from UniProtKB/Swiss-Prot  Length:4953

    Alignment length:12
                                  3570  
            RYR2_RAT   3561 KKAVWHKLLSKQ 3572
               SCOP domains ------------ SCOP domains
               CATH domains ------------ CATH domains
               Pfam domains ------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------ SAPs(SNPs)
                    PROSITE ------------ PROSITE
                 Transcript ------------ Transcript
                2k2f C    1 KKAVWHKLLSKQ   12
                                    10  


Chain D from PDB  Type:PROTEIN  Length:12
 aligned with RYR2_RAT | B0LPN4 from UniProtKB/Swiss-Prot  Length:4953

    Alignment length:12
                                  3570  
            RYR2_RAT   3561 KKAVWHKLLSKQ 3572
               SCOP domains ------------ SCOP domains
               CATH domains ------------ CATH domains
               Pfam domains ------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------ SAPs(SNPs)
                    PROSITE ------------ PROSITE
                 Transcript ------------ Transcript
                2k2f D    1 KKAVWHKLLSKQ   12
                                    10
   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)

NMR Structure
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

NMR Structure
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (2, 4)

NMR Structure
(-)
Clan: EF_hand (270)

(-) Gene Ontology  (57, 64)

NMR Structure(hide GO term definitions)
Chain A,B   (S10A1_RAT | P35467)
molecular function
    GO:0051117    ATPase binding    Interacting selectively and non-covalently with an ATPase, any enzyme that catalyzes the hydrolysis of ATP.
    GO:0044548    S100 protein binding    Interacting selectively and non-covalently with a S100 protein. S100 is a small calcium and zinc binding protein produced in astrocytes that is implicated in Alzheimer's disease, Down Syndrome and ALS.
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0048306    calcium-dependent 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), in the presence of calcium.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:1901387    positive regulation of voltage-gated calcium channel activity    Any process that activates or increases the frequency, rate or extent of voltage-gated calcium channel activity.
    GO:0008016    regulation of heart contraction    Any process that modulates the frequency, rate or extent of heart contraction. Heart contraction is the process in which the heart decreases in volume in a characteristic way to propel blood through the body.
    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:0031672    A band    The dark-staining region of a sarcomere, in which myosin thick filaments are present; the center is traversed by the paler H zone, which in turn contains the M line.
    GO:0031674    I band    A region of a sarcomere that appears as a light band on each side of the Z disc, comprising a region of the sarcomere where thin (actin) filaments are not overlapped by thick (myosin) filaments; contains actin, troponin, and tropomyosin; each sarcomere includes half of an I band at each end.
    GO:0031430    M band    The midline of aligned thick filaments in a sarcomere; location of specific proteins that link thick filaments. Depending on muscle type the M band consists of different numbers of M lines.
    GO:0030018    Z disc    Platelike region of a muscle sarcomere to which the plus ends of actin filaments are attached.
    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:0043005    neuron projection    A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    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: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.

Chain C,D   (RYR2_RAT | B0LPN4)
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: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: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:0097110    scaffold protein binding    Interacting selectively and non-covalently with a scaffold protein. Scaffold proteins are crucial regulators of many key signaling pathways. Although not strictly defined in function, they are known to interact and/or bind with multiple members of a signaling pathway, tethering them into complexes.
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:0019722    calcium-mediated signaling    Any intracellular signal transduction in which the signal is passed on within the cell via calcium ions.
    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: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:0034220    ion transmembrane transport    A process in which an ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
    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:0071421    manganese ion transmembrane transport    A process in which a manganese ion is transported from one side of a membrane to the other 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:0051481    negative regulation of cytosolic calcium ion concentration    Any process that decreases the concentration of calcium ions in the cytosol.
    GO:0051480    regulation of cytosolic calcium ion concentration    Any process involved in the maintenance of an internal steady state of calcium ions within the cytosol of a cell or between the cytosol and its surroundings.
    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:0042493    response to drug    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 drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0032026    response to magnesium 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 magnesium ion stimulus.
    GO:0007584    response to nutrient    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 nutrient stimulus.
    GO:0070296    sarcoplasmic reticulum calcium ion transport    The directed movement of calcium ions (Ca2+) into, out of or within the sarcoplasmic reticulum.
    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:0031672    A band    The dark-staining region of a sarcomere, in which myosin thick filaments are present; the center is traversed by the paler H zone, which in turn contains the M line.
    GO:0030018    Z disc    Platelike region of a muscle sarcomere to which the plus ends of actin filaments are attached.
    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:0031234    extrinsic component of cytoplasmic side of plasma membrane    The component of a plasma membrane consisting of gene products and protein complexes that are loosely bound to its cytoplasmic surface, but not integrated into the hydrophobic region.
    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:0043005    neuron projection    A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    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: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: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:0042383    sarcolemma    The outer membrane of a muscle cell, consisting of the plasma membrane, a covering basement membrane (about 100 nm thick and sometimes common to more than one fiber), and the associated loose network of collagen fibers.
    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.

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  S10A1_RAT | P35467
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(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        S10A1_RAT | P35467: 1k2h 1zfs 2kbm

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2K2F)