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(-) Description

Title :  CRYSTAL STRUCTURE OF THE MYOMESIN DOMAINS MY9-MY11
 
Authors :  N. Pinotsis, S. D. Chatziefthimiou, M. Wilmanns
Date :  13 Dec 10  (Deposition) - 21 Dec 11  (Release) - 07 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Structural Protein, Sarcomere, M-Band, Immunoglobulin- Like Domain (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Pinotsis, S. D. Chatziefthimiou, F. Berkemeier, F. Beuron, I. M. Mavridis, P. V. Konarev, D. I. Svergun, E. Morris, M. Rief, M. Wilmanns
Superhelical Architecture Of The Myosin Filament-Linking Protein Myomesin With Unusual Elastic Properties.
Plos Biol. V. 10 1261 2012
PubMed-ID: 22347812  |  Reference-DOI: 10.1371/JOURNAL.PBIO.1001261

(-) Compounds

Molecule 1 - MYOMESIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET151
    Expression System Vector Type: PLASMID
    Fragment: DOMAINS MY9, MY10, MY11, RESIDUES 1141-1447
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: 190 KDA CONNECTIN-ASSOCIATED PROTEIN, 190 KDA TITIN-ASSOCIATED PROTEIN, MYOMESIN FAMILY MEMBER 1
    Tissue: MUSCLE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1BME3Ligand/IonBETA-MERCAPTOETHANOL
2PG01Ligand/Ion2-(2-METHOXYETHOXY)ETHANOL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:1160 , LYS A:1162 , THR A:1215 , ASP A:1216 , ILE A:1218BINDING SITE FOR RESIDUE BME A2448
2AC2SOFTWAREASP A:1225 , GLU A:1226 , GLU A:1227 , HOH A:2074BINDING SITE FOR RESIDUE BME A2449
3AC3SOFTWARETYR A:1175 , LYS A:1289 , MET A:1305 , GLU A:1306 , LYS A:1307 , ASP A:1312 , HOH A:2116BINDING SITE FOR RESIDUE BME A2450
4AC4SOFTWARETYR A:1175 , VAL A:1176 , SER A:1177 , PRO A:1288 , LYS A:1289 , HOH A:2181 , HOH A:2182BINDING SITE FOR RESIDUE PG0 A2451

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Y23)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2Y23)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Y23)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Y23)

(-) Exons   (10, 10)

Asymmetric/Biological Unit (10, 10)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003564431ENSE00001400333chr18:3220106-3219801306MYOM1_HUMAN-00--
1.2ENST000003564432ENSE00001543713chr18:3215249-3214932318MYOM1_HUMAN1-97970--
1.3ENST000003564433ENSE00001403202chr18:3193956-3193816141MYOM1_HUMAN97-144480--
1.4ENST000003564434ENSE00001240625chr18:3189085-3188746340MYOM1_HUMAN144-2571140--
1.5ENST000003564435ENSE00001240622chr18:3187635-3187478158MYOM1_HUMAN258-310530--
1.6ENST000003564436ENSE00001240619chr18:3176132-317604093MYOM1_HUMAN310-341320--
1.7ENST000003564437ENSE00001240615chr18:3174206-317411889MYOM1_HUMAN341-371310--
1.8ENST000003564438ENSE00001240608chr18:3173998-317393663MYOM1_HUMAN371-392220--
1.9ENST000003564439ENSE00001240603chr18:3168979-3168815165MYOM1_HUMAN392-447560--
1.10ENST0000035644310ENSE00001240598chr18:3164437-3164276162MYOM1_HUMAN447-501550--
1.11ENST0000035644311ENSE00001240595chr18:3155086-3154945142MYOM1_HUMAN501-548480--
1.12ENST0000035644312ENSE00001240590chr18:3151891-3151692200MYOM1_HUMAN548-615680--
1.13ENST0000035644313ENSE00001240585chr18:3149199-314914357MYOM1_HUMAN615-634200--
1.14ENST0000035644314ENSE00001240581chr18:3142061-3141937125MYOM1_HUMAN634-675420--
1.15ENST0000035644315ENSE00001240577chr18:3135728-3135545184MYOM1_HUMAN676-737620--
1.16ENST0000035644316ENSE00001240573chr18:3134822-3134648175MYOM1_HUMAN737-795590--
1.17ENST0000035644317ENSE00001240567chr18:3131494-3131373122MYOM1_HUMAN795-836420--
1.18ENST0000035644318ENSE00001413714chr18:3129517-3129230288MYOM1_HUMAN836-932970--
1.19ENST0000035644319ENSE00001240558chr18:3126895-3126699197MYOM1_HUMAN932-997660--
1.20ENST0000035644320ENSE00001240553chr18:3119993-3119867127MYOM1_HUMAN998-1040430--
1.21ENST0000035644321ENSE00001240549chr18:3116513-3116329185MYOM1_HUMAN1040-1101620--
1.22ENST0000035644322ENSE00001240541chr18:3112410-3112296115MYOM1_HUMAN1102-1140390--
1.23ENST0000035644323ENSE00001240535chr18:3102628-3102472157MYOM1_HUMAN1140-1192531A:1141-119252
1.24ENST0000035644324ENSE00001240526chr18:3100424-3100318107MYOM1_HUMAN1192-1228371A:1192-122837
1.25ENST0000035644325ENSE00001240522chr18:3100201-310015745MYOM1_HUMAN1228-1243161A:1228-124316
1.26bENST0000035644326bENSE00001240516chr18:3094304-3094168137MYOM1_HUMAN1243-1288461A:1243-128846
1.27ENST0000035644327ENSE00001592917chr18:3090800-3090656145MYOM1_HUMAN1289-1337491A:1289-133749
1.28ENST0000035644328ENSE00001709505chr18:3089594-308953560MYOM1_HUMAN1337-1357211A:1337-135721
1.29ENST0000035644329ENSE00001645638chr18:3089239-308917268MYOM1_HUMAN1357-1379231A:1357-137923
1.30ENST0000035644330ENSE00001692605chr18:3086149-3086036114MYOM1_HUMAN1380-1417381A:1380-1417 (gaps)38
1.31ENST0000035644331ENSE00001738311chr18:3085130-308504388MYOM1_HUMAN1418-1447301A:1418-144730
1.32ENST0000035644332ENSE00001676386chr18:3084025-308398739MYOM1_HUMAN1447-1460141A:1447-14471
1.33ENST0000035644333ENSE00001782333chr18:3083892-3083787106MYOM1_HUMAN1460-1495360--
1.34ENST0000035644334ENSE00001735824chr18:3079340-3079177164MYOM1_HUMAN1495-1550560--
1.35ENST0000035644335ENSE00001803821chr18:3075759-307572337MYOM1_HUMAN1550-1562130--
1.36ENST0000035644336ENSE00001731412chr18:3075474-307545223MYOM1_HUMAN1562-157090--
1.37ENST0000035644337ENSE00001618984chr18:3071887-307183256MYOM1_HUMAN1570-1588190--
1.38ENST0000035644338ENSE00001615622chr18:3067553-3066805749MYOM1_HUMAN1589-1685970--

(-) 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:303
 aligned with MYOM1_HUMAN | P52179 from UniProtKB/Swiss-Prot  Length:1685

    Alignment length:307
                                  1150      1160      1170      1180      1190      1200      1210      1220      1230      1240      1250      1260      1270      1280      1290      1300      1310      1320      1330      1340      1350      1360      1370      1380      1390      1400      1410      1420      1430      1440       
         MYOM1_HUMAN   1141 TKEVVVNVDDDGVISLNFECDKMTPKSEFSWSKDYVSTEDSPRLEVESKGNKTKMTFKDLGMDDLGIYSCDVTDTDGIASSYLIDEEELKRLLALSHEHKFPTVPVKSELAVEILEKGQVRFWMQAEKLSGNAKVNYIFNEKEIFEGPKYKMHIDRNTGIIEMFMEKLQDEDEGTYTFQLQDGKATNHSTVVLVGDVFKKLQKEAEFQRQEWIRKQGPHFVEYLSWEVTGECNVLLKCKVANIKKETHIVWYKDEREISVDEKHDFKDGICTLLITEFSKKDAGIYEVILKDDRGKDKSRLKLVDEA 1447
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee.....eeeeee.........eeeee..ee......eeeeee..eeeeee...hhhhheeeeeee.......eeeeehhhhhhhhhhhhhhhhh....eeeeeeeee.....eeeeeee.......eeeeee..eee......eeeee....eeeeee...hhhhheeeeeeee....eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeee...eeeeeeeee......eeeeee..eeeeee...----.eeeeee...hhhhheeeeeeee.....eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.23  PDB: A:1141-1192 UniProt: 1140-1192      -----------------------------------Exon 1.25       ---------------------------------------------Exon 1.27  PDB: A:1289-1337 UniProt: 1289-1337   -------------------Exon 1.29              Exon 1.30  PDB: A:1380-1417 (gaps)    Exon 1.31  PDB: A:1418-1447    Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------Exon 1.24  PDB: A:1192-1228          --------------Exon 1.26b  PDB: A:1243-1288                  ------------------------------------------------Exon 1.28            -----------------------------------------------------------------------------------------1 Transcript 1 (2)
                2y23 A 1141 TKEVVVNVDDDGVISLNFECDKMTPKSEFSWSKDYVSTEDSPRLEVESKGNKTKMTFKDLGMDDLGIYSCDVTDTDGIASSYLIDEEELKRLLALSHEHKFPTVPVKSELAVEILEKGQVRFWMQAEKLSGNAKVNYIFNEKEIFEGPKYKMHIDRNTGIIEMFMEKLQDEDEGTYTFQLQDGKATNHSTVVLVGDVFKKLQKEAEFQRQEWIRKQGPHFVEYLSWEVTGECNVLLKCKVANIKKETHIVWYKDEREISVDEKH----GICTLLITEFSKKDAGIYEVILKDDRGKDKSRLKLVDEA 1447
                                  1150      1160      1170      1180      1190      1200      1210      1220      1230      1240      1250      1260      1270      1280      1290      1300      1310      1320      1330      1340      1350      1360      1370      1380      1390      1400   |  1410      1420      1430      1440       
                                                                                                                                                                                                                                                                                                1404 1409
   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  (0, 0)

(no "SCOP Domain" information available for 2Y23)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Y23)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2Y23)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MYOM1_HUMAN | P52179)
molecular function
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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.
    GO:0008307    structural constituent of muscle    The action of a molecule that contributes to the structural integrity of a muscle fiber.
biological process
    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:0002230    positive regulation of defense response to virus by host    Any host process that results in the promotion of antiviral immune response mechanisms, thereby limiting viral replication.
    GO:0098779    positive regulation of macromitophagy in response to mitochondrial depolarization    The macromitophagy process that is triggered by a detection of the loss of mitochondrial membrane potential.
    GO:0098792    xenophagy    The macroautophagy process in which a region of cytoplasm containing an intracellular pathogen or some part of an intracellular pathogen (e.g. viral capsid) is enclosed in a double membrane bound autophagosome, which then fuses with the lysosome leading to degradation of the contents.
cellular component
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0032982    myosin filament    A protein complex containing myosin heavy chains, plus associated light chains and other proteins, in which the myosin heavy chains are arranged into a filament.
    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:0005863    striated muscle myosin thick filament    Bipolar filaments formed of polymers of a muscle-specific myosin II isoform, found in the middle of sarcomeres in myofibrils.

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  2y23
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 Related Entries

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

UniProtKB/Swiss-Prot
        MYOM1_HUMAN | P52179: 2r15 2y25 3rbs 5fm4 5fm5 5fm8

(-) Related Entries Specified in the PDB File

2y25 CRYSTAL STRUCTURE OF THE MYOMESIN DOMAINS MY11-MY13