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(-) Description

Title :  CRYSTAL STRUCTURE OF THE MYOMESIN DOMAINS 12 AND 13
 
Authors :  N. Pinotsis, M. Wilmanns, S. Lange
Date :  22 Aug 07  (Deposition) - 29 Jan 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.24
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Sarcomeric Protein, Ig-Like Domains, Homodimer, Immunoglobulin Domain, Muscle Protein, Thick Filament, Contractile Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Pinotsis, S. Lange, J. C. Perriard, D. I. Svergun, M. Wilmanns
Molecular Basis Of The C-Terminal Tail-To-Tail Assembly Of The Sarcomeric Filament Protein Myomesin.
Embo J. V. 27 253 2008
PubMed-ID: 18059477  |  Reference-DOI: 10.1038/SJ.EMBOJ.7601944

(-) Compounds

Molecule 1 - MYOMESIN-1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET22B(+)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: DOMAINS 12 AND 13, UNP RESIDUES 1225-1443
    Gene: MYOM1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: 190 KDA TITIN-ASSOCIATED PROTEIN, 190 KDA CONNECTIN- ASSOCIATED PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2GOL3Ligand/IonGLYCEROL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:1652BINDING SITE FOR RESIDUE ACT A 604
2AC2SOFTWAREHOH A:109 , HOH A:236 , GLU A:1624 , TYR A:1630BINDING SITE FOR RESIDUE GOL A 601
3AC3SOFTWARETYR A:1630 , HOH B:178 , HOH B:234 , GLU B:1624BINDING SITE FOR RESIDUE GOL B 602
4AC4SOFTWARETHR A:1660 , LYS B:1643 , THR B:1660BINDING SITE FOR RESIDUE GOL B 603

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2R15)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Asp A:1599 -Pro A:1600
2Asp B:1599 -Pro B:1600

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2R15)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2R15)

(-) Exons   (6, 12)

Asymmetric/Biological Unit (6, 12)
 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_HUMAN1140-1192530--
1.24ENST0000035644324ENSE00001240526chr18:3100424-3100318107MYOM1_HUMAN1192-1228370--
1.25ENST0000035644325ENSE00001240522chr18:3100201-310015745MYOM1_HUMAN1228-1243160--
1.26bENST0000035644326bENSE00001240516chr18:3094304-3094168137MYOM1_HUMAN1243-1288460--
1.27ENST0000035644327ENSE00001592917chr18:3090800-3090656145MYOM1_HUMAN1289-1337490--
1.28ENST0000035644328ENSE00001709505chr18:3089594-308953560MYOM1_HUMAN1337-1357210--
1.29ENST0000035644329ENSE00001645638chr18:3089239-308917268MYOM1_HUMAN1357-1379230--
1.30ENST0000035644330ENSE00001692605chr18:3086149-3086036114MYOM1_HUMAN1380-1417380--
1.31ENST0000035644331ENSE00001738311chr18:3085130-308504388MYOM1_HUMAN1418-1447300--
1.32ENST0000035644332ENSE00001676386chr18:3084025-308398739MYOM1_HUMAN1447-1460140--
1.33ENST0000035644333ENSE00001782333chr18:3083892-3083787106MYOM1_HUMAN1460-1495362A:1461-1495
B:1461-1495		35
35
1.34ENST0000035644334ENSE00001735824chr18:3079340-3079177164MYOM1_HUMAN1495-1550562A:1495-1550
B:1495-1550		56
56
1.35ENST0000035644335ENSE00001803821chr18:3075759-307572337MYOM1_HUMAN1550-1562132A:1550-1562
B:1550-1562		13
13
1.36ENST0000035644336ENSE00001731412chr18:3075474-307545223MYOM1_HUMAN1562-157092A:1562-1570
B:1562-1570		9
9
1.37ENST0000035644337ENSE00001618984chr18:3071887-307183256MYOM1_HUMAN1570-1588192A:1570-1588
B:1570-1588		19
19
1.38ENST0000035644338ENSE00001615622chr18:3067553-3066805749MYOM1_HUMAN1589-1685972A:1589-1667
B:1589-1667		79
79

(-) 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:207
 aligned with MYOM1_HUMAN | P52179 from UniProtKB/Swiss-Prot  Length:1685

    Alignment length:207
                                  1470      1480      1490      1500      1510      1520      1530      1540      1550      1560      1570      1580      1590      1600      1610      1620      1630      1640      1650      1660       
         MYOM1_HUMAN   1461 LSATDLKIQSTAEGIQLYSFVTYYVEDLKVNWSHNGSAIRYSDRVKTGVTGEQIWLQINEPTPNDKGKYVMELFDGKTGHQKTVDLSGQAYDEAYAEFQRLKQAAIAEKNRARVLGGLPDVVTIQEGKALNLTCNVWGDPPPEVSWLKNEKALASDDHCNLKFEAGRTAYFTINGVSTADSGKYGLVVKNKYGSETSDFTVSVFIPE 1667
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee...eeeeeee........eeeeee..ee......eeeeee..eeeeeee..hhhhheeeeeeee....eeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhh.eeee....eeeee....eeeeeeee.....eeeeee..eee.....eeeeee...eeeeee...hhhhheeeeeeeee..eeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.33  PDB: A:1461-1495        ------------------------------------------------------Exon 1.35    -------Exon 1.37          Exon 1.38  PDB: A:1589-1667 UniProt: 1589-1685 [INCOMPLETE]                     Transcript 1 (1)
           Transcript 1 (2) ----------------------------------Exon 1.34  PDB: A:1495-1550 UniProt: 1495-1550          -----------Exon 1.36------------------------------------------------------------------------------------------------- Transcript 1 (2)
                2r15 A 1461 LSATDLKIQSTAEGIQLYSFVTYYVEDLKVNWSHNGSAIRYSDRVKTGVTGEQIWLQINEPTPNDKGKYVMELFDGKTGHQKTVDLSGQAYDEAYAEFQRLKQAAIAEKNRARVLGGLPDVVTIQEGKALNLTCNVWGDPPPEVSWLKNEKALAQTDHCNLKFEAGRTAYFTINGVSTADSGKYGLVVKNKYGSETSDFTVSVFIPE 1667
                                  1470      1480      1490      1500      1510      1520      1530      1540      1550      1560      1570      1580      1590      1600      1610      1620      1630      1640      1650      1660       


Chain B from PDB  Type:PROTEIN  Length:207
 aligned with MYOM1_HUMAN | P52179 from UniProtKB/Swiss-Prot  Length:1685

    Alignment length:207
                                  1470      1480      1490      1500      1510      1520      1530      1540      1550      1560      1570      1580      1590      1600      1610      1620      1630      1640      1650      1660       
         MYOM1_HUMAN   1461 LSATDLKIQSTAEGIQLYSFVTYYVEDLKVNWSHNGSAIRYSDRVKTGVTGEQIWLQINEPTPNDKGKYVMELFDGKTGHQKTVDLSGQAYDEAYAEFQRLKQAAIAEKNRARVLGGLPDVVTIQEGKALNLTCNVWGDPPPEVSWLKNEKALASDDHCNLKFEAGRTAYFTINGVSTADSGKYGLVVKNKYGSETSDFTVSVFIPE 1667
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee...eeeeeee........eeeeee..ee......eeeeee..eeeeeee..hhhhheeeeeeee....eeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhh.eeee....eeeee....eeeeeeee.....eeeeee..eee.....eeeeee...eeeeee...hhhhheeeeeeeee..eeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.33  PDB: B:1461-1495        ------------------------------------------------------Exon 1.35    -------Exon 1.37          Exon 1.38  PDB: B:1589-1667 UniProt: 1589-1685 [INCOMPLETE]                     Transcript 1 (1)
           Transcript 1 (2) ----------------------------------Exon 1.34  PDB: B:1495-1550 UniProt: 1495-1550          -----------Exon 1.36------------------------------------------------------------------------------------------------- Transcript 1 (2)
                2r15 B 1461 LSATDLKIQSTAEGIQLYSFVTYYVEDLKVNWSHNGSAIRYSDRVKTGVTGEQIWLQINEPTPNDKGKYVMELFDGKTGHQKTVDLSGQAYDEAYAEFQRLKQAAIAEKNRARVLGGLPDVVTIQEGKALNLTCNVWGDPPPEVSWLKNEKALAQTDHCNLKFEAGRTAYFTINGVSTADSGKYGLVVKNKYGSETSDFTVSVFIPE 1667
                                  1470      1480      1490      1500      1510      1520      1530      1540      1550      1560      1570      1580      1590      1600      1610      1620      1630      1640      1650      1660
   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 2R15)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2R15)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2R15)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (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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  2r15
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  MYOM1_HUMAN | P52179
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 Related Entries

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

UniProtKB/Swiss-Prot
        MYOM1_HUMAN | P52179: 2y23 2y25 3rbs 5fm4 5fm5 5fm8

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2R15)