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(-) Description

Title :  CRYSTAL STRUCTURE OF MYOSIN V MOTOR WITHOUT NUCLEOTIDE SOAKED IN 10 MM MGADP
 
Authors :  P. -D. Coureux, H. L. Sweeney, A. Houdusse
Date :  03 Sep 04  (Deposition) - 22 Feb 05  (Release) - 16 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Unconventional Myosin, Myosin V, Chicken, Molecular Motor, Atpase, Elc, Iq Motif, Muscle Protein, Mgadp, Motor Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. -D. Coureux, H. L. Sweeney, A. Houdusse
Three Myosin V Structures Delineate Essential Features Of Chemo-Mechanical Transduction
Embo J. V. 23 4527 2004
PubMed-ID: 15510214  |  Reference-DOI: 10.1038/SJ.EMBOJ.7600458

(-) Compounds

Molecule 1 - MYOSIN VA
    ChainsA
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System Cell LineSF9
    Expression System CommonFALL ARMYWORM
    Expression System Taxid7108
    Expression System Vector TypeBACULOVIRUS
    FragmentMOTOR DOMAIN, RESIDUES 1-792
    Organism CommonCHICKEN
    Organism ScientificGALLUS GALLUS
    Organism Taxid9031
    Other DetailsSOAKED MGADP
    SynonymMYOSIN 5A, DILUTE MYOSIN HEAVY CHAIN, NON-MUSCLE, MYOSIN HEAVY CHAIN P190, MYOSIN-V
 
Molecule 2 - MYOSIN LIGHT CHAIN 1, SLOW-TWITCH MUSCLE A ISOFORM
    ChainsB
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System Cell LineSF9
    Expression System CommonFALL ARMYWORM
    Expression System Taxid7108
    Expression System Vector TypeBACULOVIRUS
    FragmentRESIDUES 59-208
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMLC1SA

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:111 , PRO A:112 , GLU A:114 , TYR A:119 , GLY A:166 , GLY A:168 , LYS A:169 , THR A:170 , VAL A:171 , HOH A:2005BINDING SITE FOR RESIDUE ADP A1796

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1W7I)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1W7I)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1W7I)

(-) PROSITE Motifs  (3, 6)

Asymmetric/Biological Unit (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EF_HAND_2PS50222 EF-hand calcium-binding domain profile.MYL6B_HUMAN64-99
141-176
191-208
  3B:7-42
B:85-119
B:134-150
2MYOSIN_MOTORPS51456 Myosin motor domain profile.MYO5A_CHICK69-764  1A:69-764
3IQPS50096 IQ motif profile.MYO5A_CHICK767-796
790-819
815-844
838-867
863-890
888-915
  2A:767-792
A:790-792
-
-
-
-

(-) Exons   (0, 0)

(no "Exon" information available for 1W7I)

(-) 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:750
 aligned with MYO5A_CHICK | Q02440 from UniProtKB/Swiss-Prot  Length:1829

    Alignment length:791
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784       794 
          MYO5A_CHICK     5 ELYTKYARVWIPDPEEVWKSAELLKDYKPGDKVLQLRLEEGKDLEYCLDPKTKELPPLRNPDILVGENDLTALSYLHEPAVLHNLKVRFIDSKLIYTYCGIVLVAINPYEQLPIYGEDIINAYSGQNMGDMDPHIFAVAEEAYKQMARDERNQSIIVSGESGAGKTVSAKYAMRYFATVSGSASEANVEEKVLASNPIMESIGNAKTTRNDNSSRFGKYIEIGFDKRYRIIGANMRTYLLEKSRVVFQAEEERNYHIFYQLCASAALPEFKTLRLGNANYFHYTKQGGSPVIDGIDDAKEMVNTRQACTLLGISDSYQMGIFRILAGILHLGNVEFASRDSDSCAIPPKHDPLTIFCDLMGVDYEEMAHWLCHRKLATATETYIKPISKLHAINARDALAKHIYANLFNWIVDHVNKALHSTVKQHSFIGVLDIYGFETFEINSFEQFCINYANEKLQQQFNMHVFKLEQEEYMKEQIPWTLIDFYDNQPCINLIEAKMGVLDLLDEECKMPKGSDDTWAQKLYNTHLNKCALFEKPRLSNKAFIIKHFADKVEYQCEGFLEKNKDTVYEEQIKVLKSSKKFKLLPELFQDEEKAISPTSATPSGRVPLSRTPVKPAKARPGQTSKEHKKTVGHQFRNSLHLLMETLNATTPHYVRCIKPNDFKFPFTFDEKRAVQQLRACGVLETIRISAAGFPSRWTYQEFFSRYRVLMKQKDVLSDRKQTCKNVLEKLILDKDKYQFGKTKIFFRAGQVAYLEKIRADKLRAACIRIQKTIRGWLMRKKYMRMRRAAI 795
               SCOP domains d1w7ia1 A:5-62 automated matches                          d1w7ia2 A:63-795 automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------------------------------------------Myosin_head-1w7iA01 A:71-752                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              --------------------------------------IQ--- Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IQ--- Pfam domains (2)
         Sec.struct. author .......eeeeee...eeeeeee.........eeeeee..eeeeeee.............hhhhh....hhhh...hhhhhhhhhhhhhhhhh..eeee..eeeee.........hhhhhhhhh..hhhhh..hhhhhhhhhhhhhhh....eeeeee.....hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhee.......ee..eeeeeeee.....eeeeeeeee..hhhhhh........hhhhhhhhh...hhhhh.........hhhhhh.........hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh..eee...eee....hhhhhhhhhhhh.hhhhhhhhhheeee.----.eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeeee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhhhhhhh.....ee.......eeeee....eeeee..hhhhhhh...hhhhhhhhhh....hhhhhh..-------------------------------------...hhhhhhhhhhhhhhhhhhh.eeeeeeee...........hhhhhhhhhhh.hhhhhhhhhh....eeeehhhhhhhhhhhh.......hhhhhhhhhhhhhh.hhh.eee...eeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ----------------------------------------------------------------MYOSIN_MOTOR  PDB: A:69-764 UniProt: 69-764                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             -------------------------IQ     PROSITE (2)
                PROSITE (1) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IQ  PDB: A:767-792            PROSITE (1)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1w7i A   5 ELYTKYARVWIPDPEEVWKSAELLKDYKPGDKVLQLRLEEGKDLEYCLDPKTKELPPLRNPDILVGENDLTALSYLHEPAVLHNLKVRFIDSKLIYTYCGIVLVAINPYEQLPIYGEDIINAYSGQNMGDMDPHIFAVAEEAYKQMARDERNQSIIVSGESGAGKTVSAKYAMRYFATVSGSASEANVEEKVLASNPIMESIGNAKTTRNDNSSRFGKYIEIGFDKRYRIIGANMRTYLLEKSRVVFQAEEERNYHIFYQLCASAALPEFKTLRLGNANYFHYTKQGGSPVIDGIDDAKEMVNTRQACTLLGISDSYQMGIFRILAGILHLGNVEFASRDSDSCAIPPKHDPLTIFCDLMGVDYEEMAHWLCHRKLA----TYIKPISKLHAINARDALAKHIYANLFNWIVDHVNKALHSTVKQHSFIGVLDIYGFETFEINSFEQFCINYANEKLQQQFNMHVFKLEQEEYMKEQIPWTLIDFYDNQPCINLIEAKMGVLDLLDEECKMPKGSDDTWAQKLYNTHLNKCALFEKPRLSNKAFIIKHFADKVEYQCEGFLEKNKDTVYEEQIKVLKSSKKFKLLPELFQ-------------------------------------HKKTVGHQFRNSLHLLMETLNATTPHYVRCIKPNDFKFPFTFDEKRAVQQLRACGVLETIRISAAGFPSRWTYQEFFSRYRVLMKQKDVLSDRKQTCKNVLEKLILDKDKYQFGKTKIFFRAGQVAYLEKIRADKLRAACIRIQKTIRGWLMRKKYMRMRRGDA 795
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374      |  - |     394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594         -         -         -       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784       794 
                                                                                                                                                                                                                                                                                                                                                                                                                  381  386                                                                                                                                                                                                             594                                   632                                                                                                                                                                   

Chain B from PDB  Type:PROTEIN  Length:145
 aligned with MYL6B_HUMAN | P14649 from UniProtKB/Swiss-Prot  Length:208

    Alignment length:148
                                    69        79        89        99       109       119       129       139       149       159       169       179       189       199        
          MYL6B_HUMAN    60 EFNKDQLEEFKEAFELFDRVGDGKILYSQCGDVMRALGQNPTNAEVLKVLGNPKSDELKSRRVDFETFLPMLQAVAKNRGQGTYEDYLEGFRVFDKEGNGKVMGAELRHVLTTLGEKMTEEEVETVLAGHEDSNGCINYEAFLKHILS 207
               SCOP domains d1w7ib_ B: automated matches                                                                                                                         SCOP domains
               CATH domains --1w7iB01 B:5-86 EF-hand                                                            1w7iB02 B:87-148 EF-hand                                      -- CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------------EF_hand_4-1w7iB01 B:88-131                  ------------------- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------EF_hand_4-1w7iB02 B:88-131                  ------------------- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhh......eee.hhhhhhhhhh....hhhhhhhhhh..hhhhhh..eeehhhhhhhhhhhhh..---.hhhhhhhhhhh......eeehhhhhhhhhh.....hhhhhhhhh........eeehhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----EF_HAND_2  PDB: B:7-42              -----------------------------------------EF_HAND_2  PDB: B:85-119            --------------EF_HAND_2         PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1w7i B   3 EFNKDQLEEFKEAFELFDRVGDGKILYSQCGDVMRALGQNPTNAEVLKVLGNPKSDELKSRRVDFETFLPMLQAVAKNR---TYEDYLEGFRVFDKEGNGKVMGAELRHVLTTLGEKMTEEEVETVLAGHEDSNGCINYEAFLKHILS 150
                                    12        22        32        42        52        62        72        |-  |     92       102       112       122       132       142        
                                                                                                         81  85                                                                 

   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  (3, 3)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit

(-) Pfam Domains  (3, 5)

Asymmetric/Biological Unit
(-)
Clan: EF_hand (270)
(-)
Family: IQ (2)
3aIQ-1w7iA02A:791-792
3bIQ-1w7iA03A:791-792

(-) Gene Ontology  (26, 29)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MYO5A_CHICK | Q02440)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003779    actin binding    Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
    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:0000146    microfilament motor activity    Catalysis of movement along a microfilament, coupled to the hydrolysis of a nucleoside triphosphate (usually ATP).
    GO:0060001    minus-end directed microfilament motor activity    Catalysis of movement along a microfilament towards the minus end, coupled to the hydrolysis of a nucleoside triphosphate (usually ATP). The minus end of an actin filament is the end that does not preferentially add actin monomers.
    GO:0003774    motor activity    Catalysis of the generation of force resulting either in movement along a microfilament or microtubule, or in torque resulting in membrane scission, coupled to the hydrolysis of a nucleoside triphosphate.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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).
biological process
    GO:0032869    cellular response to insulin 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 insulin stimulus. Insulin is a polypeptide hormone produced by the islets of Langerhans of the pancreas in mammals, and by the homologous organs of other organisms.
    GO:0072659    protein localization to plasma membrane    A process in which a protein is transported to, or maintained in, a specific location in the plasma membrane.
    GO:0016192    vesicle-mediated transport    A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0000139    Golgi membrane    The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
    GO:0031941    filamentous actin    A two-stranded helical polymer of the protein actin.
    GO:0032593    insulin-responsive compartment    A small membrane-bounded vesicle that releases its contents by exocytosis in response to insulin stimulation; the contents are enriched in GLUT4, IRAP and VAMP2.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0016459    myosin complex    A protein complex, formed of one or more myosin heavy chains plus associated light chains and other proteins, that functions as a molecular motor; uses the energy of ATP hydrolysis to move actin filaments or to move vesicles or other cargo on fixed actin filaments; has magnesium-ATPase activity and binds actin. Myosin classes are distinguished based on sequence features of the motor, or head, domain, but also have distinct tail regions that are believed to bind specific cargoes.

Chain B   (MYL6B_HUMAN | P14649)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0003774    motor activity    Catalysis of the generation of force resulting either in movement along a microfilament or microtubule, or in torque resulting in membrane scission, coupled to the hydrolysis of a nucleoside triphosphate.
    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: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:0030049    muscle filament sliding    The sliding of actin thin filaments and myosin thick filaments past each other in muscle contraction. This involves a process of interaction of myosin located on a thick filament with actin located on a thin filament. During this process ATP is split and forces are generated.
    GO:0007519    skeletal muscle tissue development    The developmental sequence of events leading to the formation of adult skeletal muscle tissue. The main events are: the fusion of myoblasts to form myotubes that increase in size by further fusion to them of myoblasts, the formation of myofibrils within their cytoplasm and the establishment of functional neuromuscular junctions with motor neurons. At this stage they can be regarded as mature muscle fibers.
cellular component
    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: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:0005859    muscle myosin complex    A filament of myosin found in a muscle cell of any type.
    GO:0016459    myosin complex    A protein complex, formed of one or more myosin heavy chains plus associated light chains and other proteins, that functions as a molecular motor; uses the energy of ATP hydrolysis to move actin filaments or to move vesicles or other cargo on fixed actin filaments; has magnesium-ATPase activity and binds actin. Myosin classes are distinguished based on sequence features of the motor, or head, domain, but also have distinct tail regions that are believed to bind specific cargoes.
    GO:0016461    unconventional myosin complex    A portmanteau term for myosins other than myosin II.

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 Related Entries

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

UniProtKB/Swiss-Prot
        MYL6B_HUMAN | P146491oe9 1w7j
        MYO5A_CHICK | Q024401oe9 1w7j 1w8j 2dfs

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1W7I)