PDBsum entry 2oy6

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protein ligands metals Protein-protein interface(s) links
Contractile protein PDB id
Jmol PyMol
Protein chains
810 a.a. *
145 a.a. *
159 a.a. *
* Residue conservation analysis
Superseded by: 3i5f
PDB id:
Name: Contractile protein
Title: Crystal structure of squid mg.Adp myosin s1
Structure: Myosin heavy chain isoform a. Chain: a. Myosin regulatory light chain lc-2. Chain: b. Synonym: rlc. Myosin catalytic light chain lc-1. Chain: c
Source: Loligo pealei. Organism_taxid: 6621. Todarodes pacificus. Japanese flying squid. Organism_taxid: 6637. Organism_taxid: 6637
3.00Å     R-factor:   0.222     R-free:   0.312
Authors: Y.Yang,S.Gourinath,M.Kovacs,L.Nyitray,R.Reutzel,D.M.Himmel, E.O'Neall-Hennessey,L.Reshetnikova,A.G.Szent-Gyorgyi, J.H.Brown,C.Cohen
Key ref:
Y.Yang et al. (2007). Rigor-like Structures from Muscle Myosins Reveal Key Mechanical Elements in the Transduction Pathways of This Allosteric Motor. Structure, 15, 553-564. PubMed id: 17502101 DOI: 10.1016/j.str.2007.03.010
21-Feb-07     Release date:   29-May-07    
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Protein chain
Pfam   ArchSchema ?
O44934  (O44934_LOLPE) -  Myosin heavy chain isoform A
1935 a.a.
810 a.a.
Protein chain
Pfam   ArchSchema ?
P08052  (MLR_TODPA) -  Myosin regulatory light chain LC-2, mantle muscle
153 a.a.
145 a.a.
Protein chain
P05945  (MLE_TODPA) -  Myosin catalytic light chain LC-1, mantle muscle
160 a.a.
159 a.a.
Key:    PfamA domain  Secondary structure  CATH domain


DOI no: 10.1016/j.str.2007.03.010 Structure 15:553-564 (2007)
PubMed id: 17502101  
Rigor-like Structures from Muscle Myosins Reveal Key Mechanical Elements in the Transduction Pathways of This Allosteric Motor.
Y.Yang, S.Gourinath, M.Kovács, L.Nyitray, R.Reutzel, D.M.Himmel, E.O'neall-Hennessey, L.Reshetnikova, A.G.Szent-Györgyi, J.H.Brown, C.Cohen.
Unlike processive cellular motors such as myosin V, whose structure has recently been determined in a "rigor-like" conformation, myosin II from contracting muscle filaments necessarily spends most of its time detached from actin. By using squid and sea scallop sources, however, we have now obtained similar rigor-like atomic structures for muscle myosin heads (S1). The significance of the hallmark closed actin-binding cleft in these crystal structures is supported here by actin/S1-binding studies. These structures reveal how different duty ratios, and hence cellular functions, of the myosin isoforms may be accounted for, in part, on the basis of detailed differences in interdomain contacts. Moreover, the rigor-like position of switch II turns out to be unique for myosin V. The overall arrangements of subdomains in the motor are relatively conserved in each of the known contractile states, and we explore qualitatively the energetics of these states.
  Selected figure(s)  
Figure 2.
Figure 2. Comparison of the Rigor-like and Post-Rigor States of Muscle Myosin S1 and Its Active Site
(A and B) Detailed legends for all figures are supplied in Supplemental Data. (A) Schematic overlay of (squid) S1 in the two states (see text). The rigor-like state is shown in green, and the post-rigor state is shown in red. Thicker lines indicate proximity to the reader. The overall conformational differences between these (and the pre-power stroke) states are generally conserved in the different isoforms. The locations of interdomain interactions that nevertheless appear to preferentially stabilize the high-duty ratio non-muscle myosin V in a rigor-like conformation and some of the low-duty ratio myosin II isoforms in a non-rigor-like (actin-detached) conformation are indicated here with blue and red asterisks, respectively (also see text and Figure 3, Figure 4 and Figure 5). (B) The rigor-like location of switch II in the various myosin II and VI structures (green), which have small side chains at (squid) position 465, differs from that in myosin V (blue), in which 465 is a tyrosine. The locations of both switch I and switch II away from the nucleotide and near each other force the tyrosine to adopt a “g−” rotamer. The myosin V switch II is displaced toward the P loop of the N-terminal subdomain in the rigor-like state to avoid a clash of this rotamer with helix W (not shown). In the post-rigor state (red), switch I (including Ser246) is near the nucleotide and relatively far from switch II. Here, the tyrosine has room to adopt the “g+” rotamer and does not perturb the arrangement of the active site elements.
Figure 3.
Figure 3. Conserved and Variable Features of the Rigor-like 50 kDa Cleft
(A–E) The schematic S1 inset on this and subsequent figures shows the region that is magnified (box) and the viewpoint (arrow). Squid sequence numbering is used. (A) Displayed are selected interactions between the upper (dark green) and lower (light green) 50 kDa subdomains made in the squid rigor-like structure that are also made (with identical or homologous residues) in the other isoforms studied when the corresponding part of their cleft is also fully closed. Interactions include H-bonded/electrostatic contacts (dotted lines) and extensive burial of certain apolar residues (underlined labels). (B–E) Variations in crosscleft contacts, as well as in the orientations of the upper and lower 50 kDa subdomains or of subregions within them, help determine the extent of inner and outer cleft closure in the various isoforms (the green, dashed line shows squid for comparison.) (B) Myosin V displays the most closed cleft in the strut region (also see Table 1), perhaps due to a “complex H-bond link” (blue, dotted lines) between Asn424, Lys601, and Glu598 not seen in any other isoform; position 598 is aspartate in squid and sea scallop, and 424 is serine in Dictyostelium (see below for myosin VI). (C) A slightly modified orientation of helix HR relative to helix HQ yields a fully closed outer but incompletely closed inner cleft in catch and striated sea scallop S1. (D) Curvature of helix HO about a Dictyostelium-specific glycine at 435 contributes to its fully closed inner but partially open outer cleft. (E) The entire cleft of myosin VI is incompletely closed. A myosin VI-specific lysine at position 650 appears to disrupt the interdomain 602-274-431 complex salt link made from the strut.
  The above figures are reprinted by permission from Cell Press: Structure (2007, 15, 553-564) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20824272 V.Caorsi, D.S.Ushakov, T.G.West, N.Setta-Kaffetzi, and M.A.Ferenczi (2011).
FRET characterisation for cross-bridge dynamics in single-skinned rigor muscle fibres.
  Eur Biophys J, 40, 13-27.  
20801044 A.Málnási-Csizmadia, and M.Kovács (2010).
Emerging complex pathways of the actomyosin powerstroke.
  Trends Biochem Sci, 35, 684-690.  
20160108 C.V.Sindelar, and K.H.Downing (2010).
An atomic-level mechanism for activation of the kinesin molecular motors.
  Proc Natl Acad Sci U S A, 107, 4111-4116.  
20018884 H.Brzeska, J.Guag, K.Remmert, S.Chacko, and E.D.Korn (2010).
An experimentally based computer search identifies unstructured membrane-binding sites in proteins: application to class I myosins, PAKS, and CARMIL.
  J Biol Chem, 285, 5738-5747.  
20192767 H.L.Sweeney, and A.Houdusse (2010).
Structural and functional insights into the Myosin motor mechanism.
  Annu Rev Biophys, 39, 539-557.  
20459085 J.J.Frye, V.A.Klenchin, C.R.Bagshaw, and I.Rayment (2010).
Insights into the importance of hydrogen bonding in the gamma-phosphate binding pocket of myosin: structural and functional studies of serine 236.
  Biochemistry, 49, 4897-4907.
PDB codes: 3myh 3myk 3myl
20399183 M.Cecchini, Y.Alexeev, and M.Karplus (2010).
Pi release from myosin: a simulation analysis of possible pathways.
  Structure, 18, 458-470.  
20616041 M.Lorenz, and K.C.Holmes (2010).
The actin-myosin interface.
  Proc Natl Acad Sci U S A, 107, 12529-12534.  
19853615 V.Ovchinnikov, B.L.Trout, and M.Karplus (2010).
Mechanical coupling in myosin V: a simulation study.
  J Mol Biol, 395, 815-833.  
19769984 D.M.Himmel, S.Mui, E.O'Neall-Hennessey, A.G.Szent-Györgyi, and C.Cohen (2009).
The on-off switch in regulated myosins: different triggers but related mechanisms.
  J Mol Biol, 394, 496-505.
PDB codes: 3jtd 3jvt
18621839 A.C.Knowles, R.E.Ferguson, B.D.Brandmeier, Y.B.Sun, D.R.Trentham, and M.Irving (2008).
Orientation of the essential light chain region of myosin in relaxed, active, and rigor muscle.
  Biophys J, 95, 3882-3891.  
18725645 J.C.Klein, A.R.Burr, B.Svensson, D.J.Kennedy, J.Allingham, M.A.Titus, I.Rayment, and D.D.Thomas (2008).
Actin-binding cleft closure in myosin II probed by site-directed spin labeling and pulsed EPR.
  Proc Natl Acad Sci U S A, 105, 12867-12872.  
18155233 J.H.Brown, Y.Yang, L.Reshetnikova, S.Gourinath, D.Süveges, J.Kardos, F.Hóbor, R.Reutzel, L.Nyitray, and C.Cohen (2008).
An unstable head-rod junction may promote folding into the compact off-state conformation of regulated myosins.
  J Mol Biol, 375, 1434-1443.
PDB codes: 3bas 3bat
18046460 J.Ménétrey, P.Llinas, J.Cicolari, G.Squires, X.Liu, A.Li, H.L.Sweeney, and A.Houdusse (2008).
The post-rigor structure of myosin VI and implications for the recovery stroke.
  EMBO J, 27, 244-252.
PDB codes: 2vas 2vb6
18202824 L.A.Amos (2008).
Molecular motors: not quite like clockwork.
  Cell Mol Life Sci, 65, 509-515.  
18951904 L.Alamo, W.Wriggers, A.Pinto, F.Bártoli, L.Salazar, F.Q.Zhao, R.Craig, and R.Padrón (2008).
Three-dimensional reconstruction of tarantula myosin filaments suggests how phosphorylation may regulate myosin activity.
  J Mol Biol, 384, 780-797.
PDB code: 3dtp
18704171 M.Cecchini, A.Houdusse, and M.Karplus (2008).
Allosteric communication in myosin V: from small conformational changes to large directed movements.
  PLoS Comput Biol, 4, e1000129.  
18211892 M.Gyimesi, B.Kintses, A.Bodor, A.Perczel, S.Fischer, C.R.Bagshaw, and A.Málnási-Csizmadia (2008).
The mechanism of the reverse recovery step, phosphate release, and actin activation of Dictyostelium myosin II.
  J Biol Chem, 283, 8153-8163.  
18552179 M.Sun, M.B.Rose, S.K.Ananthanarayanan, D.J.Jacobs, and C.M.Yengo (2008).
Characterization of the pre-force-generation state in the actomyosin cross-bridge cycle.
  Proc Natl Acad Sci U S A, 105, 8631-8636.  
17848543 C.Cohen, and C.Cohen (2007).
Seeing and knowing in structural biology.
  J Biol Chem, 282, 32529-32538.  
17502095 C.R.Bagshaw (2007).
Myosin mechanochemistry.
  Structure, 15, 511-512.  
17956731 J.Ménétrey, P.Llinas, M.Mukherjea, H.L.Sweeney, and A.Houdusse (2007).
The structural basis for the large powerstroke of myosin VI.
  Cell, 131, 300-308.
PDB code: 2v26
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.