PDB-3dtp: Tarantula heavy meromyosin obtained by flexible docking to Tarant...

Basic information

• Entry: Database: PDB / ID: 3dtp
• Title: Tarantula heavy meromyosin obtained by flexible docking to Tarantula muscle thick filament Cryo-EM 3D-MAP

Components

• (Myosin-11,Myosin-7) x 2
• Myosin II regulatory light chain
• Myosin light polypeptide 6

• Keywords: CONTRACTILE PROTEIN / MUSCLE PROTEIN / SMOOTH MUSCLE / MYOSIN SUBFRAGMENT 2 / HEAVY MEROMYOSIN / ESSENTIAL LIGHT CHAIN / REGULATORY LIGHT CHAIN / MOTOR PROTEIN / COILED-COIL

Function / homology

Function:

myosin II filament / regulation of slow-twitch skeletal muscle fiber contraction / regulation of the force of skeletal muscle contraction / myofibril assembly / muscle myosin complex / elastic fiber assembly / myosin light chain binding / adult heart development / myosin II complex / skeletal muscle myosin thick filament assembly / regulation of the force of heart contraction / cardiac muscle hypertrophy in response to stress / transition between fast and slow fiber / actomyosin structure organization / myosin II binding / cardiac muscle fiber development / myosin filament / skeletal muscle contraction / actomyosin / muscle filament sliding / microfilament motor activity / myosin complex / actin-dependent ATPase activity / structural constituent of muscle / myosin heavy chain binding / myofibril / smooth muscle contraction / ventricular cardiac muscle tissue morphogenesis / ATP metabolic process / cardiac muscle contraction / striated muscle contraction / stress fiber / sarcomere / ADP binding / regulation of heart rate / muscle contraction / Z disc / actin filament binding / actin binding / calmodulin binding / ATPase activity / calcium ion binding / magnesium ion binding / ATP binding / cytosol

Domain/homology:

Myosin S1 fragment, N-terminal / EF-hand domain / Kinesin motor domain superfamily / IQ motif, EF-hand binding site / P-loop containing nucleoside triphosphate hydrolase / Myosin IQ motif-containing domain superfamily / EF-Hand 1, calcium-binding site / EF-hand domain pair / Myosin, N-terminal, SH3-like / Myosin head, motor domain / Myosin tail

Component:

Myosin II regulatory light chain / Myosin light polypeptide 6 / Myosin-11 / Myosin-7

• Biological species: Gallus gallus (chicken); Homo sapiens (human); Avicularia avicularia (pinktoe tarantula)
• Method: ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 20 Å
• Authors: Alamo, L. / Wriggers, W. / Pinto, A. / Bartoli, F. / Salazar, L. / Zhao, F.Q. / Craig, R. / Padron, R.

Citation

Journal: J Mol Biol / Year: 2008
Title: Three-dimensional reconstruction of tarantula myosin filaments suggests how phosphorylation may regulate myosin activity.
Authors: Lorenzo Alamo / Willy Wriggers / Antonio Pinto / Fulvia Bártoli / Leiria Salazar / Fa-Qing Zhao / Roger Craig / Raúl Padrón /
Abstract: Muscle contraction involves the interaction of the myosin heads of the thick filaments with actin subunits of the thin filaments. Relaxation occurs when this interaction is blocked by molecular switches on these filaments. In many muscles, myosin-linked regulation involves phosphorylation of the myosin regulatory light chains (RLCs). Electron microscopy of vertebrate smooth muscle myosin molecules (regulated by phosphorylation) has provided insight into the relaxed structure, revealing that myosin is switched off by intramolecular interactions between its two heads, the free head and the blocked head. Three-dimensional reconstruction of frozen-hydrated specimens revealed that this asymmetric head interaction is also present in native thick filaments of tarantula striated muscle. Our goal in this study was to elucidate the structural features of the tarantula filament involved in phosphorylation-based regulation. A new reconstruction revealed intra- and intermolecular myosin interactions in addition to those seen previously. To help interpret the interactions, we sequenced the tarantula RLC and fitted an atomic model of the myosin head that included the predicted RLC atomic structure and an S2 (subfragment 2) crystal structure to the reconstruction. The fitting suggests one intramolecular interaction, between the cardiomyopathy loop of the free head and its own S2, and two intermolecular interactions, between the cardiac loop of the free head and the essential light chain of the blocked head and between the Leu305-Gln327 interaction loop of the free head and the N-terminal fragment of the RLC of the blocked head. These interactions, added to those previously described, would help switch off the thick filament. Molecular dynamics simulations suggest how phosphorylation could increase the helical content of the RLC N-terminus, weakening these interactions, thus releasing both heads and activating the thick filament.

#1: Journal: J Mol Biol / Year: 2003
Title: Refined model of the 10S conformation of smooth muscle myosin by cryo-electron microscopy 3D image reconstruction.
Authors: Jun Liu / Thomas Wendt / Dianne Taylor / Kenneth Taylor /
Abstract: The actin-activated ATPase activity of smooth muscle myosin and heavy meromyosin (smHMM) is regulated by phosphorylation of the regulatory light chain (RLC). Complete regulation requires two intact myosin heads because single-headed myosin subfragments are always active. 2D crystalline arrays of the 10S form of intact myosin, which has a dephosphorylated RLC, were produced on a positively charged lipid monolayer and imaged in 3D at 2.0 nm resolution by cryo-electron microscopy of frozen, hydrated specimens. An atomic model of smooth muscle myosin was constructed from the X-ray structures of the smooth muscle myosin motor domain and essential light chain and a homology model of the RLC was produced based on the skeletal muscle S1 structure. The initial model of the 10S myosin, based on the previous reconstruction of smHMM, was subjected to real space refinement to obtain a quantitative fit to the density. The smHMM was likewise refined and both refined models reveal the same asymmetric interaction between the upper 50 kDa domain of the "blocked" head and parts of the catalytic, converter domains and the essential light chain of the "free" head observed previously. This observation suggests that this interaction is not simply due to crystallographic packing but is enforced by elements of the myosin heads. The 10S reconstruction shows additional alpha-helical coiled-coil not seen in the earlier smHMM reconstruction, but the location of one segment of S2 is the same in both.

#2: Journal: Proc Natl Acad Sci U S A / Year: 2006
Title: Crystal structures of human cardiac beta-myosin II S2-Delta provide insight into the functional role of the S2 subfragment.
Authors: Wulf Blankenfeldt / Nicolas H Thomä / John S Wray / Mathias Gautel / Ilme Schlichting /
Abstract: Myosin II is the major component of the muscle thick filament. It consists of two N-terminal S1 subfragments ("heads") connected to a long dimeric coiled-coil rod. The rod is in itself twofold symmetric, but in the filament, the two heads point away from the filament surface and are therefore not equivalent. This breaking of symmetry requires the initial section of the rod, subfragment 2 (S2), to be relatively flexible. S2 is an important functional element, involved in various mechanisms by which the activity of smooth and striated muscle is regulated. We have determined crystal structures of the 126 N-terminal residues of S2 from human cardiac beta-myosin II (S2-Delta), of both WT and the disease-associated E924K mutant. S2-Delta is a straight parallel dimeric coiled coil, but the N terminus of one chain is disordered in WT-S2-Delta due to crystal contacts, indicative of unstable local structure. Bulky noncanonical side chains pack into a/d positions of S2-Delta's N terminus, leading to defined local asymmetry and axial stagger, which could induce nonequivalence of the S1 subfragments. Additionally, S2 possesses a conserved charge distribution with three prominent rings of negative potential within S2-Delta, the first of which may provide a binding interface for the "blocked head" of smooth muscle myosin in the OFF state. The observation that many disease-associated mutations affect the second negatively charged ring further suggests that charge interactions play an important role in regulation of cardiac muscle activity through myosin-binding protein C.

#3: Journal: Cell / Year: 1999
Title: Atomic structure of scallop myosin subfragment S1 complexed with MgADP: a novel conformation of the myosin head.
Authors: A Houdusse / V N Kalabokis / D Himmel / A G Szent-Györgyi / C Cohen /
Abstract: The crystal structure of a proteolytic subfragment from scallop striated muscle myosin, complexed with MgADP, has been solved at 2.5 A resolution and reveals an unusual conformation of the myosin head. The converter and the lever arm are in very different positions from those in either the pre-power stroke or near-rigor state structures; moreover, in contrast to these structures, the SH1 helix is seen to be unwound. Here we compare the overall organization of the myosin head in these three states and show how the conformation of three flexible "joints" produces rearrangements of the four major subdomains in the myosin head with different bound nucleotides. We believe that this novel structure represents one of the prehydrolysis ("ATP") states of the contractile cycle in which the myosin heads stay detached from actin.

• Validation Report: SummaryFull reportAbout validation report

History

Deposition	Jul 15, 2008	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Oct 7, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Jul 22, 2015	Group: Source and taxonomy
Revision 1.3	Dec 14, 2016	Group: Other
Revision 1.4	Jan 29, 2020	Group: Author supporting evidence / Data collection / Database references / Source and taxonomy / Structure summary Category: database_2 / diffrn / em_single_particle_entity / entity / entity_name_com / entity_src_gen / entity_src_nat / struct_ref / struct_ref_seq / struct_ref_seq_dif Item: _entity.pdbx_description / _entity.pdbx_fragment / _entity_src_nat.common_name / _entity_src_nat.pdbx_beg_seq_num / _entity_src_nat.pdbx_end_seq_num / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.details

Assembly

Deposited unit

A: Myosin-11,Myosin-7

B: Myosin-11,Myosin-7

C: Myosin light polypeptide 6

D: Myosin light polypeptide 6

E: Myosin II regulatory light chain

F: Myosin II regulatory light chain

Summary:

• 301 kDa, 6 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	301,067	6
Polymers	301,067	6
Non-polymers	0	0
Water	0

1

A: Myosin-11,Myosin-7

B: Myosin-11,Myosin-7

C: Myosin light polypeptide 6

D: Myosin light polypeptide 6

E: Myosin II regulatory light chain

F: Myosin II regulatory light chain

x 36

Summary:

• representative helical assembly
• 10.8 MDa, 216 polymers
• Download structure data

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	10,838,410	216
Polymers	10,838,410	216
Non-polymers	0	0
Water	0

Symmetry operations:

Type	Name	Symmetry operation	Number
helical symmetry operation			36

2

Summary:

• Idetical with deposited unit in distinct coordinate
• helical asymmetric unit

Symmetry operations:

Type	Name	Symmetry operation	Number
helical symmetry operation			1

3

Summary:

• Idetical with deposited unit in distinct coordinate
• helical asymmetric unit, std helical frame

Symmetry operations:

Type	Name	Symmetry operation	Number
transform to helical frame			1

• Symmetry: Helical symmetry: (Circular symmetry: 4 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 36 / Rise per n subunits: 145 Å / Rotation per n subunits: 30 °)

Components

#1: Protein

A Myosin-11,Myosin-7 / Myosin heavy chain 11 / Myosin heavy chain / gizzard smooth muscle

Details:

Mass: 111851.070 Da / Num. of mol.: 1
Fragment: SUBFRAGMENT 1(S1), DELTA-S2 (residues 2-972),SUBFRAGMENT 1(S1), DELTA-S2 (residues 2-972)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken), (gene. exp.) Homo sapiens (human)
Gene: MYH11, MYH7, MYHCB / Plasmid: PVL1392 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P10587, UniProt: P12883

#2: Protein

B Myosin-11,Myosin-7 / Myosin heavy chain 11 / Myosin heavy chain / gizzard smooth muscle

Details:

Mass: 112051.328 Da / Num. of mol.: 1
Fragment: SUBFRAGMENT 1(S1), DELTA-S2 (residues 2-974),SUBFRAGMENT 1(S1), DELTA-S2 (residues 2-974)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken), (gene. exp.) Homo sapiens (human)
Gene: MYH11, MYH7, MYHCB / Plasmid: PVL1392 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P10587, UniProt: P12883

#3: Protein

C D Myosin light polypeptide 6 / G2 catalytic / LC17-GI / LC17-NM / Myosin light chain alkali smooth-muscle/non-muscle isoforms

Details:

Mass: 16873.025 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: MYL6 / Plasmid: PVL1392 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P02607

#4: Protein

E F Myosin II regulatory light chain

Details:

Mass: 21709.250 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Avicularia avicularia (pinktoe tarantula) / Tissue: leg muscle / References: UniProt: B4XT43

• Sequence details: THE CONFLICT LISTED FOR CHAINS A AND B, RESIDUE 2 ARE CONSISTENT WITH PDB ENTRY 1BR1 AND 1I84. THE SEQUENCE OF THE HEAVY CHAIN (CHICKEN) STRUCTURE REPORTED HERE DIFFERS FROM THAT REPORTED IN THE SWISS-PROT DATABASE (ID: P10587), THAT RESIDUE SER 2 WAS CHANGED BY ALA AND DECLARED AS CLONING ARTIFACT IN PDB 1BR1. PEPTIDE CHAIN DESIGNATIONS: THE TERMS "BLOCKED" AND "FREE" REFER TO THE CONFORMATIONS OF THE TWO S1 MYOSIN HEADS. "FREE" MYOSIN HEAD MYOSIN HEAVY CHAIN S1 PLUS S2 FRAGMENT IS CHAIN A ELC IS CHAIN C RLC IS CHAIN E "BLOCKED" MYOSIN HEAD MYOSIN HEAVY CHAIN S1 PLUS S2 FRAGMENT IS CHAIN B ELC IS CHAIN D RLC IS CHAIN F SEQUENCE GAPS IN THE MOLECULAR MODEL: HEAVY CHAIN UNP-P10587 CHAIN A,B: 1, 205-210, 452-457, 635-655, 853-1185 HEAVY CHAIN S2 FRAGMENT UNP-P12883 CHAIN A: 1-841, 962-1935 HEAVY CHAIN S2 FRAGMENT UNP-P12883 CHAIN B: 1-841, 964-1935 ELC UNP-P02607 CHAIN C,D: 1-2

Experimental details

Experiment

• Experiment: Method: ELECTRON MICROSCOPY
• EM experiment: Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

Sample preparation

• Component: Name: Myosin thick filaments from Tarantula striated muscle / Type: COMPLEX; Details: Polymer of a multiple myosin assembled over a paramyosin core. MODEL BUILDING: the atomic model consists of two s1 heads and a segment of s2. each heavy meromyosin consists of a chimera built by chicken smooth muscle heavy chain (1i84) for s1 plus human cardiac muscle (2fxm) for s2 (chains a,b) and two light chains, the chicken smooth muscle (1i84) for elc (chains c,d) and a homology model based on 1br1 of the tarantula skeletal muscle rlc sequence (chains e,f), this model was flexible fitted to a tarantula 3d map (emd-1535)
• Buffer solution: Name: 100mM NaCl, 3mM MgCl2, 1mM EGTA, 5mM PIPES, 5mM NaH2PO4, 1mM NaN3; pH: 7 ; Details: 100mM NaCl, 3mM MgCl2, 1mM EGTA, 5mM PIPES, 5mM NaH2PO4, 1mM NaN3
• Specimen: Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
• Specimen support: Details: Holey carbon grids, 400 mesh
• Vitrification: Details: Plunging in a liquid ethane. Blotting was performed from one side of the grid till a thin sample film on it using Whatman No 42 filter paper, then the grid was immediately plunged under gravity into liquid ethane cooled by liquid nitrogen. Grids were stored under liquid nitrogen.

Electron microscopy imaging

• Microscopy: Model: FEI/PHILIPS CM120T / Date: Sep 19, 2001; Details: Holey carbon grids Cryo preserved in Liquid ethane were observed in a Philips CM120 electron microscope under low dose conditions. Only filaments on thin carbon over holes were photographed
• Electron gun: Electron source: LAB6 / Accelerating voltage: 120 kV / Illumination mode: FLOOD BEAM
• Electron lens: Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 35000 X / Calibrated magnification: 35000 X / Nominal defocus max: 1950 nm / Nominal defocus min: 1950 nm / Cs: 2 mm
• Specimen holder: Temperature: 88 K
• Image scans: Num. digital images: 465

Processing

EM software

ID	Name	Version	Category
1	Situs	3.2	model fitting
2	X-PLOR	3.851	model fitting

• CTF correction: Details: no corrected
• 3D reconstruction: Method: Single particle reconstruction with a modification of the IHRSR method; Resolution: 20 Å / Num. of particles: 15504 / Nominal pixel size: 2.48 Å / Actual pixel size: 2.48 Å / Magnification calibration: Tropomyosin paracrystal; Details: three-dimensional single particle reconstruction was carried out by a modification of the ihrsr method, using spider. low-dose electron micrographs of 1008 frozen-hydrated thick filaments halves were digitized at 0.248 nm per pixel using a nikon super coolscan 8000 ed scanner. filaments were aligned with the bare zone at the top, to ensure correct polarity in subsequent steps. a total of 15,504 segments, each 62 nm long, with an overlap of 55.8 nm, and containing aprox. 40,000 unique pairs of interacting myosin heads went into the reconstruction. as an initial reference model we used the tarantula negatively stained 3d-map, which was axially rotated, axially shifted and also out of plane tilted up to plus-minus12deg. for projection matching, giving a total of 4,095 projections (13 tilted projections plus-minus 12 deg. every 2 deg., 45 reference rotated projections (0-90 deg., every 2 deg. rotation angle), and 7 image axial shifts of 2.2 nm. the resulting 3d-map combines about 10,700 out of 15,504 filament segments, a yield of 69 percent of included segments.; Symmetry type: HELICAL
• Atomic model building: Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Constrained Molecular Dynamics; Details: METHOD--Flexible Fitting REFINEMENT PROTOCOL--Custom skeleton of 31 positional markers

Atomic model building

ID	PDB-ID	3D fitting-ID
1	1I84 1i84	1
2	2FXM 2fxm	1
3	1B7T 1b7t	1

Refinement step

Cycle: LAST

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	20580	0	0	0	20580