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- PDB-5h53: The structure of rabbit skeletal muscle actomyosin rigor complex ... -

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Basic information

Entry
Database: PDB / ID: 5h53
TitleThe structure of rabbit skeletal muscle actomyosin rigor complex at 5.2 angstrom.
Components
  • Actin, alpha skeletal muscle
  • Myosin light chain 1/3, skeletal muscle isoform
  • Myosin regulatory light chain 2, skeletal muscle isoform type 1
  • Skeletal muscle myosin heavy chain MyHC-EO/IIL
KeywordsMOTOR PROTEIN / Actin / Myosin / Muscle / rigor complex
Function / homology
Function and homology information


myosin complex / structural constituent of muscle / cytoskeletal motor activator activity / tropomyosin binding / myofibril / myosin heavy chain binding / mesenchyme migration / troponin I binding / actin filament bundle / filamentous actin ...myosin complex / structural constituent of muscle / cytoskeletal motor activator activity / tropomyosin binding / myofibril / myosin heavy chain binding / mesenchyme migration / troponin I binding / actin filament bundle / filamentous actin / actin filament bundle assembly / skeletal muscle thin filament assembly / cytoskeletal motor activity / striated muscle thin filament / skeletal muscle myofibril / actin monomer binding / skeletal muscle fiber development / stress fiber / titin binding / actin filament polymerization / cellular response to starvation / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / calcium-dependent protein binding / actin filament binding / lamellipodium / cell body / hydrolase activity / protein domain specific binding / calcium ion binding / positive regulation of gene expression / magnesium ion binding / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
Myosin-13, motor domain / : / EF-hand domain / Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain / Myosin S1 fragment, N-terminal / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Myosin head, motor domain ...Myosin-13, motor domain / : / EF-hand domain / Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain / Myosin S1 fragment, N-terminal / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / IQ motif, EF-hand binding site / Actins signature 1. / Actin, conserved site / Actins signature 2. / Kinesin motor domain superfamily / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / EF-hand, calcium binding motif / ATPase, nucleotide binding domain / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Myosin light chain 1/3, skeletal muscle isoform / Myosin regulatory light chain 2, skeletal muscle isoform type 1 / Actin, alpha skeletal muscle / Skeletal muscle myosin heavy chain MyHC-EO/IIL
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 5.2 Å
AuthorsFujii, T. / Namba, K.
CitationJournal: Nat Commun / Year: 2017
Title: Structure of actomyosin rigour complex at 5.2 Å resolution and insights into the ATPase cycle mechanism.
Authors: Takashi Fujii / Keiichi Namba /
Abstract: Muscle contraction is driven by cyclic association and dissociation of myosin head of the thick filament with thin actin filament coupled with ATP binding and hydrolysis by myosin. However, because ...Muscle contraction is driven by cyclic association and dissociation of myosin head of the thick filament with thin actin filament coupled with ATP binding and hydrolysis by myosin. However, because of the absence of actomyosin rigour structure at high resolution, it still remains unclear how the strong binding of myosin to actin filament triggers the release of hydrolysis products and how ATP binding causes their dissociation. Here we report the structure of mammalian skeletal muscle actomyosin rigour complex at 5.2 Å resolution by electron cryomicroscopy. Comparison with the structures of myosin in various states shows a distinctly large conformational change, providing insights into the ATPase-coupled reaction cycle of actomyosin. Based on our observations, we hypothesize that asymmetric binding along the actin filament could function as a Brownian ratchet by favouring directionally biased thermal motions of myosin and actin.
History
DepositionNov 4, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2017Group: Database references

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Assembly

Deposited unit
A: Skeletal muscle myosin heavy chain MyHC-EO/IIL
B: Myosin regulatory light chain 2, skeletal muscle isoform type 1
C: Myosin light chain 1/3, skeletal muscle isoform
D: Actin, alpha skeletal muscle
E: Actin, alpha skeletal muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,0717
Polymers214,2165
Non-polymers8542
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area11900 Å2
ΔGint-90 kcal/mol
Surface area96330 Å2

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Components

#1: Protein Skeletal muscle myosin heavy chain MyHC-EO/IIL / Uncharacterized protein


Mass: 96770.133 Da / Num. of mol.: 1 / Fragment: UNP residues 1-845 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: Q9GJP9
#2: Protein Myosin regulatory light chain 2, skeletal muscle isoform type 1 / DTNB / Fast skeletal myosin light chain 2 / MLC-2


Mass: 16507.588 Da / Num. of mol.: 1 / Fragment: UNP residues 25-170 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P24732
#3: Protein Myosin light chain 1/3, skeletal muscle isoform / MLC1F/MLC3F / Myosin light chain alkali 1/2 / Myosin light chain A1/A2


Mass: 17187.293 Da / Num. of mol.: 1 / Fragment: UNP residues 41-192 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P02602
#4: Protein Actin, alpha skeletal muscle / / Alpha-actin-1


Mass: 41875.633 Da / Num. of mol.: 2 / Fragment: UNP residues 3-377 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P68135
#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Actomyosin rigor complex / Type: COMPLEX / Entity ID: #1-#4 / Source: NATURAL
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: JEOL 3200FSC
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 20 e/Å2 / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 166.7 ° / Axial rise/subunit: 27.6 Å / Axial symmetry: C1
3D reconstructionResolution: 5.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 31535 / Symmetry type: HELICAL

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