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- PDB-5mva: Structure of the thin filament at high calcium concentration -

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Basic information

Entry
Database: PDB / ID: 5mva
TitleStructure of the thin filament at high calcium concentration
ComponentsActin, alpha skeletal muscle
KeywordsSTRUCTURAL PROTEIN / Thin filament / troponin / actin / tropomyosin
Function / homology
Function and homology information


cytoskeletal motor activator activity / myosin heavy chain binding / tropomyosin binding / troponin I binding / filamentous actin / mesenchyme migration / actin filament bundle / actin filament bundle assembly / skeletal muscle myofibril / striated muscle thin filament ...cytoskeletal motor activator activity / myosin heavy chain binding / tropomyosin binding / troponin I binding / filamentous actin / mesenchyme migration / actin filament bundle / actin filament bundle assembly / skeletal muscle myofibril / striated muscle thin filament / skeletal muscle thin filament assembly / actin monomer binding / stress fiber / skeletal muscle fiber development / titin binding / actin filament polymerization / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / calcium-dependent protein 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
Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / negative staining / Resolution: 27.7 Å
AuthorsPaul, D.M. / Squire, J.M. / Morris, E.P.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
British Heart FoundationFS/14/18/30711 United Kingdom
CitationJournal: J Struct Biol / Year: 2017
Title: Relaxed and active thin filament structures; a new structural basis for the regulatory mechanism.
Authors: Danielle M Paul / John M Squire / Edward P Morris /
Abstract: The structures of muscle thin filaments reconstituted using skeletal actin and cardiac troponin and tropomyosin have been determined with and without bound Ca using electron microscopy and reference- ...The structures of muscle thin filaments reconstituted using skeletal actin and cardiac troponin and tropomyosin have been determined with and without bound Ca using electron microscopy and reference-free single particle analysis. The resulting density maps have been fitted with atomic models of actin, tropomyosin and troponin showing that: (i) the polarity of the troponin complex is consistent with our 2009 findings, with large shape changes in troponin between the two states; (ii) without Ca the tropomyosin pseudo-repeats all lie at almost equivalent positions in the 'blocked' position on actin (over subdomains 1 and 2); (iii) in the active state the tropomyosin pseudo-repeats are all displaced towards subdomains 3 and 4 of actin, but the extent of displacement varies within the regulatory unit depending upon the axial location of the pseudo-repeats with respect to troponin. Individual pseudo-repeats with Ca bound to troponin can be assigned either to the 'closed' state, a partly activated conformation, or the 'M-state', a fully activated conformation which has previously been thought to occur only when myosin heads bind. These results lead to a modified view of the steric blocking model of thin filament regulation in which cooperative activation is governed by troponin-mediated local interactions of the pseudo-repeats of tropomyosin with actin.
History
DepositionJan 16, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.0Nov 29, 2017Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Nov 29, 2017Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 29, 2017Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update
Revision 1.1Apr 9, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / Category: database_2 / em_admin / Data content type: EM metadata / EM metadata / EM metadata
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update

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Assembly

Deposited unit
A: Actin, alpha skeletal muscle
B: Actin, alpha skeletal muscle
C: Actin, alpha skeletal muscle
D: Actin, alpha skeletal muscle
E: Actin, alpha skeletal muscle
F: Actin, alpha skeletal muscle
G: Actin, alpha skeletal muscle
H: Actin, alpha skeletal muscle
I: Actin, alpha skeletal muscle
J: Actin, alpha skeletal muscle
K: Actin, alpha skeletal muscle
L: Actin, alpha skeletal muscle
M: Actin, alpha skeletal muscle
N: Actin, alpha skeletal muscle
O: Actin, alpha skeletal muscle
P: Actin, alpha skeletal muscle
Q: Actin, alpha skeletal muscle
R: Actin, alpha skeletal muscle
S: Actin, alpha skeletal muscle
T: Actin, alpha skeletal muscle
U: Actin, alpha skeletal muscle
V: Actin, alpha skeletal muscle
W: Actin, alpha skeletal muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)972,96546
Polymers963,14023
Non-polymers9,82623
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area69640 Å2
ΔGint-425 kcal/mol
Surface area371690 Å2
MethodPISA

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Components

#1: Protein ...
Actin, alpha skeletal muscle / Alpha-actin-1


Mass: 41875.633 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P68135
#2: Chemical...
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Alpha-actin-1


Mass: 427.201 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Thin filament at high calcium concentration / Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: NO
EM stainingType: NEGATIVE / Material: Uranyl Acetate

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Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS CM12
Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 12 e/Å2 / Film or detector model: AGFA SCIENTA FILM
Image scansScanner model: ZEISS SCAI

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 27.7 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 1680 / Symmetry type: POINT

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