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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 / Structural protein
Function / homologyActin, conserved site / Actin/actin-like conserved site / Actin family / Actins and actin-related proteins signature. / Actins signature 2. / Actins signature 1. / Actin / positive regulation of actin-dependent ATPase activity / mesenchyme migration / tropomyosin binding ...Actin, conserved site / Actin/actin-like conserved site / Actin family / Actins and actin-related proteins signature. / Actins signature 2. / Actins signature 1. / Actin / positive regulation of actin-dependent ATPase activity / mesenchyme migration / tropomyosin binding / myosin heavy chain binding / troponin I binding / skeletal muscle thin filament assembly / striated muscle thin filament / actin filament bundle / filamentous actin / actin monomer binding / skeletal muscle fiber development / actin filament bundle assembly / skeletal muscle myofibril / stress fiber / titin binding / actin filament polymerization / actin filament / filopodium / cell body / calcium-dependent protein binding / lamellipodium / protein domain specific binding / positive regulation of gene expression / magnesium ion binding / calcium ion binding / ATP binding / identical protein binding / cytoplasm / Actin, alpha skeletal muscle
Function and homology information
Specimen sourceOryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / negative staining / 27.7 Å resolution
AuthorsPaul, D.M. / Squire, J.M. / Morris, E.P.
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 ...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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 16, 2017 / Release: Nov 29, 2017

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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
Polyers963,14023
Non-polymers9,82623
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)69640
ΔGint (kcal/M)-425
Surface area (Å2)371690
MethodPISA

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Components

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


Mass: 41875.633 Da / Num. of mol.: 23 / 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 / Formula: C10H15N5O10P2 / Adenosine diphosphate / Comment: ADP (energy-carrying molecule) *YM

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Thin filament at high calcium concentrationActin / 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

MicroscopyMicroscope model: FEI/PHILIPS CM12
Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
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 / Number of particles: 1680 / Symmetry type: POINT

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