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- EMDB-3576: Structure of the thin filament at high calcium concentration -

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Basic information

Entry
Database: EMDB / ID: 3576
TitleStructure of the thin filament at high calcium concentration
Map dataThin Filament at High Calcium concentrationActin
SampleThin filament at high calcium concentrationActin:
Actin, alpha skeletal muscle / ligand
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
SourceOryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / 27.7 Å resolution
AuthorsPaul DM / Squire JM
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 ReportPDB-ID: 5mva

SummaryFull reportAbout validation report
DateDeposition: Jan 16, 2017 / Header (metadata) release: Aug 30, 2017 / Map release: Nov 29, 2017 / Last update: Nov 29, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_3576.map.gz (map file in CCP4 format, 3539 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
96 pix
6.6 Å/pix.
= 633.6 Å
96 pix
6.6 Å/pix.
= 633.6 Å
96 pix
6.6 Å/pix.
= 633.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 6.6 Å
Density
Contour Level:2 (by author), 2 (movie #1):
Minimum - Maximum-12.902359 - 24.301378
Average (Standard dev.)0.0013400215 (0.9243033)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions969696
Origin-50-50-50
Limit454545
Spacing969696
CellA=B=C: 633.6 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z6.66.66.6
M x/y/z969696
origin x/y/z0.0000.0000.000
length x/y/z633.600633.600633.600
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-50-50-50
NC/NR/NS969696
D min/max/mean-12.90224.3010.001

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Supplemental data

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Sample components

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Entire Thin filament at high calcium concentration

EntireName: Thin filament at high calcium concentration / Number of components: 3

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Component #1: protein, Thin filament at high calcium concentration

ProteinName: Thin filament at high calcium concentrationActin / Recombinant expression: No
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Component #2: protein, Actin, alpha skeletal muscle

ProteinName: Actin, alpha skeletal muscle / Recombinant expression: No
MassTheoretical: 41.875633 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Component #3: ligand, ADENOSINE-5'-DIPHOSPHATE

LigandName: ADENOSINE-5'-DIPHOSPHATE / Number of Copies: 23 / Recombinant expression: No
MassTheoretical: 0.427201 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: filament
Sample solutionpH: 7
VitrificationCryogen name: NONE

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Electron microscopy imaging

ImagingMicroscope: FEI/PHILIPS CM12
Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Electron dose: 12 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: AGFA SCIENTA FILM

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Image acquisition

Image acquisitionScanner: ZEISS SCAI

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 1680
3D reconstructionResolution: 27.7 Å / Resolution method: FSC 0.5 CUT-OFF

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Atomic model buiding

Output model

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