[English] 日本語
Yorodumi
- EMDB-1950: 3D-Structure of tarantula myosin filament obtained by cryo-electr... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 1950
Title3D-Structure of tarantula myosin filament obtained by cryo-electron microscopy
Keywordscryo-EM / thick filament / flexible docking / single particle reconstruction / Iterative Helical Real Space Reconstruction (IHRSR) / Myosin regulation / myosin regulatory light chain / phosphorylation
SampleMyosin filaments from Tarantula striated muscle
SourceAphonopelma sp. / arthropod / Tarantula
Map dataThis is a density map of tarantula thick filaments, the initial view is from the Z line perspective, if the map is rotated by 90 degress in x direction, the J motif of the interacting heads features and the backbone subfilaments can be seen clearly
Methodhelical reconstruction, at 20 A resolution
AuthorsAlamo L / Wriggers W / Pinto A / Bartoli F / Salazar L / Zhao F / Craig R / Padron R
CitationJ. Mol. Biol., 2011, 414, 44-61

primary. J. Mol. Biol., 2011, 414, 44-61 StrPapers
A molecular model of phosphorylation-based activation and potentiation of tarantula muscle thick filaments.
Reicy Brito / Lorenzo Alamo / Ulf Lundberg / José R Guerrero / Antonio Pinto / Guidenn Sulbarán / Mary Ann Gawinowicz / Roger Craig / Raúl Padrón

1. J. Mol. Biol., 2008, 384, 780-797 StrPapers
Three-dimensional reconstruction of tarantula myosin filaments suggests how phosphorylation may regulate myosin activity.
Lorenzo Alamo / Willy Wriggers / Antonio Pinto / Fulvia Bártoli / Leiria Salazar / Fa-Qing Zhao / Roger Craig / Raúl Padrón

DateDeposition: Aug 23, 2011 / Header (metadata) release: Sep 2, 2011 / Map release: Sep 2, 2011 / Last update: Aug 23, 2011

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 25
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 25
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-3jbh
  • Surface level: 25
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-3jbh
  • Surface level: 25
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


View / / Stereo:
Center
Zoom
Scale
Slabnear <=> far

fix: /
Orientation
Orientation Rotation
Misc. /
Show/hide
Supplemental images

Downloads & links

-
Map

Fileemd_1950.map.gz (map file in CCP4 format, 61037 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
250 pix
2.48 A/pix
= 620.5 A
250 pix
2.48 A/pix
= 620. A
250 pix
2.48 A/pix
= 620. A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

(generated in cubic-lattice coordinate)

Voxel sizeX: 2.48 A / Y: 2.48 A / Z: 2.482 A
Density
Contour Level:25 (by author), 25 (movie #1):
Minimum - Maximum-0.0374444 - 247.077
Average (Standard dev.)10.0232 (28.5667)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions250250250
Origin-124-1240
Limit125125249
Spacing250250250
CellA: 620 A / B: 620 A / C: 620.5 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z2.482.482.482
M x/y/z250250250
origin x/y/z0.0000.0000.000
length x/y/z620.000620.000620.500
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ454586
MAP C/R/S123
start NC/NR/NS-124-1240
NC/NR/NS250250250
D min/max/mean-0.037247.07710.023

-
Supplemental data

-
Sample components

-
Entire Myosin filaments from Tarantula striated muscle

EntireName: Myosin filaments from Tarantula striated muscle / Number of components: 2
Oligomeric State: Polymer of a multiple myosin assembled over a paramyosin core

-
Component #1: protein, Myosin II

ProteinName: Myosin II / a.k.a: Myosin Type II / Oligomeric Details: Polymer / Recombinant expression: No
SourceSpecies: Aphonopelma sp. / arthropod / Tarantula
Source (natural)Location in cell: Sarcomere / Cell: Myofibrils / Organ or tissue: Muscle

+
Experimental details

-
Sample preparation

Specimen statefilament
Helical parametersAxial symmetry: C4 (4 fold cyclic) / Hand: RIGHT HANDED / Delta z: 100 A / Delta phi: 30 deg.
Sample solutionBuffer solution: 100mM NaCl,3mM MgCl2,1mM EGTA, 5mM PIPES, 5mM NaH2PO4,1mM NaN3.
pH: 7
Support filmHoley carbon grids 400 mesh
StainingA 6 ul aliquot of native purified tarantula thick filaments suspension (Hidalgo et al. 2001) was applied to a 400 mesh grid coated with a holey carbon film that had been rendered hydrophilic by glow discharge in n-amylamine vapor for 3 minutes before use. After allowing the filaments to adsorb to the grid for 30 seconds, the grid was rinsed with the relaxing rinse, then placed in a humidity chamber (aprox. 80% relative humidity). 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.
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 93 K / Humidity: 80 % / Method: Plunging in a liquid ethane
Details: Vitrification instrument: Home-made plunger. 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

ImagingMicroscope: FEI/PHILIPS CM120T / Date: Oct 23, 2002
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 gunElectron source: LAB6 / Accelerating voltage: 120 kV / Illumination mode: FLOOD BEAM
LensMagnification: 35000 X (nominal), 35000 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1950 nm
Specimen HolderHolder: Eucentric / Model: GATAN LIQUID NITROGEN / Temperature: K ( 88 - 90 K)
CameraDetector: KODAK SO-163 FILM

-
Image acquisition

Image acquisitionNumber of digital images: 1008 / Scanner: OTHER / Sampling size: 8.47 microns / Bit depth: 14

-
Image processing

ProcessingMethod: helical reconstruction
Details: There are 4 helices of myosin heads, rotated 30 degrees, every 145 Angstroms. The filament segments were selected based on visual judgement of good helical order
3D reconstructionAlgorithm: Single particle reconstruction with a modification of the IHRSR method
Software: SPIDER
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 ere 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-minus12deg. every 2deg., 45 reference rotated projections (0-90 degrees, 2deg. 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.
Resolution: 20 A / Resolution method: FSC 0.5

-
Atomic model buiding

Modeling #1Software: Situs 2.3 / Refinement protocol: flexible / Target criteria: Correlation / Refinement space: REAL
Details: Protocol: Flexible Fitting. The flexible docking procedure is based on a connected (motion capture) network of identified features within the atomic model. The atomic model is allowed to move according to displacements tracked by 31 control points defined by the network, in order to find the best match to the cryo-EM map
Input PDB model: 3DTP
Chain ID: 3DTP_A, 3DTP_B, 3DTP_C, 3DTP_D, 3DTP_E, 3DTP_F
Output model

+
About Yorodumi

-
News

-
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

-
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

+
Mar 3, 2016. Presentation (PDF format) at IPR seminar on Feb 19.

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

Read more