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- EMDB-10113: Basketweave Z-band of sonic muscle in midshipman fish -

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Basic information

Entry
Database: EMDB / ID: EMD-10113
TitleBasketweave Z-band of sonic muscle in midshipman fish
Map dataSubtomogram average of a tomogram of basketweave Z-band found in sonic muscle in the swimbladder of male Type 1 midshipman fish.
Sample
  • Organelle or cellular component: Z-band of vertebrate striated muscle in basketweave form
Biological speciesPorichthys notatus (plainfin midshipman)
Methodsubtomogram averaging / cryo EM / negative staining / Resolution: 39.0 Å
AuthorsLuther PK / Heumann J / Burgoyne T / Morris EP
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
British Heart FoundationRG/11/21/29335 United Kingdom
CitationJournal: Proc Natl Acad Sci U S A / Year: 2019
Title: Three-dimensional structure of the basketweave Z-band in midshipman fish sonic muscle.
Authors: Thomas Burgoyne / John M Heumann / Edward P Morris / Carlo Knupp / Jun Liu / Michael K Reedy / Kenneth A Taylor / Kuan Wang / Pradeep K Luther /
Abstract: Striated muscle enables movement in all animals by the contraction of myriads of sarcomeres joined end to end by the Z-bands. The contraction is due to tension generated in each sarcomere between ...Striated muscle enables movement in all animals by the contraction of myriads of sarcomeres joined end to end by the Z-bands. The contraction is due to tension generated in each sarcomere between overlapping arrays of actin and myosin filaments. At the Z-band, actin filaments from adjoining sarcomeres overlap and are cross-linked in a regular pattern mainly by the protein α-actinin. The Z-band is dynamic, reflected by the 2 regular patterns seen in transverse section electron micrographs; the so-called small-square and basketweave forms. Although these forms are attributed, respectively, to relaxed and actively contracting muscles, the basketweave form occurs in certain relaxed muscles as in the muscle studied here. We used electron tomography and subtomogram averaging to derive the 3D structure of the Z-band in the swimbladder sonic muscle of type I male plainfin midshipman fish (, into which we docked the crystallographic structures of actin and α-actinin. The α-actinin links run diagonally between connected pairs of antiparallel actin filaments and are oriented at an angle of about 25° away from the actin filament axes. The slightly curved and flattened structure of the α-actinin rod has a distinct fit into the map. The Z-band model provides a detailed understanding of the role of α-actinin in transmitting tension between actin filaments in adjoining sarcomeres.
History
DepositionJul 6, 2019-
Header (metadata) releaseJul 31, 2019-
Map releaseJul 31, 2019-
UpdateAug 7, 2019-
Current statusAug 7, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 165
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 165
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10113.png

Downloads & links

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Map

FileDownload / File: emd_10113.map.gz / Format: CCP4 / Size: 4.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubtomogram average of a tomogram of basketweave Z-band found in sonic muscle in the swimbladder of male Type 1 midshipman fish.
Voxel sizeX=Y=Z: 6.42 Å
Density
Contour LevelBy AUTHOR: 165.0 / Movie #1: 165
Minimum - Maximum125.395294000000007 - 176.195979999999992
Average (Standard dev.)146.525599999999997 (±8.73213)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions8080200
Spacing8080200
CellA: 513.6 Å / B: 513.6 Å / C: 1284.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z6.426.426.42
M x/y/z8080200
origin x/y/z0.0000.0000.000
length x/y/z513.600513.6001284.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ10810112
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS8080200
D min/max/mean125.395176.196146.526

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Supplemental data

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Sample components

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Entire : Z-band of vertebrate striated muscle in basketweave form

EntireName: Z-band of vertebrate striated muscle in basketweave form
Components
  • Organelle or cellular component: Z-band of vertebrate striated muscle in basketweave form

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Supramolecule #1: Z-band of vertebrate striated muscle in basketweave form

SupramoleculeName: Z-band of vertebrate striated muscle in basketweave form
type: organelle_or_cellular_component / ID: 1 / Parent: 0
Details: Z-band studied in sonic muscle in the swimbladder of male Type 1 midshipman fish.
Source (natural)Organism: Porichthys notatus (plainfin midshipman) / Organ: Swimbladder muscle / Tissue: Muscle / Organelle: Z-band / Location in cell: Myofibrillar

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsubtomogram averaging
Aggregation statetissue

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Sample preparation

BufferpH: 7
Component:
ConcentrationNameFormula
4.0 mMmagnesium acetate
5.0 mMK2EGTA
5.0 mMNa2.ATP
20.0 mMMOPS
164.0 mMKMeSO3
Sigma Cocktail
50.0 mMbutanedione-monoxime (BDM)

Details: This is the relaxing solution
StainingType: POSITIVE / Material: Uranyl acetate and lead citrate
Details: Conventionally stained with 2% uranyl acetate and Reynolds lead citrate
Sugar embeddingMaterial: Araldite
Details: Sample was freeze-substituted in acetone and then embedded in araldiate
GridMaterial: COPPER / Mesh: 700
VitrificationCryogen name: ETHANE / Instrument: REICHERT-JUNG PLUNGER
Details: Sample was cryo-protected with 30% sucrose (added to the relaxing solution).
DetailsFibers of swimbladder muscle (sonic muscle) of midshipman fish were rapidly frozen, freeze-substituted, embedded in resin, ~100 nm thin transverse sections cut, coated with 10 nm gold fiducials and stained with uranyl acetate and lead citrate.

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus min: 0.005 µm / Nominal magnification: 27000
Sample stageSpecimen holder model: OTHER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Average exposure time: 1.0 sec. / Average electron dose: 5.0 e/Å2

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Image processing

Crystal parametersUnit cell - A: 262 Å / Unit cell - B: 262 Å / Unit cell - C: 768 Å / Unit cell - γ: 90 ° / Unit cell - α: 90 ° / Unit cell - β: 90 ° / Space group: P43212
ExtractionNumber tomograms: 1 / Number images used: 483 / Method: Semi-Automatic particle picking / Software - Name: PEET (ver. 1.11.0 alpha)
Details: Automatic particle picking was performed by iterative refinement starting from a manually chosen initial reference and a uniform 2D grid of initial locations with spacing approximating that ...Details: Automatic particle picking was performed by iterative refinement starting from a manually chosen initial reference and a uniform 2D grid of initial locations with spacing approximating that of the unit cell. Selected points were windowed via cross-correlation thresholding and manual editing before further alignment and averaging.
Final 3D classificationNumber classes: 1 / Avg.num./class: 5796 / Software - Name: PEET (ver. 1.11.0 alpha)
Final angle assignmentType: OTHER / Software - Name: PEET (ver. 1.11.0 alpha)
Details: Normalised cross-correlation and weighted averaging in reciprocal space
Final reconstructionNumber classes used: 1 / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 39.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: PEET (ver. 1.11.0 alpha) / Number subtomograms used: 5796

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Atomic model buiding 1

Initial model(PDB ID:

1atn

,

3lue

)

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