[English] 日本語
Yorodumi
- EMDB-1561: Electron tomography of isometrically contracting insect flight muscle -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-1561
TitleElectron tomography of isometrically contracting insect flight muscle
Map dataThis is a dual axis tomogram of quick frozen, freeze This is a dual axis tomogram of quick frozen, freeze substituted, plastic embedded, thin sectioned insect flight muscle from Lethocerus sp.
Sample
  • Sample: Isometrically contracting asynchronous insect flight muscle
  • Organelle or cellular component: myofibril
Keywordsinsect / muscle / myosin / troponin / tropomyosin / actin / light chains / thin filament / thick filament / electron microscopy / image processing / isometric contraction / freezing / freeze substitution / microtomy / multivariate data analysis
Function / homology
Function and homology information


troponin C binding / contractile muscle fiber / troponin complex / Striated Muscle Contraction / regulation of muscle contraction / myosin filament / myosin II complex / myosin complex / sarcomere organization / cytoskeletal motor activator activity ...troponin C binding / contractile muscle fiber / troponin complex / Striated Muscle Contraction / regulation of muscle contraction / myosin filament / myosin II complex / myosin complex / sarcomere organization / cytoskeletal motor activator activity / microfilament motor activity / tropomyosin binding / myofibril / myosin heavy chain binding / mesenchyme migration / troponin I binding / actin filament bundle / filamentous actin / actin filament bundle assembly / skeletal muscle thin filament assembly / cytoskeletal motor activity / striated muscle thin filament / skeletal muscle myofibril / skeletal muscle contraction / actin monomer binding / skeletal muscle fiber development / skeletal muscle tissue development / stress fiber / titin binding / cardiac muscle contraction / actin filament polymerization / filopodium / muscle contraction / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / calcium-dependent protein binding / actin filament binding / actin cytoskeleton / lamellipodium / cell body / actin binding / calmodulin binding / hydrolase activity / protein heterodimerization activity / protein domain specific binding / calcium ion binding / positive regulation of gene expression / magnesium ion binding / protein homodimerization activity / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
Troponin T / Tropomyosins signature. / Tropomyosin / Troponin / Troponin domain superfamily / Tropomyosin / Troponin / EF-hand domain / DNA repair protein XRCC4-like, C-terminal / Myosin tail ...Troponin T / Tropomyosins signature. / Tropomyosin / Troponin / Troponin domain superfamily / Tropomyosin / Troponin / EF-hand domain / DNA repair protein XRCC4-like, C-terminal / Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain / Myosin S1 fragment, N-terminal / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Short calmodulin-binding motif containing conserved Ile and Gln residues. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / IQ motif, EF-hand binding site / Actins signature 1. / Actin, conserved site / Actins signature 2. / Kinesin motor domain superfamily / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / EF-hand domain pair / EF-hand, calcium binding motif / ATPase, nucleotide binding domain / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Troponin C, skeletal muscle / Myosin light chain 3, skeletal muscle isoform / Myosin regulatory light chain 11 / Myosin essential light chain, striated adductor muscle / Troponin T, fast skeletal muscle isoforms / Myosin heavy chain, skeletal muscle, adult / Myosin regulatory light chain, striated adductor muscle / Myosin heavy chain, striated muscle / Tropomyosin alpha-1 chain / Actin, alpha skeletal muscle / Troponin I, fast skeletal muscle
Similarity search - Component
Biological speciesLethocerus indicus (insect)
Methodelectron tomography / cryo EM / negative staining
AuthorsWu S / Liu J / Reedy MC / Tregear RT / Winkler H / Franzini-Armstrong C / Sasaki H / Lucaveche C / Goldman YE / Reedy MK / Taylor KA
CitationJournal: J Struct Biol / Year: 2009
Title: Methods for identifying and averaging variable molecular conformations in tomograms of actively contracting insect flight muscle.
Authors: Shenping Wu / Jun Liu / Mary C Reedy / Hanspeter Winkler / Michael K Reedy / Kenneth A Taylor /
Abstract: During active muscle contraction, tension is generated through many simultaneous, independent interactions between the molecular motor myosin and the actin filaments. The ensemble of myosin motors ...During active muscle contraction, tension is generated through many simultaneous, independent interactions between the molecular motor myosin and the actin filaments. The ensemble of myosin motors displays heterogeneous conformations reflecting different mechanochemical steps of the ATPase pathway. We used electron tomography of actively contracting insect flight muscle fast-frozen, freeze substituted, Araldite embedded, thin-sectioned and stained, to obtain 3D snapshots of the multiplicity of actin-attached myosin structures. We describe procedures for alignment of the repeating lattice of sub-volumes (38.7 nm cross-bridge repeats bounded by troponin) and multivariate data analysis to identify self-similar repeats for computing class averages. Improvements in alignment and classification of repeat sub-volumes reveals (for the first time in active muscle images) the helix of actin subunits in the thin filament and the troponin density with sufficient clarity that a quasiatomic model of the thin filament can be built into the class averages independent of the myosin cross-bridges. We show how quasiatomic model building can identify both strong and weak myosin attachments to actin. We evaluate the accuracy of image classification to enumerate the different types of actin-myosin attachments.
History
DepositionSep 26, 2008-
Header (metadata) releaseSep 29, 2008-
Map releaseApr 12, 2010-
UpdateAug 12, 2015-
Current statusAug 12, 2015Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
  • Download
  • Close-up
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1561.gif

Downloads & links

-
Map

FileDownload / File: emd_1561.map.gz / Format: CCP4 / Size: 560.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a dual axis tomogram of quick frozen, freeze This is a dual axis tomogram of quick frozen, freeze substituted, plastic embedded, thin sectioned insect flight muscle from Lethocerus sp.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
6.9 Å/pix.
x 70 pix.
= 483. Å		6.9 Å/pix.
x 1344 pix.
= 11040. Å		6.9 Å/pix.
x 1600 pix.
= 9273.601 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 6.9 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-3296.960000000000036 - 4848.859999999999673
Average (Standard dev.)5.83993 (±532.039999999999964)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions1344160070
Spacing1344160070
CellA: 9273.6 Å / B: 11040 Å / C: 483 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z6.90000074404766.96.9
M x/y/z1344160070
origin x/y/z0.0000.0000.000
length x/y/z9273.60111040.000483.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS1600134470
D min/max/mean-3296.9594848.8645.840

-
Supplemental data

-
Sample components

-
Entire : Isometrically contracting asynchronous insect flight muscle

EntireName: Isometrically contracting asynchronous insect flight muscle
Components
  • Sample: Isometrically contracting asynchronous insect flight muscle
  • Organelle or cellular component: myofibril

-
Supramolecule #1000: Isometrically contracting asynchronous insect flight muscle

SupramoleculeName: Isometrically contracting asynchronous insect flight muscle
type: sample / ID: 1000
Details: This specimen is obtained from a quick frozen, isometrically contracting asynchronous insect flight muscle that has been freeze substituted, plastic embedded, and thin sectioned
Oligomeric state: tissue / Number unique components: 8

-
Supramolecule #1: myofibril

SupramoleculeName: myofibril / type: organelle_or_cellular_component / ID: 1 / Name.synonym: muscle
Details: The sample was enblock stained using uranyl acetate and tannic acid, and post stained with lead citrate and potassium permanganate
Oligomeric state: muscle fibril / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Lethocerus indicus (insect) / synonym: Water bug / Tissue: asynchronous dorsal longitudinal flight muscle / Organelle: myofibril / Location in cell: myooplasm

-
Experimental details

-
Structure determination

Methodnegative staining, cryo EM
Processingelectron tomography

-
Sample preparation

BufferDetails: 20 mM MOPS buffer, 5 mM NaN3, and MgCl2, ATP, CaCl2, and EGTA in varying millimolar concentrations
StainingType: NEGATIVE
Details: Freeze slammed fibers were freeze-substituted in acetone using a tannic aciduranyl acetate sequence, and ultimately embedded in Araldite-506 for thin-section electron microscopy. Ultrathin ...Details: Freeze slammed fibers were freeze-substituted in acetone using a tannic aciduranyl acetate sequence, and ultimately embedded in Araldite-506 for thin-section electron microscopy. Ultrathin (25-30 nm) longitudinal sections were stained by permanganate-lead.
VitrificationCryogen name: HELIUM / Chamber temperature: 4.5 K / Instrument: HOMEMADE PLUNGER
Details: Vitrification instrument: modified Heuser Cryopress freezing head
Method: smash against a liquid helium cooled Au-coated Cu mirror

-
Electron microscopy

MicroscopeFEI/PHILIPS CM300FEG/T
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm
Sample stageSpecimen holder: Gatan model 670 Ultrahigh tilt analytical holder
Specimen holder model: OTHER / Tilt series - Axis1 - Min angle: -72 ° / Tilt series - Axis1 - Max angle: 72 °
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F224 (2k x 2k)
Details: Images recorded on a TVIPS Tem-Cam F224 2k x 2k CCD camera
Bits/pixel: 16

-
Image processing

Final reconstructionAlgorithm: OTHER / Resolution method: FSC 0.5 CUT-OFF / Software - Name: PROTOMO, IMOD
Details: Two tilt series at 90 degrees to one another were first independently aligned using marker-free alignment and area matching. The two resulting tomograms were then merged by patch correlation ...Details: Two tilt series at 90 degrees to one another were first independently aligned using marker-free alignment and area matching. The two resulting tomograms were then merged by patch correlation and volume warp using IMOD. Tomogram computed using weighted back projection.
Number images used: 70

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more