[English] 日本語
Yorodumi
- EMDB-22975: Lethocerus Myosin II complete coiled-coil domain resolved in its ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-22975
TitleLethocerus Myosin II complete coiled-coil domain resolved in its native environment
Map data
SampleLethocerus flight muscle myosin filament:
Myosin heavy chain isoform Mhc_X1
Biological speciesLethocerus indicus (insect)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.25 Å
AuthorsRahmani H / Hu Z / Daneshparvar N / Taylor D / Taylor KA
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM30598 United States
American Heart Association20PRE35120273 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2021
Title: The myosin II coiled-coil domain atomic structure in its native environment.
Authors: Hamidreza Rahmani / Wen Ma / Zhongjun Hu / Nadia Daneshparvar / Dianne W Taylor / J Andrew McCammon / Thomas C Irving / Robert J Edwards / Kenneth A Taylor /
Abstract: The atomic structure of the complete myosin tail within thick filaments isolated from flight muscle is described and compared to crystal structures of recombinant, human cardiac myosin tail segments. ...The atomic structure of the complete myosin tail within thick filaments isolated from flight muscle is described and compared to crystal structures of recombinant, human cardiac myosin tail segments. Overall, the agreement is good with three exceptions: the proximal S2, in which the filament has heads attached but the crystal structure doesn't, and skip regions 2 and 4. At the head-tail junction, the tail α-helices are asymmetrically structured encompassing well-defined unfolding of 12 residues for one myosin tail, ∼4 residues of the other, and different degrees of α-helix unwinding for both tail α-helices, thereby providing an atomic resolution description of coiled-coil "uncoiling" at the head-tail junction. Asymmetry is observed in the nonhelical C termini; one C-terminal segment is intercalated between ribbons of myosin tails, the other apparently terminating at Skip 4 of another myosin tail. Between skip residues, crystal and filament structures agree well. Skips 1 and 3 also agree well and show the expected α-helix unwinding and coiled-coil untwisting in response to skip residue insertion. Skips 2 and 4 are different. Skip 2 is accommodated in an unusual manner through an increase in α-helix radius and corresponding reduction in rise/residue. Skip 4 remains helical in one chain, with the other chain unfolded, apparently influenced by the acidic myosin C terminus. The atomic model may shed some light on thick filament mechanosensing and is a step in understanding the complex roles that thick filaments of all species undergo during muscle contraction.
Validation ReportSummary, Full report, XML, About validation report
History
DepositionNov 9, 2020-
Header (metadata) releaseMar 24, 2021-
Map releaseMar 24, 2021-
UpdateApr 14, 2021-
Current statusApr 14, 2021Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.12
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.12
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7kog
  • Surface level: 0.12
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7kog
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_22975.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.98 Å/pix.
x 1712 pix.
= 1677.76 Å
0.98 Å/pix.
x 182 pix.
= 178.36 Å
0.98 Å/pix.
x 140 pix.
= 137.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 0.98 Å
Density
Contour LevelBy AUTHOR: 0.12 / Movie #1: 0.12
Minimum - Maximum-0.07149465 - 3.2776268
Average (Standard dev.)0.0024193982 (±0.046974123)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin9361044239
Dimensions1821401712
Spacing1401821712
CellA: 137.2 Å / B: 178.36 Å / C: 1677.76 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.980.980.98
M x/y/z1401821712
origin x/y/z0.0000.0000.000
length x/y/z137.200178.3601677.760
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS1044936239
NC/NR/NS1401821712
D min/max/mean-0.0713.2780.002

-
Supplemental data

-
Sample components

-
Entire Lethocerus flight muscle myosin filament

EntireName: Lethocerus flight muscle myosin filament
Details: The sample is a bipolar helical structure, with helical repeat 145 Angstrom and helical turn 33.98 degree. The sample has C4 symmetry. The map contains 6 unique features: myosin molecule ...Details: The sample is a bipolar helical structure, with helical repeat 145 Angstrom and helical turn 33.98 degree. The sample has C4 symmetry. The map contains 6 unique features: myosin molecule with completely resolved rods, 4 resolved non-myosin densities among the myosin rods and an annular region inside of annulus occupied by myosin rods that most likely contains paramyosin. The 4 non-myosin densities may contain parts of the proteins myofilin and flightin.
Number of components: 2

-
Component #1: cellular-component, Lethocerus flight muscle myosin filament

Cellular-componentName: Lethocerus flight muscle myosin filament
Details: The sample is a bipolar helical structure, with helical repeat 145 Angstrom and helical turn 33.98 degree. The sample has C4 symmetry. The map contains 6 unique features: myosin molecule ...Details: The sample is a bipolar helical structure, with helical repeat 145 Angstrom and helical turn 33.98 degree. The sample has C4 symmetry. The map contains 6 unique features: myosin molecule with completely resolved rods, 4 resolved non-myosin densities among the myosin rods and an annular region inside of annulus occupied by myosin rods that most likely contains paramyosin. The 4 non-myosin densities may contain parts of the proteins myofilin and flightin.
Recombinant expression: No
SourceSpecies: Lethocerus indicus (insect)
Source (natural)Organelle: Sarcomere / Location in cell: myofibril / Organ or tissue: myocyte

-
Component #2: protein, Myosin heavy chain isoform Mhc_X1

ProteinName: Myosin heavy chain isoform Mhc_X1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 225.227562 kDa
SourceSpecies: Lethocerus indicus (insect)

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: Filament / Method: cryo EM
Sample solutionpH: 6.8
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 60 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: DIRECT ELECTRON DE-64 (8k x 8k)

-
Image acquisition

Image acquisitionNumber of digital images: 3507

-
Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 173515
3D reconstructionSoftware: cisTEM / Resolution: 4.25 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

-
Atomic model buiding

Output model

+
About Yorodumi

-
News

-
Aug 12, 2020. New: Covid-19 info

New: Covid-19 info

  • 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. New: 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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

Read more

-
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.

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