[English] 日本語
Yorodumi
- EMDB-6664: The structure of rabbit skeletal muscle actomyosin rigor complex ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-6664
TitleThe structure of rabbit skeletal muscle actomyosin rigor complex at 5.2 angstrom.
Map data
Sample
  • Complex: Actomyosin rigor complex
    • Protein or peptide: Skeletal muscle myosin heavy chain MyHC-EO/IIL
    • Protein or peptide: Myosin regulatory light chain 2, skeletal muscle isoform type 1
    • Protein or peptide: Myosin light chain 1/3, skeletal muscle isoform
    • Protein or peptide: Actin, alpha skeletal muscle
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
Function / homology
Function and homology information


myosin complex / structural constituent of muscle / cytoskeletal motor activator activity / tropomyosin binding / myofibril / myosin heavy chain binding / mesenchyme migration / troponin I binding / actin filament bundle / filamentous actin ...myosin complex / structural constituent of muscle / cytoskeletal motor activator 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 / actin monomer binding / skeletal muscle fiber development / stress fiber / titin binding / actin filament polymerization / cellular response to starvation / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / calcium-dependent protein binding / actin filament binding / lamellipodium / cell body / hydrolase activity / protein domain specific binding / calcium ion binding / positive regulation of gene expression / magnesium ion binding / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
Myosin-13, motor domain / : / EF-hand domain / 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. / Myosin head, motor domain ...Myosin-13, motor domain / : / EF-hand domain / 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. / 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, 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
Myosin light chain 1/3, skeletal muscle isoform / Myosin regulatory light chain 2, skeletal muscle isoform type 1 / Actin, alpha skeletal muscle / Skeletal muscle myosin heavy chain MyHC-EO/IIL
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit) / Rabbit (rabbit)
Methodhelical reconstruction / cryo EM / Resolution: 5.2 Å
AuthorsFujii T / Namba K
CitationJournal: Nat Commun / Year: 2017
Title: Structure of actomyosin rigour complex at 5.2 Å resolution and insights into the ATPase cycle mechanism.
Authors: Takashi Fujii / Keiichi Namba /
Abstract: Muscle contraction is driven by cyclic association and dissociation of myosin head of the thick filament with thin actin filament coupled with ATP binding and hydrolysis by myosin. However, because ...Muscle contraction is driven by cyclic association and dissociation of myosin head of the thick filament with thin actin filament coupled with ATP binding and hydrolysis by myosin. However, because of the absence of actomyosin rigour structure at high resolution, it still remains unclear how the strong binding of myosin to actin filament triggers the release of hydrolysis products and how ATP binding causes their dissociation. Here we report the structure of mammalian skeletal muscle actomyosin rigour complex at 5.2 Å resolution by electron cryomicroscopy. Comparison with the structures of myosin in various states shows a distinctly large conformational change, providing insights into the ATPase-coupled reaction cycle of actomyosin. Based on our observations, we hypothesize that asymmetric binding along the actin filament could function as a Brownian ratchet by favouring directionally biased thermal motions of myosin and actin.
History
DepositionNov 4, 2016-
Header (metadata) releaseNov 23, 2016-
Map releaseJan 18, 2017-
UpdateJan 25, 2017-
Current statusJan 25, 2017Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.52
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.52
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-5h53
  • Surface level: 1.52
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-5h53
  • Surface level: 1.52
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5h53
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6664.png

Downloads & links

-
Map

FileDownload / File: emd_6664.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.35 Å
Density
Contour LevelBy AUTHOR: 1.52 / Movie #1: 1.52
Minimum - Maximum-6.852589 - 9.438276
Average (Standard dev.)0.0037829473 (±0.74621767)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions250250250
Spacing250250250
CellA=B=C: 337.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z250250250
origin x/y/z0.0000.0000.000
length x/y/z337.500337.500337.500
α/β/γ90.00090.00090.000
start NX/NY/NZ-190-190-190
NX/NY/NZ380380380
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS250250250
D min/max/mean-6.8539.4380.004

-
Supplemental data

-
Sample components

-
Entire : Actomyosin rigor complex

EntireName: Actomyosin rigor complex
Components
  • Complex: Actomyosin rigor complex
    • Protein or peptide: Skeletal muscle myosin heavy chain MyHC-EO/IIL
    • Protein or peptide: Myosin regulatory light chain 2, skeletal muscle isoform type 1
    • Protein or peptide: Myosin light chain 1/3, skeletal muscle isoform
    • Protein or peptide: Actin, alpha skeletal muscle
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

-
Supramolecule #1: Actomyosin rigor complex

SupramoleculeName: Actomyosin rigor complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Oryctolagus cuniculus (rabbit)

-
Macromolecule #1: Skeletal muscle myosin heavy chain MyHC-EO/IIL

MacromoleculeName: Skeletal muscle myosin heavy chain MyHC-EO/IIL / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rabbit (rabbit)
Molecular weightTheoretical: 96.770133 KDa
SequenceString: MSSDAEMAIF GEAAPYLRKP EKERIEAQNR PFDSKKACFA VDDKEMYVKG MIQSRENDKV TVKTLDDRTL TLNSDQVFPM NPPKFDKIE DMAMMTHLHE PAVLYNLKER YAAWMIYTYS GLFCVTVNPY KWLPVYNPEV VTAYRGKKRQ EAPPHIFSIS D NAYQFMLT ...String:
MSSDAEMAIF GEAAPYLRKP EKERIEAQNR PFDSKKACFA VDDKEMYVKG MIQSRENDKV TVKTLDDRTL TLNSDQVFPM NPPKFDKIE DMAMMTHLHE PAVLYNLKER YAAWMIYTYS GLFCVTVNPY KWLPVYNPEV VTAYRGKKRQ EAPPHIFSIS D NAYQFMLT DRDNQSILIT GESGAGKTVN TKRVIQYFAT IAVTGDKKKE QQPGKMQGTL EDQIIQANPL LEAFGNAKTV RN DNSSRFG KFIRIHFGAT GKLASADIET YLLEKSRVTF QLSSERSYHI FYQIMSNKKP ELIDLLLIST NPFDFPFVSQ GEV TVASID DSEELLATDN AIDILGFSSE EKVGIYKLTG AVMHYGNMKF KQKQREEQAE PDGTEVADKA GYLMGLNSAE MLKG LCCPR VKVGNEYVTK GQNVQQVTNS VGALAKAVYE KMFLWMVTRI NQQLDTKQPR QYFIGVLDIA GFEIFDFNSL EQLCI NFTN EKLQQFFNHH MFVLEQEEYK KEGIEWEFID FGMDLAACIE LIEKPMGIFS ILEEECMFPK ATDTSFKNKL YDQHLG KSN NFQKPKPAKG KAEAHFSLVH YAGTVDYNIA GWLDKNKDPL NETVVGLYQK SALKLLSFLF SNYAGAEAGD SGGSKKG GK KKGSSFQTVS AVFRENLNKL MTNLRSTHPH FVRCLIPNET KTPGVMDHYL VMHQLRCNGV LEGIRICRKG FPSRILYA D FKQRYRILNA SAIPEGQFID SKNASEKLLN SIDVDREQYR FGHTKVFFKA GLLGLLEEMR DEKLVTLMTR TQALCRGYL MRVEFKKMME RRDSIFCIQY NIRAFMNVKH WPWMNLFFKI KPLLK

-
Macromolecule #2: Myosin regulatory light chain 2, skeletal muscle isoform type 1

MacromoleculeName: Myosin regulatory light chain 2, skeletal muscle isoform type 1
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rabbit (rabbit)
Molecular weightTheoretical: 16.507588 KDa
SequenceString:
QTQIQEFKEA FTVIDQNRDG IIDKEDLRDT FAAMGRLNVK NEELDAMMKE ASGPINFTVF LTMFGEKLKG ADPEDVITGA FKVLDPEGK GTIKKQFLEE LLITQCDRFS QEEIKNMWAA FSPDVGGNVD YKNICYVITH GDAKDQE

-
Macromolecule #3: Myosin light chain 1/3, skeletal muscle isoform

MacromoleculeName: Myosin light chain 1/3, skeletal muscle isoform / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rabbit (rabbit)
Molecular weightTheoretical: 17.187293 KDa
SequenceString:
IKIEFSKEQQ DEFKEAFLLY DRTGDSKITL SQVGDVLRAL GTNPTNAEVK KVLGNPSNEE MNAKKIEFEQ FLPMLQAISN NKDQGTYED FVEGLRVFDK EGNGTVMGAE LRHVLATLGE KMKEEEVEAL MAGQEDSNGC INYEAFVKHI MSID

-
Macromolecule #4: Actin, alpha skeletal muscle

MacromoleculeName: Actin, alpha skeletal muscle / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rabbit (rabbit)
Molecular weightTheoretical: 41.875633 KDa
SequenceString: DEDETTALVC DNGSGLVKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IE(HIC)GII TNW DDMEKIWHHT FYNELRVAPE EHPTLLTEAP LNPKANREKM TQIMFETFNV PAMYVAIQAV LSLYASGRTT GIVLDSG DG VTHNVPIYEG ...String:
DEDETTALVC DNGSGLVKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IE(HIC)GII TNW DDMEKIWHHT FYNELRVAPE EHPTLLTEAP LNPKANREKM TQIMFETFNV PAMYVAIQAV LSLYASGRTT GIVLDSG DG VTHNVPIYEG YALPHAIMRL DLAGRDLTDY LMKILTERGY SFVTTAEREI VRDIKEKLCY VALDFENEMA TAASSSSL E KSYELPDGQV ITIGNERFRC PETLFQPSFI GMESAGIHET TYNSIMKCDI DIRKDLYANN VMSGGTTMYP GIADRMQKE ITALAPSTMK IKIIAPPERK YSVWIGGSIL ASLSTFQQMW ITKQEYDEAG PSIVHRKCF

-
Macromolecule #5: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 2 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM / Adenosine diphosphate

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeJEOL 3200FSC
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Average electron dose: 20.0 e/Å2

-
Image processing

Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Helical parameters - Δz: 27.6 Å
Applied symmetry - Helical parameters - Δ&Phi: 166.7 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 5.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 31535

+
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