[English] 日本語
Yorodumi
- EMDB-7116: CryoEM structure of MyosinVI-actin complex in the rigor (nucleoti... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-7116
TitleCryoEM structure of MyosinVI-actin complex in the rigor (nucleotide-free) state
Map dataCryo-EM structure of myosin VI-actin complex, B factor sharpened to -150
Sample
  • Complex: myosin VI-actin in the rigor (nucleotide-free) state
    • Complex: myosin VI
      • Protein or peptide: Unconventional myosin-VI
    • Complex: actin
      • Protein or peptide: Actin, alpha skeletal muscle
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsCytoskeleton / Filament / complex / CONTRACTILE PROTEIN
Function / homology
Function and homology information


CH domain binding / regulation of secretion / inner ear auditory receptor cell differentiation / actin filament-based movement / myosin complex / clathrin-coated vesicle / inner ear morphogenesis / cytoskeletal motor activator activity / microfilament motor activity / myosin binding ...CH domain binding / regulation of secretion / inner ear auditory receptor cell differentiation / actin filament-based movement / myosin complex / clathrin-coated vesicle / inner ear morphogenesis / cytoskeletal motor activator activity / microfilament motor activity / myosin binding / tropomyosin binding / myosin heavy chain binding / troponin I binding / mesenchyme migration / filamentous actin / actin filament bundle / cytoskeletal motor activity / microvillus / striated muscle thin filament / actin filament bundle assembly / skeletal muscle thin filament assembly / skeletal muscle myofibril / actin monomer binding / DNA damage response, signal transduction by p53 class mediator / stress fiber / skeletal muscle fiber development / clathrin-coated pit / titin binding / ruffle / actin filament polymerization / actin filament organization / filopodium / actin filament / intracellular protein transport / sensory perception of sound / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / ADP binding / ruffle membrane / endocytosis / calcium-dependent protein binding / actin filament binding / disordered domain specific binding / actin cytoskeleton / protein localization / lamellipodium / myelin sheath / cell body / cell cortex / cytoplasmic vesicle / nuclear membrane / calmodulin binding / hydrolase activity / protein domain specific binding / centrosome / calcium ion binding / positive regulation of gene expression / perinuclear region of cytoplasm / Golgi apparatus / magnesium ion binding / protein-containing complex / nucleoplasm / ATP binding / identical protein binding / nucleus / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Myosin VI, cargo binding domain / Class VI myosin, motor domain / : / Myosin VI cargo binding domain / Myosin VI, lever arm / 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 VI, cargo binding domain / Class VI myosin, motor domain / : / Myosin VI cargo binding domain / Myosin VI, lever arm / 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. / Kinesin motor domain superfamily / : / Actins signature 1. / Actin, conserved site / Actins signature 2. / 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
Unconventional myosin-VI / Calmodulin / Actin, alpha skeletal muscle / Unconventional myosin-VI
Similarity search - Component
Biological speciesSus scrofa (pig) / Oryctolagus cuniculus (rabbit)
Methodhelical reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsGurel PS / Alushin GA
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/Office of the Director5DP5OD017885 United States
CitationJournal: Nat Nanotechnol / Year: 2018
Title: Controllable molecular motors engineered from myosin and RNA.
Authors: Tosan Omabegho / Pinar S Gurel / Clarence Y Cheng / Laura Y Kim / Paul V Ruijgrok / Rhiju Das / Gregory M Alushin / Zev Bryant /
Abstract: Engineering biomolecular motors can provide direct tests of structure-function relationships and customized components for controlling molecular transport in artificial systems or in living cells . ...Engineering biomolecular motors can provide direct tests of structure-function relationships and customized components for controlling molecular transport in artificial systems or in living cells . Previously, synthetic nucleic acid motors and modified natural protein motors have been developed in separate complementary strategies to achieve tunable and controllable motor function. Integrating protein and nucleic-acid components to form engineered nucleoprotein motors may enable additional sophisticated functionalities. However, this potential has only begun to be explored in pioneering work harnessing DNA scaffolds to dictate the spacing, number and composition of tethered protein motors . Here, we describe myosin motors that incorporate RNA lever arms, forming hybrid assemblies in which conformational changes in the protein motor domain are amplified and redirected by nucleic acid structures. The RNA lever arm geometry determines the speed and direction of motor transport and can be dynamically controlled using programmed transitions in the lever arm structure . We have characterized the hybrid motors using in vitro motility assays, single-molecule tracking, cryo-electron microscopy and structural probing . Our designs include nucleoprotein motors that reversibly change direction in response to oligonucleotides that drive strand-displacement reactions. In multimeric assemblies, the controllable motors walk processively along actin filaments at speeds of 10-20 nm s. Finally, to illustrate the potential for multiplexed addressable control, we demonstrate sequence-specific responses of RNA variants to oligonucleotide signals.
History
DepositionNov 17, 2017-
Header (metadata) releaseJan 10, 2018-
Map releaseJan 10, 2018-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 6
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 6
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6bnp
  • Surface level: 6
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6bnv
  • Surface level: 6
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6bnp
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6bnv
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7116_1.png

emd_7116_2.png

Downloads & links

-
Map

FileDownload / File: emd_7116.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of myosin VI-actin complex, B factor sharpened to -150
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.27 Å/pix.
x 512 pix.
= 650.24 Å		1.27 Å/pix.
x 512 pix.
= 650.24 Å		1.27 Å/pix.
x 512 pix.
= 650.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.27 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 6.0 / Movie #1: 6
Minimum - Maximum-9.431532000000001 - 20.607714000000001
Average (Standard dev.)0.000000001548081 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-256-256-256
Dimensions512512512
Spacing512512512
CellA=B=C: 650.24 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.271.271.27
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z650.240650.240650.240
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-256-256-256
NC/NR/NS512512512
D min/max/mean-9.43220.6080.000

-
Supplemental data

-
Mask #1

Fileemd_7116_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Mask #2

Fileemd_7116_msk_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: unsharpened density map of myosin VI-actin complex

Fileemd_7116_additional.map
Annotationunsharpened density map of myosin VI-actin complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map of the full myosin VI-actin reconstruction

Fileemd_7116_half_map_1.map
AnnotationHalf map of the full myosin VI-actin reconstruction
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map of the full myosin VI-actin reconstruction

Fileemd_7116_half_map_2.map
AnnotationHalf map of the full myosin VI-actin reconstruction
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : myosin VI-actin in the rigor (nucleotide-free) state

EntireName: myosin VI-actin in the rigor (nucleotide-free) state
Components
  • Complex: myosin VI-actin in the rigor (nucleotide-free) state
    • Complex: myosin VI
      • Protein or peptide: Unconventional myosin-VI
    • Complex: actin
      • Protein or peptide: Actin, alpha skeletal muscle
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

-
Supramolecule #1: myosin VI-actin in the rigor (nucleotide-free) state

SupramoleculeName: myosin VI-actin in the rigor (nucleotide-free) state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Molecular weightTheoretical: 42 KDa

-
Supramolecule #2: myosin VI

SupramoleculeName: myosin VI / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Sus scrofa (pig)

-
Supramolecule #3: actin

SupramoleculeName: actin / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Oryctolagus cuniculus (rabbit)

-
Macromolecule #1: Unconventional myosin-VI

MacromoleculeName: Unconventional myosin-VI / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 79.837367 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: EDGKPVWAPH PTDGFQVGNI VDIGPDSLTI EPLNQKGKTF LALINQVFPA EEDSKKDVED NCSLMYLNEA TLLHNIKVRY SKDRIYTYV ANILIAVNPY FDIPKIYSSE TIKSYQGKSL GTMPPHVFAI ADKAFRDMKV LKLSQSIIVS GESGAGKTEN T KFVLRYLT ...String:
EDGKPVWAPH PTDGFQVGNI VDIGPDSLTI EPLNQKGKTF LALINQVFPA EEDSKKDVED NCSLMYLNEA TLLHNIKVRY SKDRIYTYV ANILIAVNPY FDIPKIYSSE TIKSYQGKSL GTMPPHVFAI ADKAFRDMKV LKLSQSIIVS GESGAGKTEN T KFVLRYLT ESYGTGQDID DRIVEANPLL EAFGNAKTVR NNNSSRFGKF VEIHFNEKSS VVGGFVSHYL LEKSRICVQG KE ERNYHIF YRLCAGASED IRERLHLSSP DNFRYLNRGC TRYFANKETD KQILQNRKSP EYLKAGSLKD PLLDDHGDFI RMC TAMKKI GLDDEEKLDL FRVVAGVLHL GNIDFEEAGS TSGGCNLKNK STQALEYCAE LLGLDQDDLR VSLTTRVMLT TAGG AKGTV IKVPLKVEQA NNARDALAKT VYSHLFDHVV NRVNQCFPFE TSSYFIGVLD IAGFEYFEHN SFEQFCINYC NEKLQ QFFN ERILKEEQEL YQKEGLGVNE VHYVDNQDCI DLIEARLVGI LDILDEENRL PQPSDQHFTS AVHQKHKDHF RLSIPR KSK LAIHRNIRDD EGFIIRHFAG AVCYETTQFV EKNNDALHMS LESLICESRD KFIRELFESS TNNNKDTKQK AGKLSFI SV GNKFKTQLNL LLDKLRSTGA SFIRCIKPNL KMTSHHFEGA QILSQLQCSG MVSVLDLMQG GF

UniProtKB: Unconventional myosin-VI

-
Macromolecule #2: Actin, alpha skeletal muscle

MacromoleculeName: Actin, alpha skeletal muscle / type: protein_or_peptide / ID: 2 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit) / Tissue: Skeletal Muscle
Molecular weightTheoretical: 41.560266 KDa
SequenceString: MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTLK YPIEHGIITN WDDMEKIWH HTFYNELRVA PEEHPTLLTE APLNPKANRE KMTQIMFETF NVPAMYVAIQ AVLSLYASGR TTGIVLDSGD G VTHNVPIY ...String:
MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTLK YPIEHGIITN WDDMEKIWH HTFYNELRVA PEEHPTLLTE APLNPKANRE KMTQIMFETF NVPAMYVAIQ AVLSLYASGR TTGIVLDSGD G VTHNVPIY EGYALPHAIM RLDLAGRDLT DYLMKILTER GYSFVTTAER EIVRDIKEKL CYVALDFENE MATAASSSSL EK SYELPDG QVITIGNERF RCPETLFQPS FIGMESAGIH ETTYNSIMKC DIDIRKDLYA NNVMSGGTTM YPGIADRMQK EIT ALAPST MKIKIIAPPE RKYSVWIGGS ILASLSTFQQ MWITKQEYDE AGPSIVH

UniProtKB: Actin, alpha skeletal muscle

-
Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 8 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Macromolecule #4: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 8 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

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

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

-
Sample preparation

Concentration0.45 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMKClpotassium chloride
1.0 mMMgCl2magnesium chloride
1.0 mMC14H24N2O10EGTA
10.0 mMC3H4N2imidazole
2.0 mMC4H11NO3Tris hydrochloride
0.5 mMC4H10O2S2dithiothreitol
200.0 mMC10H16N5O13P3adenosine triphosphate
0.01 %NaN3sodium azide
10.0 U/mLApyraseApyrase

Details: Buffer was filtered through 0.44 um filter and degassed.
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 6 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 298 K / Instrument: LEICA EM GP
Details: Sample was applied to a glow-discharged holey carbon grid. 3 uL actin was incubated for 60 seconds. 3 uL of myosin VI was added and incubated for 60 seconds. 3 uL solution was removed. An ...Details: Sample was applied to a glow-discharged holey carbon grid. 3 uL actin was incubated for 60 seconds. 3 uL of myosin VI was added and incubated for 60 seconds. 3 uL solution was removed. An additional 3 uL of myosin VI was applied. After 60 seconds, 3 uL solution was removed, and the grid was blotted for 3 seconds from the backside with filter paper..
Details0.45 mg/mL myosin VI was added to 0.025 mg/mL actin

-
Electron microscopy

MicroscopeFEI TECNAI 20
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-24 / Number grids imaged: 3 / Number real images: 778 / Average exposure time: 0.25 sec. / Average electron dose: 1.5 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 29000
Sample stageSpecimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN

-
Image processing

Final reconstructionNumber classes used: 1
Applied symmetry - Helical parameters - Δz: 28.06 Å
Applied symmetry - Helical parameters - Δ&Phi: -166.73 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: FREALIGN (ver. 9.11) / Number images used: 56116
Startup modelType of model: EMDB MAP
EMDB ID:

1990


Details: low-pass filtered to 35 A
Final angle assignmentType: NOT APPLICABLE / Software - Name: FREALIGN (ver. 9.11)
FSC plot (resolution estimation)

-
Atomic model buiding 1

DetailsInitial models were assembled from 8 actins (3J8A) and 6 myosins (2BKI) through rigid body docking in Chimera, followed by flexible fitting with DireX. Resulting models were subjected to MDFF.
RefinementProtocol: FLEXIBLE FIT / Overall B value: 150
Output model

PDB-6bnp:
CryoEM structure of MyosinVI-actin complex in the rigor (nucleotide-free) state

PDB-6bnv:
CryoEM structure of MyosinVI-actin complex in the rigor (nucleotide-free) state, backbone-averaged with side chains truncated to alanine

+
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