[English] 日本語
Yorodumi
- EMDB-7117: CryoEM structure of Myosin VI-Actin complex in the ADP state -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 7117
TitleCryoEM structure of Myosin VI-Actin complex in the ADP state
Map dataCryoEM density map of myosin VI-actin complex in the ADP state, B factor sharpened to -200.
Samplemyosin VI-actin in the ADP state:
myosin VI / actin / Unconventional myosin-VI / Actin, alpha skeletal muscle / (ligand) x 2
Function / homologyKinesin motor domain superfamily / Myosin motor domain profile. / Actins signature 1. / Myosin VI cargo binding domain / Myosin head (motor domain) / Myosin head, motor domain / Actin family / Myosin, N-terminal, SH3-like / Actins signature 2. / Actins and actin-related proteins signature. ...Kinesin motor domain superfamily / Myosin motor domain profile. / Actins signature 1. / Myosin VI cargo binding domain / Myosin head (motor domain) / Myosin head, motor domain / Actin family / Myosin, N-terminal, SH3-like / Actins signature 2. / Actins and actin-related proteins signature. / Actin, conserved site / Myosin N-terminal SH3-like domain profile. / Actin/actin-like conserved site / Class VI myosin, motor domain / Myosin VI, cargo binding domain / P-loop containing nucleoside triphosphate hydrolase / Gap junction degradation / Actin / Trafficking of AMPA receptors / Myosin S1 fragment, N-terminal / regulation of secretion / RNA polymerase II, holoenzyme / actin filament-based movement / clathrin-coated endocytic vesicle / positive regulation of actin-dependent ATPase activity / myosin complex / mesenchyme migration / tropomyosin binding / myosin heavy chain binding / troponin I binding / skeletal muscle thin filament assembly / striated muscle thin filament / actin filament bundle / filamentous actin / motor activity / skeletal muscle fiber development / actin filament bundle assembly / actin monomer binding / DNA damage response, signal transduction by p53 class mediator / titin binding / skeletal muscle myofibril / stress fiber / ADP binding / actin filament polymerization / microtubule motor activity / actin filament / microtubule-based movement / filopodium / calcium-dependent protein binding / intracellular protein transport / ruffle / sensory perception of sound / cell body / cell cortex / endocytosis / actin filament binding / lamellipodium / cytoplasmic vesicle / nuclear membrane / microtubule binding / calmodulin binding / protein domain specific binding / positive regulation of gene expression / magnesium ion binding / calcium ion binding / Golgi apparatus / perinuclear region of cytoplasm / positive regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / identical protein binding / nucleus / cytoplasm / Unconventional myosin-VI / Actin, alpha skeletal muscle / Unconventional myosin-VI
Function and homology information
SourceSus scrofa (pig) / Oryctolagus cuniculus (rabbit)
Methodhelical reconstruction / cryo EM / 5.5 Å resolution
AuthorsGurel PG / Alushin GM
Citation
Journal: Elife / Year: 2017
Title: Cryo-EM structures reveal specialization at the myosin VI-actin interface and a mechanism of force sensitivity.
Authors: Pinar S Gurel / Laura Y Kim / Paul V Ruijgrok / Tosan Omabegho / Zev Bryant / Gregory M Alushin
#1: Journal: 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
Validation ReportPDB-ID: 6bnq

SummaryFull report
PDB-ID: 6bnw

SummaryFull report
About validation report
DateDeposition: Nov 17, 2017 / Header (metadata) release: Jan 10, 2018 / Map release: Jan 10, 2018 / Last update: Jan 17, 2018

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5.8
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 5.8
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6bnq
  • Surface level: 5.8
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6bnw
  • Surface level: 5.8
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6bnq
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6bnw
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

Fileemd_7117.map.gz (map file in CCP4 format, 536871 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
512 pix
1.27 Å/pix.
= 650.24 Å
512 pix
1.27 Å/pix.
= 650.24 Å
512 pix
1.27 Å/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
Contour Level:5.8 (by author), 5.8 (movie #1):
Minimum - Maximum-7.0485396 - 18.04262
Average (Standard dev.)-1.499693E-9 (0.99999994)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions512512512
Origin-256-256-256
Limit255255255
Spacing512512512
CellA=B=C: 650.24 Å
α=β=γ: 90 deg.

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
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-256-256-256
NC/NR/NS512512512
D min/max/mean-7.04918.043-0.000

-
Supplemental data

-
Mask #1

Fileemd_7117_msk_1.map ( map file in CCP4 format, 536871 KB )
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms
Data typeImage stored as Reals
Annotation detailsHalf map of the myosin VI-actin complex in the ADP state, masked at 90A to exclude lower density portions of the density map including the lever arm
Space group number1

-
Mask #2

Fileemd_7117_msk_2.map ( map file in CCP4 format, 536871 KB )
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms
Data typeImage stored as Reals
Annotation detailsHalf map of the myosin VI-actin complex in the ADP state, masked at 90A to exclude lower density portions of the density map including the lever arm
Space group number1

-
Mask #2~

Fileemd_7117_msk_2.map
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

-
Sample components

+
Entire myosin VI-actin in the ADP state

EntireName: myosin VI-actin in the ADP state / Number of components: 7
MassTheoretical: 122 kDa

+
Component #1: protein, myosin VI-actin in the ADP state

ProteinName: myosin VI-actin in the ADP state / Recombinant expression: No
MassTheoretical: 122 kDa

+
Component #2: protein, myosin VI

ProteinName: myosin VI / Recombinant expression: No
SourceSpecies: Sus scrofa (pig)
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

+
Component #3: protein, actin

ProteinName: actin / Recombinant expression: No
SourceSpecies: Oryctolagus cuniculus (rabbit)

+
Component #4: protein, Unconventional myosin-VI

ProteinName: Unconventional myosin-VI / Recombinant expression: No
MassTheoretical: 79.837367 kDa
Source (engineered)Expression System: Sus scrofa (pig) / Vector: pBiex-1

+
Component #5: protein, Actin, alpha skeletal muscle

ProteinName: Actin, alpha skeletal muscle / Recombinant expression: No
MassTheoretical: 41.560266 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)
Source (natural)Organ or tissue: Skeletal Muscle

+
Component #6: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 8 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

+
Component #7: ligand, ADENOSINE-5'-DIPHOSPHATE

LigandName: ADENOSINE-5'-DIPHOSPHATE / Number of Copies: 8 / Recombinant expression: No
MassTheoretical: 0.427201 kDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: filament / Method: cryo EM
Helical parametersAxial symmetry: C1 (asymmetric) / Delta z: 28.06 Å / Delta phi: -166.69 deg.
Sample solutionSpecimen conc.: 0.45 mg/ml
Buffer solution: Buffer was filtered through 0.44 um filter and degassed.
pH: 7.5
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Temperature: 298 K / Humidity: 95 %
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.

-
Electron microscopy imaging

ImagingMicroscope: FEI TECNAI 20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 1.5 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 29000 X (nominal) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1500 - 3000 nm
Specimen HolderModel: GATAN LIQUID NITROGEN
CameraDetector: GATAN K2 (4k x 4k)

-
Image acquisition

Image acquisitionNumber of digital images: 377 / Sampling size: 5 microns

-
Image processing

ProcessingMethod: helical reconstruction
3D reconstructionAlgorithm: FOURIER SPACE / Software: FREALIGN / Resolution: 5.5 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

-
Atomic model buiding

Output model

+
About Yorodumi

-
News

-
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

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

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