[English] 日本語
Yorodumi
- EMDB-7115: Structure of bare actin filament -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 7115
TitleStructure of bare actin filament
Map datacryoEM density map of actin alone, sharpened with a -350 B factor
Samplebare actin filament
Function/homologypositive regulation of actin-dependent ATPase activity / mesenchyme migration / tropomyosin binding / myosin heavy chain binding / skeletal muscle thin filament assembly / troponin I binding / striated muscle thin filament / actin filament bundle / Actins signature 1. / Actins signature 2. ...positive regulation of actin-dependent ATPase activity / mesenchyme migration / tropomyosin binding / myosin heavy chain binding / skeletal muscle thin filament assembly / troponin I binding / striated muscle thin filament / actin filament bundle / Actins signature 1. / Actins signature 2. / Actin, conserved site / filamentous actin / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin family / actin monomer binding / skeletal muscle fiber development / actin filament bundle assembly / skeletal muscle myofibril / stress fiber / titin binding / actin filament polymerization / actin filament / Actin / filopodium / calcium-dependent protein binding / cell body / lamellipodium / protein domain specific binding / positive regulation of gene expression / magnesium ion binding / calcium ion binding / ATP binding / identical protein binding / cytoplasm / Actin, alpha skeletal muscle
Function and homology information
SourceOryctolagus cuniculus / mammal / European rabbit /
Methodhelical reconstruction, at 5.5 Å resolution
AuthorsGurel PS / Alushin GA
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
Abstract: Despite extensive scrutiny of the myosin superfamily, the lack of high-resolution structures of actin-bound states has prevented a complete description of its mechanochemical cycle and limited ...Despite extensive scrutiny of the myosin superfamily, the lack of high-resolution structures of actin-bound states has prevented a complete description of its mechanochemical cycle and limited insight into how sequence and structural diversification of the motor domain gives rise to specialized functional properties. Here we present cryo-EM structures of the unique minus-end directed myosin VI motor domain in rigor (4.6 Å) and Mg-ADP (5.5 Å) states bound to F-actin. Comparison to the myosin IIC-F-actin rigor complex reveals an almost complete lack of conservation of residues at the actin-myosin interface despite preservation of the primary sequence regions composing it, suggesting an evolutionary path for motor specialization. Additionally, analysis of the transition from ADP to rigor provides a structural rationale for force sensitivity in this step of the mechanochemical cycle. Finally, we observe reciprocal rearrangements in actin and myosin accompanying the transition between these states, supporting a role for actin structural plasticity during force generation by myosin VI.
#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
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.
Validation ReportPDB-ID: 6bno

SummaryFull report
PDB-ID: 6bnu

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: 12
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 12
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6bno
  • Surface level: 12
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6bnu
  • Surface level: 12
  • Imaged by UCSF CHIMERA
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6bno
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6bnu
  • Imaged by Jmol
  • Download
3D viewer
Supplemental images

Downloads & links

-
Map

Fileemd_7115.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 package.

Voxel sizeX=Y=Z: 1.27 Å
Density
Contour Level:12 (by author), 12 (movie #1):
Minimum - Maximum-14.238342 - 35.01912
Average (Standard dev.)-5.170885E-9 (1)
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-14.23835.019-0.000

-
Supplemental data

-
Sample components

-
Entire bare actin filament

EntireName: bare actin filament / Details: Actin filament in the ADP state / Number of components: 4
MassExperimental: 42 kDa

-
Component #1: protein, bare actin filament

ProteinName: bare actin filament / Details: Actin filament in the ADP state / Recombinant expression: No
MassExperimental: 42 kDa
SourceSpecies: Oryctolagus cuniculus / mammal / European rabbit /

-
Component #2: protein, Actin, alpha skeletal muscle

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

-
Component #3: ligand, MAGNESIUM ION

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

-
Component #4: ligand, ADENOSINE-5'-DIPHOSPHATE

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

-
Experimental details

-
Sample preparation

Specimen statefilament
Helical parametersAxial symmetry: C1 (asymmetric) / Delta z: 28.11 Å / Delta phi: -166.6 deg.
Sample solutionSpecimen conc.: 0.025 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, incubated for 60 seconds and 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: 442 / 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 assessment)

-
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 / EM Navigator (legacy version) / Yorodumi (legacy version)

+
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 / EM Navigator (legacy version) / Yorodumi (legacy version)

+
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.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more