|Entry||Database: PDB / ID: 6bnv|
|Title||CryoEM structure of MyosinVI-actin complex in the rigor (nucleotide-free) state, backbone-averaged with side chains truncated to alanine|
|Keywords||CONTRACTILE PROTEIN / Cytoskeleton / Filament / complex|
|Function / homology|
Function and homology information
CH domain binding / Trafficking of AMPA receptors / regulation of secretion / Gap junction degradation / RNA polymerase II, holoenzyme / actin filament-based movement / inner ear auditory receptor cell differentiation / vesicle transport along actin filament / inner ear morphogenesis / microfilament motor activity ...CH domain binding / Trafficking of AMPA receptors / regulation of secretion / Gap junction degradation / RNA polymerase II, holoenzyme / actin filament-based movement / inner ear auditory receptor cell differentiation / vesicle transport along actin filament / inner ear morphogenesis / microfilament motor activity / myosin binding / microfilament motor activity => GO:0000146 / positive regulation of microfilament motor activity => GO:0120081 / myosin complex / mesenchyme migration / clathrin-coated vesicle / tropomyosin binding / myosin heavy chain binding / troponin I binding / DNA damage response, signal transduction by p53 class mediator / skeletal muscle thin filament assembly / striated muscle thin filament / actin filament bundle / filamentous actin / actin filament bundle assembly / actin monomer binding / motor activity / skeletal muscle fiber development / skeletal muscle myofibril / endocytic vesicle / stress fiber / clathrin-coated pit / titin binding / actin filament polymerization / enzyme regulator activity / ruffle / filopodium / actin filament / actin filament organization / ADP binding / sensory perception of sound / ruffle membrane / intracellular protein transport / cell cortex / microvillus / cell body / protein transport / calcium-dependent protein binding / actin filament binding / endocytosis / actin cytoskeleton / lamellipodium / disordered domain specific binding / cytoplasmic vesicle / nuclear membrane / vesicle / calmodulin binding / protein C-terminus binding / protein domain specific binding / positive regulation of gene expression / calcium ion binding / magnesium ion binding / perinuclear region of cytoplasm / Golgi apparatus / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / ATP binding / identical protein binding / plasma membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Myosin VI cargo binding domain / Myosin VI, cargo binding domain / Class VI myosin, motor domain / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Myosin S1 fragment, N-terminal / Myosin head, motor domain / Myosin. Large ATPases. / Myosin head (motor domain) / Myosin motor domain profile. ...Myosin VI cargo binding domain / Myosin VI, cargo binding domain / Class VI myosin, motor domain / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Myosin S1 fragment, N-terminal / Myosin head, motor domain / Myosin. Large ATPases. / Myosin head (motor domain) / Myosin motor domain profile. / Actins signature 1. / Actins signature 2. / Actin, conserved site / Actins and actin-related proteins signature. / Actin/actin-like conserved site / Actin / Actin / Actin family / Kinesin motor domain superfamily / EF-hand domain pair / ATPase, nucleotide binding domain / EF-hand, calcium binding motif / EF-hand calcium-binding domain profile. / EF-Hand 1, calcium-binding site / EF-hand domain / EF-hand calcium-binding domain. / EF-hand domain pair / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Unconventional myosin-6 / Calmodulin / Actin, alpha skeletal muscle / Unconventional myosin-VI
Similarity search - Component
|Biological species||Sus scrofa (pig)|
Gallus gallus (chicken)
Oryctolagus cuniculus (rabbit)
|Method||ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4.6 Å|
|Authors||Gurel, P.S. / Alushin, G.A.|
|Funding support|| United States, 1items |
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.
|Structure viewer||Molecule: |
Downloads & links
I: Unconventional myosin-VI
J: Unconventional myosin-VI
K: Unconventional myosin-VI
L: Unconventional myosin-VI
M: Unconventional myosin-VI
N: Unconventional myosin-VI
A: Actin, alpha skeletal muscle
B: Actin, alpha skeletal muscle
C: Actin, alpha skeletal muscle
D: Actin, alpha skeletal muscle
E: Actin, alpha skeletal muscle
F: Actin, alpha skeletal muscle
G: Actin, alpha skeletal muscle
H: Actin, alpha skeletal muscle
Mass: 93207.297 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Tissue: skeletal muscle / Gene: MYO6 / Plasmid: pBiex1 / Cell line (production host): sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: F1RQI7, UniProt: Q29122*PLUS
Mass: 41560.266 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: skeletal muscle / References: UniProt: P68135
Mass: 16406.004 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: CALM, CAM, RCJMB04_24e7 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P62149
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction|
|Molecular weight||Value: 0.139 MDa / Experimental value: NO|
|Buffer solution||pH: 7.5 |
Details: Buffer was filtered through 0.44 um filter and degassed.
|Specimen||Conc.: 0.045 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES|
Details: 0.45 mg/mL myosin VI was added to 0.025 mg/mL actin
|Specimen support||Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: C-flat-1.2/1.3|
|Vitrification||Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 298 K|
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.
-Electron microscopy imaging
|Microscopy||Model: FEI TECNAI 20|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM|
|Electron lens||Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 29000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm / Cs: 2 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE|
|Specimen holder||Cryogen: NITROGEN|
Model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
|Image recording||Average exposure time: 0.25 sec. / Electron dose: 1.5 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 3 / Num. of real images: 778|
|Image scans||Sampling size: 5 µm / Width: 3838 / Height: 3711 / Movie frames/image: 24 / Used frames/image: 1-24|
|CTF correction||Type: PHASE FLIPPING AND AMPLITUDE CORRECTION|
|Helical symmerty||Angular rotation/subunit: -166.73 ° / Axial rise/subunit: 28.06 Å / Axial symmetry: C1|
|3D reconstruction||Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 56116 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: HELICAL|
|Atomic model building||B value: 150 / Protocol: FLEXIBLE FIT / Space: REAL|
Details: 2BKI chain B was grafted onto Chains A-F of 6BNP, then assembled by rigid body docking into the 7.5 A low pass-filtered density map, followed by flexible fitting with DireX. The resulting ...Details: 2BKI chain B was grafted onto Chains A-F of 6BNP, then assembled by rigid body docking into the 7.5 A low pass-filtered density map, followed by flexible fitting with DireX. The resulting model was subjected to MDFF using the 7.5 A low pass-filtered density map. Atomistic models were backbone-averaged in Phenix and side chains were truncated to alanine. This treatment has resulted in the errors noted in the associated caveats.
-Aug 12, 2020. New: Covid-19 info
New: Covid-19 info
Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data
-Mar 5, 2020. Novel coronavirus structure data
Novel coronavirus structure data
- International Committee on Taxonomy of Viruses (ICTV) defined the short name of the 2019 coronavirus as "SARS-CoV-2".
The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 - nature microbiology
- In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Related info.:Yorodumi Speices / Aug 12, 2020. New: Covid-19 info
+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
+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.
+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
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