|Entry||Database: PDB / ID: 7pmf|
|Title||Cryo-EM structure of the actomyosin-V complex in the post-rigor transition state (AppNHp, central 1er, class 1)|
|Keywords||MOTOR PROTEIN / myosin / cytoskeleton / F-actin / phalloidin|
|Function / homology|
Function and homology information
minus-end directed microfilament motor activity / unconventional myosin complex / insulin-responsive compartment / muscle myosin complex / muscle filament sliding / myosin II complex / vesicle transport along actin filament / myosin complex / cytoskeletal motor activator activity / microfilament motor activity ...minus-end directed microfilament motor activity / unconventional myosin complex / insulin-responsive compartment / muscle myosin complex / muscle filament sliding / myosin II complex / vesicle transport along actin filament / myosin complex / cytoskeletal motor activator activity / microfilament motor activity / structural constituent of muscle / mesenchyme migration / tropomyosin binding / myosin heavy chain binding / troponin I binding / actin filament bundle / skeletal muscle thin filament assembly / striated muscle thin filament / filamentous actin / Smooth Muscle Contraction / actin filament bundle assembly / actin monomer binding / cytoskeletal motor activity / skeletal muscle myofibril / skeletal muscle fiber development / skeletal muscle tissue development / stress fiber / titin binding / actin filament polymerization / actin filament organization / filopodium / muscle contraction / actin filament / vesicle-mediated transport / protein localization to plasma membrane / cell body / cellular response to insulin stimulus / calcium-dependent protein binding / actin cytoskeleton / actin filament binding / lamellipodium / calmodulin binding / vesicle / Golgi membrane / protein domain specific binding / calcium ion binding / positive regulation of gene expression / magnesium ion binding / extracellular exosome / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Myosin 5a, cargo-binding domain / Class V myosin, motor domain / Dilute domain / Dilute domain profile. / DIL domain / DIL / IQ calmodulin-binding motif / Myosin N-terminal SH3-like domain profile. / Myosin, N-terminal, SH3-like / Short calmodulin-binding motif containing conserved Ile and Gln residues. ...Myosin 5a, cargo-binding domain / Class V myosin, motor domain / Dilute domain / Dilute domain profile. / DIL domain / DIL / IQ calmodulin-binding motif / Myosin N-terminal SH3-like domain profile. / Myosin, N-terminal, SH3-like / Short calmodulin-binding motif containing conserved Ile and Gln residues. / Myosin head (motor domain) / Myosin. Large ATPases. / Myosin motor domain profile. / Myosin head, motor domain / IQ motif profile. / IQ motif, EF-hand binding site / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / Kinesin motor domain superfamily / ATPase, nucleotide binding domain / EF-hand, calcium binding motif / 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 6B / Actin, alpha skeletal muscle / : / ADENOSINE-5'-DIPHOSPHATE / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Unconventional myosin-Va
Similarity search - Component
|Biological species||Homo sapiens (human)|
Gallus gallus (chicken)
Oryctolagus cuniculus (rabbit)
Amanita phalloides (death cap)
|Method||ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.4 Å|
|Authors||Pospich, S. / Sweeney, H.L. / Houdusse, A. / Raunser, S.|
|Funding support|| Germany, European Union, France, United States, 5items |
|Citation||Journal: Elife / Year: 2021|
Title: High-resolution structures of the actomyosin-V complex in three nucleotide states provide insights into the force generation mechanism.
Authors: Sabrina Pospich / H Lee Sweeney / Anne Houdusse / Stefan Raunser /
Abstract: The molecular motor myosin undergoes a series of major structural transitions during its force-producing motor cycle. The underlying mechanism and its coupling to ATP hydrolysis and actin binding are ...The molecular motor myosin undergoes a series of major structural transitions during its force-producing motor cycle. The underlying mechanism and its coupling to ATP hydrolysis and actin binding are only partially understood, mostly due to sparse structural data on actin-bound states of myosin. Here, we report 26 high-resolution cryo-EM structures of the actomyosin-V complex in the strong-ADP, rigor, and a previously unseen post-rigor transition state that binds the ATP analog AppNHp. The structures reveal a high flexibility of myosin in each state and provide valuable insights into the structural transitions of myosin-V upon ADP release and binding of AppNHp, as well as the actomyosin interface. In addition, they show how myosin is able to specifically alter the structure of F-actin.
|Structure viewer||Molecule: |
Downloads & links
B: Myosin light chain 6B
A: Unconventional myosin-Va
C: Actin, alpha skeletal muscle
-Protein , 3 types, 3 molecules B
|#1: Protein|| |
Mass: 17090.277 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MYL6B, MLC1SA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P14649
|#2: Protein|| |
Mass: 91363.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: MYO5A / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q02440
|#3: Protein|| |
Mass: 42109.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P68135
-Protein/peptide , 1 types, 1 molecules H
|#4: Protein/peptide|| |
Type: Peptide-like / Class: Toxin / Mass: 808.899 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Amanita phalloides (death cap) / References: BIRD: PRD_002366
-Non-polymers , 3 types, 5 molecules
|#5: Chemical|| ChemComp-ANP / |
|#6: Chemical||#7: Chemical|| ChemComp-ADP / |
|Has ligand of interest||N|
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction|
|Component||Name: Actomyosin-V complex in the post-rigor transition stateMyofibril|
Details: Aged ADP-bound F-actin stabilized with phalloidin and decorated with myosin-Va-LC in a post-rigor transition state (Mg2+-AppNHp)
Entity ID: #1-#4 / Source: MULTIPLE SOURCES
|Molecular weight||Experimental value: NO|
|Buffer solution||pH: 7.5|
|Specimen||Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Rise 27.8 A, Twist -167.3 degrees|
|Specimen support||Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1|
|Vitrification||Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Details: On grid decoration, two data sets combined|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Microscopy||Model: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN|
|Electron lens||Mode: BRIGHT FIELDBright-field microscopy / Cs: 0 mm|
|Specimen holder||Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER|
|Image recording||Average exposure time: 15 sec. / Electron dose: 81 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 12475|
|EM imaging optics||Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV / Spherical aberration corrector: Cs-corrected microscope|
|Image scans||Movie frames/image: 40|
|Software||Name: PHENIX / Version: 1.17.1_3660: / Classification: refinement|
|CTF correction||Type: PHASE FLIPPING AND AMPLITUDE CORRECTION|
|Helical symmerty||Angular rotation/subunit: -167.3 ° / Axial rise/subunit: 27.8 Å / Axial symmetry: C1|
|3D reconstruction||Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 330197 / Num. of class averages: 1 / Symmetry type: POINT|
|Atomic model building||Space: REAL|
Details: Starting from average model and ChimeraX-Isolde session
|Atomic model building||PDB-ID: 7PMD|
|Refine LS restraints|
-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
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
- 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. 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.
- 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.
- 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.
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