[English] 日本語
Yorodumi
- PDB-9szr: shutdown state non-muscle myosin 2A heads region -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9szr
Titleshutdown state non-muscle myosin 2A heads region
Components
  • (Isoform 1 of ...) x 2
  • Myosin regulatory light polypeptide 9
KeywordsMOTOR PROTEIN / Myosin / coiled coil
Function / homology
Function and homology information


Ephrin signaling / Smooth Muscle Contraction / negative regulation of actin filament severing / uropod organization / regulation of plasma membrane repair / establishment of meiotic spindle localization / cytokinetic process / myosin II filament / cortical granule exocytosis / establishment of T cell polarity ...Ephrin signaling / Smooth Muscle Contraction / negative regulation of actin filament severing / uropod organization / regulation of plasma membrane repair / establishment of meiotic spindle localization / cytokinetic process / myosin II filament / cortical granule exocytosis / establishment of T cell polarity / myofibril assembly / cortical granule / blood vessel endothelial cell migration / actomyosin contractile ring / positive regulation of protein processing in phagocytic vesicle / uropod / regulated exocytosis / myosin II binding / actin filament-based movement / muscle myosin complex / meiotic spindle organization / lysosome localization / plasma membrane repair / actomyosin / myosin filament / myoblast fusion / RHO GTPases activate CIT / RHO GTPases Activate ROCKs / actomyosin structure organization / Sema4D induced cell migration and growth-cone collapse / myosin II complex / Sensory processing of sound by outer hair cells of the cochlea / structural constituent of muscle / platelet formation / CD163 mediating an anti-inflammatory response / Sensory processing of sound by inner hair cells of the cochlea / leukocyte migration / phagocytosis, engulfment / EPHA-mediated growth cone collapse / myosin heavy chain binding / microfilament motor activity / endodermal cell differentiation / cell leading edge / RHO GTPases activate PAKs / cleavage furrow / brush border / membrane protein ectodomain proteolysis / cytoskeletal motor activity / monocyte differentiation / immunological synapse / RHO GTPases activate PKNs / stress fiber / protein-membrane adaptor activity / ruffle / integrin-mediated signaling pathway / Translocation of SLC2A4 (GLUT4) to the plasma membrane / FCGR3A-mediated phagocytosis / adherens junction / neuromuscular junction / ADP binding / Regulation of actin dynamics for phagocytic cup formation / platelet aggregation / spindle / cytoplasmic side of plasma membrane / integrin binding / actin filament binding / Signaling by ALK fusions and activated point mutants / protein transport / regulation of cell shape / actin cytoskeleton / actin binding / virus receptor activity / actin cytoskeleton organization / cell cortex / angiogenesis / in utero embryonic development / calmodulin binding / nuclear body / cadherin binding / protein domain specific binding / focal adhesion / calcium ion binding / symbiont entry into host cell / magnesium ion binding / cell surface / protein homodimerization activity / protein-containing complex / RNA binding / extracellular exosome / ATP binding / identical protein binding / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
DJBP, EF-hand domain / EF-hand domain / : / RGS domain superfamily / Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain / Myosin S1 fragment, N-terminal / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. ...DJBP, EF-hand domain / EF-hand domain / : / RGS domain superfamily / Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain / Myosin S1 fragment, N-terminal / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / Kinesin motor domain superfamily / : / EF-hand domain pair / EF-hand, calcium binding motif / 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
ADENOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / Myosin light polypeptide 6 / Myosin-9 / Myosin regulatory light polypeptide 9
Similarity search - Component
Biological speciesHomo sapiens (human)
Gallus gallus (chicken)
Bos taurus (domestic cattle)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.3 Å
AuthorsPeckham, M. / Carrington, G.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome TrustRGIMCB124415 United Kingdom
CitationJournal: To Be Published
Title: Cryo-EM structure of shutdown non-muscle myosin 2A
Authors: Casas-Mao, D. / Carrington, G. / Peckham, M.
History
DepositionOct 15, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Isoform 1 of Myosin-9
B: Isoform 1 of Myosin-9
C: Isoform 1 of Myosin light polypeptide 6
D: Isoform 1 of Myosin light polypeptide 6
E: Myosin regulatory light polypeptide 9
F: Myosin regulatory light polypeptide 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)528,70814
Polymers527,5666
Non-polymers1,1428
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

-
Isoform 1 of ... , 2 types, 4 molecules ABCD

#1: Protein Isoform 1 of Myosin-9 / Cellular myosin heavy chain / type A / Myosin heavy chain 9 / Myosin heavy chain / non-muscle IIa / ...Cellular myosin heavy chain / type A / Myosin heavy chain 9 / Myosin heavy chain / non-muscle IIa / Non-muscle myosin heavy chain A / NMMHC-A / Non-muscle myosin heavy chain IIa / NMMHC II-a / NMMHC-IIA


Mass: 226888.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MYH9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P35579
#2: Protein Isoform 1 of Myosin light polypeptide 6 / G2 catalytic / LC17-GI / LC17-NM / Myosin light chain alkali smooth-muscle/non-muscle isoforms


Mass: 17004.221 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: MYL6 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P02607

-
Protein , 1 types, 2 molecules EF

#3: Protein Myosin regulatory light polypeptide 9 / Myosin regulatory light chain 2 / smooth muscle isoform / Myosin regulatory light chain 9


Mass: 19890.211 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: MYL9, MYRL2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q5E9E2

-
Non-polymers , 3 types, 8 molecules

#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: NM2A complex with essential and regulatory light chains in the shutdown state
Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightValue: 0.527 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.2
Details: 140 mM KCl, 10 mM MOPS pH 7.2, 0.1 mM EGTA, 2 mM MgCl2, 1 mM ATP. 1 mM Bissulfosuccinimidyl suberate
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 90 %

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 96000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 900 nm / Cs: 2.7 mm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 3.42 sec. / Electron dose: 36.94 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 27549

-
Processing

EM software
IDNameVersionCategory
1cryoSPARCv4.7.0particle selection
2EPU3.3image acquisition
4cryoSPARCCTF correction
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 6.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 15167 / Num. of class averages: 1 / Symmetry type: POINT

+
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