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- EMDB-55354: shutdown state non-muscle myosin 2A heads region -

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Basic information

Entry
Database: EMDB / ID: EMD-55354
Titleshutdown state non-muscle myosin 2A heads region
Map dataDeepEMhancer map
Sample
  • Complex: NM2A complex with essential and regulatory light chains in the shutdown state
    • Protein or peptide: Isoform 1 of Myosin-9
    • Protein or peptide: Isoform 1 of Myosin light polypeptide 6
    • Protein or peptide: Myosin regulatory light polypeptide 9
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: PHOSPHATE ION
  • Ligand: MAGNESIUM ION
KeywordsMyosin / coiled coil / MOTOR PROTEIN
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
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.98 Å
AuthorsPeckham M / Carrington G
Funding support United Kingdom, 1 items
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 14, 2025-
Header (metadata) releaseOct 22, 2025-
Map releaseOct 22, 2025-
UpdateOct 22, 2025-
Current statusOct 22, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55354.png

Downloads & links

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Map

FileDownload / File: emd_55354.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDeepEMhancer map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 480 pix.
= 393.6 Å		0.82 Å/pix.
x 480 pix.
= 393.6 Å		0.82 Å/pix.
x 480 pix.
= 393.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.0073517985 - 2.1098995
Average (Standard dev.)0.0011630098 (±0.024391958)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 393.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: sharpened cryosparc map

Fileemd_55354_additional_1.map
Annotationsharpened cryosparc map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: unsharpened cryosparc map

Fileemd_55354_additional_2.map
Annotationunsharpened cryosparc map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_55354_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_55354_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : NM2A complex with essential and regulatory light chains in the sh...

EntireName: NM2A complex with essential and regulatory light chains in the shutdown state
Components
  • Complex: NM2A complex with essential and regulatory light chains in the shutdown state
    • Protein or peptide: Isoform 1 of Myosin-9
    • Protein or peptide: Isoform 1 of Myosin light polypeptide 6
    • Protein or peptide: Myosin regulatory light polypeptide 9
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: PHOSPHATE ION
  • Ligand: MAGNESIUM ION

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Supramolecule #1: NM2A complex with essential and regulatory light chains in the sh...

SupramoleculeName: NM2A complex with essential and regulatory light chains in the shutdown state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 527 KDa

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Macromolecule #1: Isoform 1 of Myosin-9

MacromoleculeName: Isoform 1 of Myosin-9 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 226.888781 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAQQAADKYL YVDKNFINNP LAQADWAAKK LVWVPSDKSG FEPASLKEEV GEEAIVELVE NGKKVKVNKD DIQKMNPPKF SKVEDMAEL TCLNEASVLH NLKERYYSGL IYTYSGLFCV VINPYKNLPI YSEEIVEMYK GKKRHEMPPH IYAITDTAYR S MMQDREDQ ...String:
MAQQAADKYL YVDKNFINNP LAQADWAAKK LVWVPSDKSG FEPASLKEEV GEEAIVELVE NGKKVKVNKD DIQKMNPPKF SKVEDMAEL TCLNEASVLH NLKERYYSGL IYTYSGLFCV VINPYKNLPI YSEEIVEMYK GKKRHEMPPH IYAITDTAYR S MMQDREDQ SILCTGESGA GKTENTKKVI QYLAYVASSH KSKKDQGELE RQLLQANPIL EAFGNAKTVK NDNSSRFGKF IR INFDVNG YIVGANIETY LLEKSRAIRQ AKEERTFHIF YYLLSGAGEH LKTDLLLEPY NKYRFLSNGH VTIPGQQDKD MFQ ETMEAM RIMGIPEEEQ MGLLRVISGV LQLGNIVFKK ERNTDQASMP DNTAAQKVSH LLGINVTDFT RGILTPRIKV GRDY VQKAQ TKEQADFAIE ALAKATYERM FRWLVLRINK ALDKTKRQGA SFIGILDIAG FEIFDLNSFE QLCINYTNEK LQQLF NHTM FILEQEEYQR EGIEWNFIDF GLDLQPCIDL IEKPAGPPGI LALLDEECWF PKATDKSFVE KVMQEQGTHP KFQKPK QLK DKADFCIIHY AGKVDYKADE WLMKNMDPLN DNIATLLHQS SDKFVSELWK DVDRIIGLDQ VAGMSETALP GAFKTRK GM FRTVGQLYKE QLAKLMATLR NTNPNFVRCI IPNHEKKAGK LDPHLVLDQL RCNGVLEGIR ICRQGFPNRV VFQEFRQR Y EILTPNSIPK GFMDGKQACV LMIKALELDS NLYRIGQSKV FFRAGVLAHL EEERDLKITD VIIGFQACCR GYLARKAFA KRQQQLTAMK VLQRNCAAYL KLRNWQWWRL FTKVKPLLQV SRQEEEMMAK EEELVKVREK QLAAENRLTE METLQSQLMA EKLQLQEQL QAETELCAEA EELRARLTAK KQELEEICHD LEARVEEEEE RCQHLQAEKK KMQQNIQELE EQLEEEESAR Q KLQLEKVT TEAKLKKLEE EQIILEDQNC KLAKEKKLLE DRIAEFTTNL TEEEEKSKSL AKLKNKHEAM ITDLEERLRR EE KQRQELE KTRRKLEGDS TDLSDQIAEL QAQIAELKMQ LAKKEEELQA ALARVEEEAA QKNMALKKIR ELESQISELQ EDL ESERAS RNKAEKQKRD LGEELEALKT ELEDTLDSTA AQQELRSKRE QEVNILKKTL EEEAKTHEAQ IQEMRQKHSQ AVEE LAEQL EQTKRVKANL EKAKQTLENE RGELANEVKV LLQGKGDSEH KRKKVEAQLQ ELQVKFNEGE RVRTELADKV TKLQV ELDN VTGLLSQSDS KSSKLTKDFS ALESQLQDTQ ELLQEENRQK LSLSTKLKQV EDEKNSFREQ LEEEEEAKHN LEKQIA TLH AQVADMKKKM EDSVGCLETA EEVKRKLQKD LEGLSQRHEE KVAAYDKLEK TKTRLQQELD DLLVDLDHQR QSACNLE KK QKKFDQLLAE EKTISAKYAE ERDRAEAEAR EKETKALSLA RALEEAMEQK AELERLNKQF RTEMEDLMSS KDDVGKSV H ELEKSKRALE QQVEEMKTQL EELEDELQAT EDAKLRLEVN LQAMKAQFER DLQGRDEQSE EKKKQLVRQV REMEAELED ERKQRSMAVA ARKKLEMDLK DLEAHIDSAN KNRDEAIKQL RKLQAQMKDC MRELDDTRAS REEILAQAKE NEKKLKSMEA EMIQLQEEL AAAERAKRQA QQERDELADE IANSSGKGAL ALEEKRRLEA RIAQLEEELE EEQGNTELIN DRLKKANLQI D QINTDLNL ERSHAQKNEN ARQQLERQNK ELKVKLQEME GTVKSKYKAS ITALEAKIAQ LEEQLDNETK ERQAACKQVR RT EKKLKDV LLQVDDERRN AEQYKDQADK ASTRLKQLKR QLEEAEEEAQ RANASRRKLQ RELEDATETA DAMNREVSSL KNK LRRGDL PFVVPRRMAR KGAGDGSDEE VDGKADGAEA KPAE

UniProtKB: Myosin-9

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Macromolecule #2: Isoform 1 of Myosin light polypeptide 6

MacromoleculeName: Isoform 1 of Myosin light polypeptide 6 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Gallus gallus (chicken)
Molecular weightTheoretical: 17.004221 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MCDFSEEQTA EFKEAFQLFD RTGDGKILYS QCGDVMRALG QNPTNAEVMK VLGNPKSDEM NLKTLKFEQF LPMMQTIAKN KDQGCFEDY VEGLRVFDKE GNGTVMGAEI RHVLVTLGEK MTEEEVEQLV AGHEDSNGCI NYEELVRMVL SG

UniProtKB: Myosin light polypeptide 6

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Macromolecule #3: Myosin regulatory light polypeptide 9

MacromoleculeName: Myosin regulatory light polypeptide 9 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 19.890211 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MSSKRAKTKT TKKRPQRATS NVFAMFDQSQ IQEFKEAFNM IDQNRDGFID KEDLHDMLAS LGKNPTDEYL DAMMNEAPGP INFTMFLTM FGEKLNGTDP EDVIRNAFAC FDEEATGTIQ EDYLRELLTT MGDRFTDEEV DELYREAPID KKGNFNYIEF T RILKHGAK DKDD

UniProtKB: Myosin regulatory light polypeptide 9

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Macromolecule #4: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 2 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #5: PHOSPHATE ION

MacromoleculeName: PHOSPHATE ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: PO4
Molecular weightTheoretical: 94.971 Da
Chemical component information

ChemComp-PO4:
PHOSPHATE ION

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Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 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
GridModel: UltrAuFoil / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 90 %

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 2 / Number real images: 27549 / Average exposure time: 3.42 sec. / Average electron dose: 36.94 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 96000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE / Details: Initial model built with ModelAngelo
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 186265
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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