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- EMDB-8165: Cryo-EM structure of a human cytoplasmic actomyosin complex at ne... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-8165 | |||||||||
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Title | Cryo-EM structure of a human cytoplasmic actomyosin complex at near-atomic resolution | |||||||||
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Function / homology | ![]() RHOBTB2 GTPase cycle / RHOU GTPase cycle / RHOV GTPase cycle / contractile vacuole / COPI-mediated anterograde transport / Platelet degranulation / basal body patch / sorocarp development / myosin II filament / tight junction assembly ...RHOBTB2 GTPase cycle / RHOU GTPase cycle / RHOV GTPase cycle / contractile vacuole / COPI-mediated anterograde transport / Platelet degranulation / basal body patch / sorocarp development / myosin II filament / tight junction assembly / macropinocytic cup / Neutrophil degranulation / regulation of transepithelial transport / morphogenesis of a polarized epithelium / actin crosslink formation / actin filament-based movement / structural constituent of postsynaptic actin cytoskeleton / profilin binding / protein localization to bicellular tight junction / dense body / vocalization behavior / Formation of annular gap junctions / Gap junction degradation / Cell-extracellular matrix interactions / actomyosin / myosin filament / RHO GTPases Activate ROCKs / hyperosmotic response / Adherens junctions interactions / regulation of stress fiber assembly / RHO GTPases activate CIT / actomyosin structure organization / Sema4D induced cell migration and growth-cone collapse / Sensory processing of sound by outer hair cells of the cochlea / Interaction between L1 and Ankyrins / Sensory processing of sound by inner hair cells of the cochlea / regulation of synaptic vesicle endocytosis / apical junction complex / regulation of focal adhesion assembly / myosin II complex / cortical actin cytoskeleton / microfilament motor activity / positive regulation of wound healing / maintenance of blood-brain barrier / myofibril / sarcomere organization / NuA4 histone acetyltransferase complex / EPHA-mediated growth cone collapse / cell leading edge / pseudopodium / Recycling pathway of L1 / filamentous actin / RHO GTPases activate PAKs / brush border / calyx of Held / actin filament bundle assembly / skeletal muscle contraction / mitotic cytokinesis / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate WASPs and WAVEs / neuronal action potential / RHO GTPases activate IQGAPs / RHOBTB2 GTPase cycle / phagocytosis / stress fiber / skeletal muscle tissue development / RHO GTPases activate PKNs / EPHB-mediated forward signaling / phagocytic vesicle / cellular response to starvation / mitochondrion organization / axonogenesis / extracellular matrix / cell projection / Translocation of SLC2A4 (GLUT4) to the plasma membrane / RHO GTPases Activate Formins / cell motility / actin filament / FCGR3A-mediated phagocytosis / sensory perception of sound / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Signaling by high-kinase activity BRAF mutants / Schaffer collateral - CA1 synapse / MAP2K and MAPK activation / structural constituent of cytoskeleton / Regulation of actin dynamics for phagocytic cup formation / platelet aggregation / VEGFA-VEGFR2 Pathway / cellular response to type II interferon / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by BRAF and RAF1 fusions / cell-cell junction / actin filament binding / cell junction / Clathrin-mediated endocytosis / protein-macromolecule adaptor activity / cell cortex Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
![]() | von der Ecken J / Heissler SM / Pathan-Chhatbar S / Manstein DJ / Raunser S | |||||||||
![]() | ![]() Title: Cryo-EM structure of a human cytoplasmic actomyosin complex at near-atomic resolution. Abstract: The interaction of myosin with actin filaments is the central feature of muscle contraction and cargo movement along actin filaments of the cytoskeleton. The energy for these movements is generated ...The interaction of myosin with actin filaments is the central feature of muscle contraction and cargo movement along actin filaments of the cytoskeleton. The energy for these movements is generated during a complex mechanochemical reaction cycle. Crystal structures of myosin in different states have provided important structural insights into the myosin motor cycle when myosin is detached from F-actin. The difficulty of obtaining diffracting crystals, however, has prevented structure determination by crystallography of actomyosin complexes. Thus, although structural models exist of F-actin in complex with various myosins, a high-resolution structure of the F-actin–myosin complex is missing. Here, using electron cryomicroscopy, we present the structure of a human rigor actomyosin complex at an average resolution of 3.9 Å. The structure reveals details of the actomyosin interface, which is mainly stabilized by hydrophobic interactions. The negatively charged amino (N) terminus of actin interacts with a conserved basic motif in loop 2 of myosin, promoting cleft closure in myosin. Surprisingly, the overall structure of myosin is similar to rigor-like myosin structures in the absence of F-actin, indicating that F-actin binding induces only minimal conformational changes in myosin. A comparison with pre-powerstroke and intermediate (Pi-release) states of myosin allows us to discuss the general mechanism of myosin binding to F-actin. Our results serve as a strong foundation for the molecular understanding of cytoskeletal diseases, such as autosomal dominant hearing loss and diseases affecting skeletal and cardiac muscles, in particular nemaline myopathy and hypertrophic cardiomyopathy. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 47.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 21.3 KB 21.3 KB | Display Display | ![]() |
Images | ![]() | 249 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 289.3 KB | Display | ![]() |
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Full document | ![]() | 288.4 KB | Display | |
Data in XML | ![]() | 6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5jlhMC ![]() 8162C ![]() 8163C ![]() 8164C ![]() 5jlfC C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | None | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : F-actin-myosin-tropomyosin complex
Entire | Name: F-actin-myosin-tropomyosin complex |
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Components |
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-Supramolecule #1: F-actin-myosin-tropomyosin complex
Supramolecule | Name: F-actin-myosin-tropomyosin complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Filament |
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Source (natural) | Organism: ![]() |
-Supramolecule #2: F-actin
Supramolecule | Name: F-actin / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() |
-Supramolecule #3: Myosin
Supramolecule | Name: Myosin / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() ![]() |
-Supramolecule #4: tropomyosin
Supramolecule | Name: tropomyosin / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3 |
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-Macromolecule #1: Actin, cytoplasmic 2
Macromolecule | Name: Actin, cytoplasmic 2 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: EEEIAALVID NGSGMCKAGF AGDDAPRAVF PSIVGRPRHQ GVMVGMGQKD SYVGDEAQSK RGILTLKYPI EHGIVTNWDD MEKIWHHTF YNELRVAPEE HPVLLTEAPL NPKANREKMT QIMFETFNTP AMYVAIQAVL SLYASGRTTG IVMDSGDGVT H TVPIYEGY ...String: EEEIAALVID NGSGMCKAGF AGDDAPRAVF PSIVGRPRHQ GVMVGMGQKD SYVGDEAQSK RGILTLKYPI EHGIVTNWDD MEKIWHHTF YNELRVAPEE HPVLLTEAPL NPKANREKMT QIMFETFNTP AMYVAIQAVL SLYASGRTTG IVMDSGDGVT H TVPIYEGY ALPHAILRLD LAGRDLTDYL MKILTERGYS FTTTAEREIV RDIKEKLCYV ALDFEQEMAT AASSSSLEKS YE LPDGQVI TIGNERFRCP EALFQPSFLG MESCGIHETT FNSIMKCDVD IRKDLYANTV LSGGTTMYPG IADRMQKEIT ALA PSTMKI KIIAPPERKY SVWIGGSILA SLSTFQQMWI SKQEYDESGP SIVHRKCF |
-Macromolecule #2: NON MUSCLE MYOSIN 2C, ALPHA-ACTININ
Macromolecule | Name: NON MUSCLE MYOSIN 2C, ALPHA-ACTININ / type: protein_or_peptide / ID: 2 Details: NON MUSCLE MYOSIN 2C HEAVY CHAIN, MOTOR DOMAIN RESIDUES 1-799 LINKED TO ALPHA-ACTININ 3, REPEATS 1 AND 2 RESIDUES 800-1039 FRAGMENT: UNP Q7Z406-1 RESIDUES 1-799, UNP P05095 RESIDUES 265-502 Enantiomer: LEVO / EC number: ec: 3.6.4.1 |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MAAVTMSVPG RKAPPRPGPV PEAAQPFLFT PRGPSAGGGP GSGTSPQVEW TARRLVWVPS ELHGFEAAAL RDEGEEEAEV ELAESGRRL RLPRDQIQRM NPPKFSKAED MAELTCLNEA SVLHNLRERY YSGLIYTYSG LFCVVINPYK QLPIYTEAIV E MYRGKKRH ...String: MAAVTMSVPG RKAPPRPGPV PEAAQPFLFT PRGPSAGGGP GSGTSPQVEW TARRLVWVPS ELHGFEAAAL RDEGEEEAEV ELAESGRRL RLPRDQIQRM NPPKFSKAED MAELTCLNEA SVLHNLRERY YSGLIYTYSG LFCVVINPYK QLPIYTEAIV E MYRGKKRH EVPPHVYAVT EGAYRSMLQD REDQSILCTG ESGAGKTENT KKVIQYLAHV ASSPKGRKEP GVPGELERQL LQ ANPILEA FGNAKTVKND NSSRFGKFIR INFDVAGYIV GANIETYLLE KSRAIRQAKD ECSFHIFYQL LGGAGEQLKA DLL LEPCSH YRFLTNGPSS SPGQERELFQ ETLESLRVLG FSHEEIISML RMVSAVLQFG NIALKRERNT DQATMPDNTA AQKL CRLLG LGVTDFSRAL LTPRIKVGRD YVQKAQTKEQ ADFALEALAK ATYERLFRWL VLRLNRALDR SPRQGASFLG ILDIA GFEI FQLNSFEQLC INYTNEKLQQ LFNHTMFVLE QEEYQREGIP WTFLDFGLDL QPCIDLIERP ANPPGLLALL DEECWF PKA TDKSFVEKVA QEQGGHPKFQ RPRHLRDQAD FSVLHYAGKV DYKANEWLMK NMDPLNDNVA ALLHQSTDRL TAEIWKD VE GIVGLEQVSS LGDGPPGGRP RRGMFRTVGQ LYKESLSRLM ATLSNTNPSF VRCIVPNHEK RAGKLEPRLV LDQLRCNG V LEGIRICRQG FPNRILFQEF RQRYEILTPN AIPKGFMDGK QACEKMIQAL ELDPNLYRVG QSKIFFRAGV LAQLEEERA SEQTKSDYLK RANELVQWIN DKQASLESRD FGDSIESVQS FMNAHKEYKK TEKPPKGQEV SELEAIYNSL QTKLRLIKRE PFVAPAGLT PNEIDSTWSA LEKAEQEHAE ALRIELKRQK KIAVLLQKYN RILKKLENWA TTKSVYLGSN ETGDSITAVQ A KLKNLEAF DGECQSLEGQ SNSDLLSILA QLTELNYNGV PELTERKDTF FAQQWTGVKS SAETYKNTLL AELERLQKIE D |
-Macromolecule #3: Tropomyosin alpha-3 chain
Macromolecule | Name: Tropomyosin alpha-3 chain / type: protein_or_peptide / ID: 3 Details: Human TROPOMYSIN WAS USED (UNP P06753-2,TPM3_HUMAN, RESIDUES 62-196). DUE TO THE LIMITED RESOLUTION OF THE CRYO-EM DENSITY IN THE REGION OF TROPOMYOSIN, TROPOMYOSIN HAS BEEN REPRESENTED AS POLY(UNK). Enantiomer: LEVO |
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Sequence | String: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | filament |
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Sample preparation
Buffer | pH: 7.5 Component:
Details: 5 mM Tris-HCl pH 7.5, 1 mM DTT, 100 mM KCl, and 2 mM MgCl2 | ||||||||||
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Sugar embedding | Material: I | ||||||||||
Grid | Model: C-flat-2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE | ||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Instrument: GATAN CRYOPLUNGE 3 Details: Sample (2 uL of F-actin-tropomyosin solution) was applied to a glow-discharged holey carbon grid, incubated for 20 s and manually blotted from the backside for less than a second with filter ...Details: Sample (2 uL of F-actin-tropomyosin solution) was applied to a glow-discharged holey carbon grid, incubated for 20 s and manually blotted from the backside for less than a second with filter paper. Afterwards 1.5 uL of myosin solution (3 uM without nucleotide) were added directly on the grid, incubated for 10 s and then manually blotted for 5 s from the backside with filter paper.. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Details | Cs corrected microscope |
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 2-8 / Number real images: 6300 / Average exposure time: 0.475 sec. / Average electron dose: 16.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated defocus max: 2.8 µm / Calibrated defocus min: 0.7 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal magnification: 59000 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Initial model |
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Refinement | Protocol: BACKBONE TRACE / Overall B value: 180 | ||||||
Output model | ![]() PDB-5jlh: |