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Yorodumi- EMDB-8164: Cryo-EM structure of a human cytoplasmic actomyosin complex at ne... -
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-Basic information
Entry | Database: EMDB / ID: EMD-8164 | |||||||||
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Title | Cryo-EM structure of a human cytoplasmic actomyosin complex at near-atomic resolution (tropomyosin filtered to 7 Angstrom) | |||||||||
Map data | None | |||||||||
Sample |
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Keywords | CONTRACTILE FILAMENT / MUSCLE / THIN FILAMENT / CYTOSKELETON / STRUCTURAL PROTEIN / HYDROLASE COMPLEX / F-actin / tropomyosin / filament / myosin / protein polymers / cryo EM / Contractile protein | |||||||||
Function / homology | Function and homology information 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 / macropinocytic cup ...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 / macropinocytic cup / tight junction assembly / Neutrophil degranulation / regulation of transepithelial transport / morphogenesis of a polarized epithelium / actin crosslink formation / actin filament-based movement / protein localization to bicellular tight junction / profilin binding / structural constituent of postsynaptic actin cytoskeleton / vocalization behavior / Formation of annular gap junctions / dense body / actomyosin / Gap junction degradation / Cell-extracellular matrix interactions / myosin filament / actomyosin structure organization / RHO GTPases Activate ROCKs / hyperosmotic response / regulation of stress fiber assembly / RHO GTPases activate CIT / Sema4D induced cell migration and growth-cone collapse / Adherens junctions interactions / myosin II complex / Interaction between L1 and Ankyrins / Sensory processing of sound by outer hair cells of the cochlea / Sensory processing of sound by inner hair cells of the cochlea / regulation of synaptic vesicle endocytosis / apical junction complex / regulation of focal adhesion assembly / sarcomere organization / microfilament motor activity / positive regulation of wound healing / myofibril / cortical actin cytoskeleton / maintenance of blood-brain barrier / EPHA-mediated growth cone collapse / NuA4 histone acetyltransferase complex / cell leading edge / pseudopodium / filamentous actin / RHO GTPases activate PAKs / Recycling pathway of L1 / brush border / actin filament bundle assembly / skeletal muscle contraction / calyx of Held / neuronal action potential / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / RHOBTB2 GTPase cycle / phagocytosis / phagocytic vesicle / stress fiber / RHO GTPases activate PKNs / skeletal muscle tissue development / EPHB-mediated forward signaling / cellular response to starvation / axonogenesis / extracellular matrix / cell projection / mitochondrion organization / cell motility / Translocation of SLC2A4 (GLUT4) to the plasma membrane / actin filament / RHO GTPases Activate Formins / 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 / MAP2K and MAPK activation / Schaffer collateral - CA1 synapse / cellular response to type II interferon / structural constituent of cytoskeleton / platelet aggregation / Regulation of actin dynamics for phagocytic cup formation / VEGFA-VEGFR2 Pathway / 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 / actin filament binding / cell-cell junction / cell junction / Clathrin-mediated endocytosis / regulation of cell shape / cell cortex / protein-macromolecule adaptor activity Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Dictyostelium discoideum (eukaryote) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | von der Ecken J / Heissler SM / Pathan-Chhatbar S / Manstein DJ / Raunser S | |||||||||
Funding support | Germany, 2 items
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Citation | Journal: Nature / Year: 2016 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 |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_8164.map.gz | 48.3 MB | EMDB map data format | |
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Header (meta data) | emd-8164-v30.xml emd-8164.xml | 24.2 KB 24.2 KB | Display Display | EMDB header |
Images | emd_8164.png | 156.3 KB | ||
Filedesc metadata | emd-8164.cif.gz | 8.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8164 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8164 | HTTPS FTP |
-Validation report
Summary document | emd_8164_validation.pdf.gz | 426.9 KB | Display | EMDB validaton report |
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Full document | emd_8164_full_validation.pdf.gz | 426.5 KB | Display | |
Data in XML | emd_8164_validation.xml.gz | 6.2 KB | Display | |
Data in CIF | emd_8164_validation.cif.gz | 7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8164 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8164 | HTTPS FTP |
-Related structure data
Related structure data | 5jlhMC 8162C 8163C 8165C 5jlfC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_8164.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | None | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
-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: #1-#3 / Details: Filament |
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Molecular weight | Theoretical: 440 KDa |
-Supramolecule #2: actin, myosin
Supramolecule | Name: actin, myosin / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #3: tropomyosin
Supramolecule | Name: tropomyosin / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Actin, cytoplasmic 2
Macromolecule | Name: Actin, cytoplasmic 2 / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 41.70757 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
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 UniProtKB: Actin, cytoplasmic 2 |
-Macromolecule #2: Myosin-14,Alpha-actinin A
Macromolecule | Name: Myosin-14,Alpha-actinin A / 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 Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Dictyostelium discoideum (eukaryote) |
Molecular weight | Theoretical: 117.570633 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
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 UniProtKB: Myosin-14, Alpha-actinin A |
-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). Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 11.507176 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
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) |
-Macromolecule #4: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 5 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-Macromolecule #5: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 5 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | filament |
-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.. |
-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: FIELD EMISSION GUN |
Electron optics | Calibrated defocus max: 2.8000000000000003 µm / Calibrated defocus min: 0.7000000000000001 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal magnification: 59000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model |
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Refinement | Protocol: BACKBONE TRACE / Overall B value: 180 | ||||||||||||||
Output model | PDB-5jlh: |
-Atomic model buiding 2
Initial model |
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Details | tropomyosin fitting | ||||||
Refinement | Protocol: RIGID BODY FIT | ||||||
Output model | PDB-5jlh: |