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Yorodumi- EMDB-7330: High-Resolution Cryo-EM Structures of Actin-bound Myosin States R... -
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-Basic information
Entry | Database: EMDB / ID: EMD-7330 | |||||||||
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Title | High-Resolution Cryo-EM Structures of Actin-bound Myosin States Reveal the Mechanism of Myosin Force Sensing | |||||||||
Map data | Actin-bound Myosin | |||||||||
Sample |
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Keywords | Mechanochemistry / Mechanobiology / Structural Biology / Cytoskeleton / Molecular Motor / Myosin-I / STRUCTURAL PROTEIN | |||||||||
Function / homology | Function and homology information post-Golgi vesicle-mediated transport / transferrin transport / actin filament-based movement / myosin complex / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Reduction of cytosolic Ca++ levels / Calmodulin induced events / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde ...post-Golgi vesicle-mediated transport / transferrin transport / actin filament-based movement / myosin complex / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Reduction of cytosolic Ca++ levels / Calmodulin induced events / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Activation of Ca-permeable Kainate Receptor / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / organelle localization by membrane tethering / negative regulation of high voltage-gated calcium channel activity / CaMK IV-mediated phosphorylation of CREB / autophagosome membrane docking / mitochondrion-endoplasmic reticulum membrane tethering / Glycogen breakdown (glycogenolysis) / positive regulation of cyclic-nucleotide phosphodiesterase activity / cytoskeletal motor activator activity / negative regulation of calcium ion export across plasma membrane / CLEC7A (Dectin-1) induces NFAT activation / Activation of RAC1 downstream of NMDARs / regulation of cardiac muscle cell action potential / microfilament motor activity / tropomyosin binding / positive regulation of ryanodine-sensitive calcium-release channel activity / myosin heavy chain binding / mesenchyme migration / regulation of cell communication by electrical coupling involved in cardiac conduction / Synthesis of IP3 and IP4 in the cytosol / negative regulation of peptidyl-threonine phosphorylation / Negative regulation of NMDA receptor-mediated neuronal transmission / troponin I binding / Phase 0 - rapid depolarisation / Unblocking of NMDA receptors, glutamate binding and activation / negative regulation of ryanodine-sensitive calcium-release channel activity / adenylate cyclase activator activity / protein phosphatase activator activity / RHO GTPases activate PAKs / filamentous actin / Ion transport by P-type ATPases / actin filament bundle / brush border / cytoskeletal motor activity / phosphatidylinositol-3,4,5-trisphosphate binding / : / skeletal muscle thin filament assembly / microvillus / actin filament bundle assembly / striated muscle thin filament / Uptake and function of anthrax toxins / Long-term potentiation / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / catalytic complex / skeletal muscle myofibril / DARPP-32 events / regulation of cardiac muscle contraction / detection of calcium ion / actin monomer binding / Smooth Muscle Contraction / regulation of ryanodine-sensitive calcium-release channel activity / trans-Golgi network membrane / cellular response to interferon-beta / RHO GTPases activate IQGAPs / calcium channel inhibitor activity / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / eNOS activation / Protein methylation / voltage-gated potassium channel complex / skeletal muscle fiber development / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Activation of AMPK downstream of NMDARs / stress fiber / Ion homeostasis / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / : / phosphatidylinositol-4,5-bisphosphate binding / titin binding / positive regulation of protein autophosphorylation / regulation of calcium-mediated signaling / sperm midpiece / calcium channel complex / substantia nigra development / Ras activation upon Ca2+ influx through NMDA receptor / actin filament polymerization / sarcomere / regulation of heart rate / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / protein serine/threonine kinase activator activity / VEGFR2 mediated vascular permeability / regulation of cytokinesis / VEGFR2 mediated cell proliferation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / actin filament organization / filopodium Similarity search - Function | |||||||||
Biological species | unidentified (others) / Rattus norvegicus (Norway rat) / Oryctolagus cuniculus (rabbit) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Mentes A / Huehn A | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2018 Title: High-resolution cryo-EM structures of actin-bound myosin states reveal the mechanism of myosin force sensing. Authors: Ahmet Mentes / Andrew Huehn / Xueqi Liu / Adam Zwolak / Roberto Dominguez / Henry Shuman / E Michael Ostap / Charles V Sindelar / Abstract: Myosins adjust their power outputs in response to mechanical loads in an isoform-dependent manner, resulting in their ability to dynamically adapt to a range of motile challenges. Here, we reveal the ...Myosins adjust their power outputs in response to mechanical loads in an isoform-dependent manner, resulting in their ability to dynamically adapt to a range of motile challenges. Here, we reveal the structural basis for force-sensing based on near-atomic resolution structures of one rigor and two ADP-bound states of myosin-IB (myo1b) bound to actin, determined by cryo-electron microscopy. The two ADP-bound states are separated by a 25° rotation of the lever. The lever of the first ADP state is rotated toward the pointed end of the actin filament and forms a previously unidentified interface with the N-terminal subdomain, which constitutes the upper half of the nucleotide-binding cleft. This pointed-end orientation of the lever blocks ADP release by preventing the N-terminal subdomain from the pivoting required to open the nucleotide binding site, thus revealing how myo1b is inhibited by mechanical loads that restrain lever rotation. The lever of the second ADP state adopts a rigor-like orientation, stabilized by class-specific elements of myo1b. We identify a role for this conformation as an intermediate in the ADP release pathway. Moreover, comparison of our structures with other myosins reveals structural diversity in the actomyosin binding site, and we reveal the high-resolution structure of actin-bound phalloidin, a potent stabilizer of filamentous actin. These results provide a framework to understand the spectrum of force-sensing capacities among the myosin superfamily. | |||||||||
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_7330.map.gz | 194.4 MB | EMDB map data format | |
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Header (meta data) | emd-7330-v30.xml emd-7330.xml | 17.7 KB 17.7 KB | Display Display | EMDB header |
Images | emd_7330.png | 163.8 KB | ||
Masks | emd_7330_msk_1.map | 244.1 MB | Mask map | |
Filedesc metadata | emd-7330.cif.gz | 6.2 KB | ||
Others | emd_7330_half_map_1.map.gz emd_7330_half_map_2.map.gz | 194.2 MB 194.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-7330 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7330 | HTTPS FTP |
-Validation report
Summary document | emd_7330_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_7330_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_7330_validation.xml.gz | 15.4 KB | Display | |
Data in CIF | emd_7330_validation.cif.gz | 18.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7330 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7330 | HTTPS FTP |
-Related structure data
Related structure data | 6c1gMC 7329C 7331C 5v7xC 6c1dC 6c1hC 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_7330.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Actin-bound Myosin | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_7330_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Actin-bound Myosin, half mask 1
File | emd_7330_half_map_1.map | ||||||||||||
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Annotation | Actin-bound Myosin, half mask 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Actin-bound Myosin, half mask 2
File | emd_7330_half_map_2.map | ||||||||||||
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Annotation | Actin-bound Myosin, half mask 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex of actin, myosin-1b, and calmodulin with ADP
Entire | Name: Complex of actin, myosin-1b, and calmodulin with ADP |
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Components |
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-Supramolecule #1: Complex of actin, myosin-1b, and calmodulin with ADP
Supramolecule | Name: Complex of actin, myosin-1b, and calmodulin with ADP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: unidentified (others) |
-Macromolecule #1: Unconventional myosin-Ib
Macromolecule | Name: Unconventional myosin-Ib / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) |
Molecular weight | Theoretical: 84.14393 KDa |
Sequence | String: VKSSLLDNMI GVGDTVLLEP LNEETFIDNL KKRFDHNEIY TYIGSVVISV NPYRSLPIYS PEKVEDYRNR NFYELSPHIF ALSDEAYRS LRDQDKDQCI LITGESGAGK TEASKLVMSY VAAVCGKGAE VNQVKEQLLQ STPVLEAFGN AKTVRNDNSS R FGKYMDIE ...String: VKSSLLDNMI GVGDTVLLEP LNEETFIDNL KKRFDHNEIY TYIGSVVISV NPYRSLPIYS PEKVEDYRNR NFYELSPHIF ALSDEAYRS LRDQDKDQCI LITGESGAGK TEASKLVMSY VAAVCGKGAE VNQVKEQLLQ STPVLEAFGN AKTVRNDNSS R FGKYMDIE FDFKGDPLGG VISNYLLEKS RVVKQPRGER NFHVFYQLLS GASEELLHKL KLERDFSRYN YLSLDSAKVN GV DDAANFR TVRNAMQIVG FSDPEAESVL EVVAAVLKLG NIEFKPESRM NGLDESKIKD KNELKEICEL TSIDQVVLER AFS FRTVEA KQEKVSTTLN VAQAYYARDA LAKNLYSRLF SWLVNRINES IKAQTKVRKK VMGVLDIYGF EIFEDNSFEQ FIIN YCNEK LQQIFIELTL KEEQEEYIRE DIEWTHIDYF NNAIICDLIE NNTNGILAML DEECLRPGTV TDETFLEKLN QVCAT HQHF ESRMSKCSRF LNDTTLPHSC FRIQHYAGKV LYQVEGFVDK NNDLLYRDLS QAMWKAGHAL IKSLFPEGNP AKVNLK RPP TAGSQFKASV ATLMKNLQTK NPNYIRCIKP NDKKAAHIFS ESLVCHQIRY LGLLENVRVR RAGYAFRQAY EPCLERY KM LCKQTWPHWK GPARSGVEVL FNELEIPVEE YSFGRSKIFI RNPRTLFQLE DLRKQRLEDL ATLIQKIYRG WKCRTHFL L MKGLNDIF UniProtKB: Unconventional myosin-Ib |
-Macromolecule #2: Calmodulin
Macromolecule | Name: Calmodulin / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: unidentified (others) |
Molecular weight | Theoretical: 16.72135 KDa |
Sequence | String: ADQLTEEQIA EFKEAFSLFD KDGDGTITTK ELGTVMRSLG QNPTEAELQD MINEVDADGN GTIDFPEFLT MMARKMKDTD SEEEIREAF RVFDKDGNGY ISAAELRHVM TNLGEKLTDE EVDEMIREAD IDGDGQVNYE EFVQMMTAK |
-Macromolecule #3: Actin, alpha skeletal muscle
Macromolecule | Name: Actin, alpha skeletal muscle / type: protein_or_peptide / ID: 3 / Number of copies: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: Oryctolagus cuniculus (rabbit) |
Molecular weight | Theoretical: 41.862613 KDa |
Sequence | String: DEDETTALVC DNGSGLVKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IEHGIITNWD DMEKIWHHT FYNELRVAPE EHPTLLTEAP LNPKANREKM TQIMFETFNV PAMYVAIQAV LSLYASGRTT GIVLDSGDGV T HNVPIYEG ...String: DEDETTALVC DNGSGLVKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IEHGIITNWD DMEKIWHHT FYNELRVAPE EHPTLLTEAP LNPKANREKM TQIMFETFNV PAMYVAIQAV LSLYASGRTT GIVLDSGDGV T HNVPIYEG YALPHAIMRL DLAGRDLTDY LMKILTERGY SFVTTAEREI VRDIKEKLCY VALDFENEMA TAASSSSLEK SY ELPDGQV ITIGNERFRC PETLFQPSFI GMESAGIHET TYNSIMKCDI DIRKDLYANN VMSGGTTMYP GIADRMQKEI TAL APSTMK IKIIAPPERK YSVWIGGSIL ASLSTFQQMW ITKQEYDEAG PSIVHRKCF UniProtKB: Actin, alpha skeletal muscle |
-Macromolecule #4: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 6 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #5: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 6 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | helical array |
-Sample preparation
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average exposure time: 11.0 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Helical parameters - Δz: 27.5 Å Applied symmetry - Helical parameters - Δ&Phi: -167.4 ° Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric) Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF Details: Resolution estimated by post-processing in RELION using a mask with soft edges that included only the central subunit. Number images used: 7700 |
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Startup model | Type of model: OTHER |
Final angle assignment | Type: NOT APPLICABLE |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
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Output model | PDB-6c1g: |