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Yorodumi- EMDB-7329: High-Resolution Cryo-EM Structures of Actin-bound Myosin States R... -
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-Basic information
Entry | Database: EMDB / ID: EMD-7329 | |||||||||
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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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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 / Calmodulin induced events / Reduction of cytosolic Ca++ levels / 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 / Calmodulin induced events / Reduction of cytosolic Ca++ levels / 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 / negative regulation of high voltage-gated calcium channel activity / cytoskeletal motor activator activity / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / positive regulation of cyclic-nucleotide phosphodiesterase activity / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / CLEC7A (Dectin-1) induces NFAT activation / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / microfilament motor activity / regulation of cardiac muscle cell action potential / Activation of RAC1 downstream of NMDARs / tropomyosin binding / positive regulation of ryanodine-sensitive calcium-release channel activity / mesenchyme migration / regulation of cell communication by electrical coupling involved in cardiac conduction / Negative regulation of NMDA receptor-mediated neuronal transmission / negative regulation of peptidyl-threonine phosphorylation / troponin I binding / Synthesis of IP3 and IP4 in the cytosol / Unblocking of NMDA receptors, glutamate binding and activation / myosin heavy chain binding / Phase 0 - rapid depolarisation / negative regulation of ryanodine-sensitive calcium-release channel activity / protein phosphatase activator activity / filamentous actin / actin filament bundle / RHO GTPases activate PAKs / cytoskeletal motor activity / brush border / phosphatidylinositol-3,4,5-trisphosphate binding / : / Ion transport by P-type ATPases / skeletal muscle thin filament assembly / microvillus / striated muscle thin filament / actin filament bundle assembly / Long-term potentiation / Uptake and function of anthrax toxins / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / skeletal muscle myofibril / catalytic complex / DARPP-32 events / actin monomer binding / detection of calcium ion / regulation of cardiac muscle contraction / regulation of ryanodine-sensitive calcium-release channel activity / Smooth Muscle Contraction / cellular response to interferon-beta / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium channel inhibitor activity / Protein methylation / eNOS activation / skeletal muscle fiber development / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Activation of AMPK downstream of NMDARs / stress fiber / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / : / Ion homeostasis / titin binding / regulation of calcium-mediated signaling / positive regulation of protein autophosphorylation / voltage-gated potassium channel complex / sperm midpiece / calcium channel complex / phosphatidylinositol-4,5-bisphosphate binding / substantia nigra development / adenylate cyclase activator activity / Ras activation upon Ca2+ influx through NMDA receptor / regulation of heart rate / actin filament polymerization / sarcomere / FCERI mediated Ca+2 mobilization / protein serine/threonine kinase activator activity / FCGR3A-mediated IL10 synthesis / VEGFR2 mediated vascular permeability / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / VEGFR2 mediated cell proliferation / regulation of cytokinesis / trans-Golgi network membrane / positive regulation of peptidyl-threonine phosphorylation / filopodium Similarity search - Function | |||||||||
Biological species | unidentified (others) / Rabbit (rabbit) / Rat (rat) / death cap (death cap) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Mentes A / Huehn A / Liu X / Zwolak A / Dominguez R / Shuman H / Ostap EM / Sindelar CV | |||||||||
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_7329.map.gz | 194.1 MB | EMDB map data format | |
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Header (meta data) | emd-7329-v30.xml emd-7329.xml | 18.7 KB 18.7 KB | Display Display | EMDB header |
Images | emd_7329.png | 237.4 KB | ||
Masks | emd_7329_msk_1.map | 244.1 MB | Mask map | |
Others | emd_7329_half_map_1.map.gz emd_7329_half_map_2.map.gz | 194.8 MB 194 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-7329 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7329 | HTTPS FTP |
-Validation report
Summary document | emd_7329_validation.pdf.gz | 838.4 KB | Display | EMDB validaton report |
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Full document | emd_7329_full_validation.pdf.gz | 838 KB | Display | |
Data in XML | emd_7329_validation.xml.gz | 15.3 KB | Display | |
Data in CIF | emd_7329_validation.cif.gz | 18.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7329 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7329 | HTTPS FTP |
-Related structure data
Related structure data | 6c1dMC 7330C 7331C 5v7xC 6c1gC 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_7329.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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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_7329_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_7329_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_7329_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 and phalloidin
Entire | Name: Complex of actin, myosin-1b, and calmodulin with ADP and phalloidin |
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Components |
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-Supramolecule #1: Complex of actin, myosin-1b, and calmodulin with ADP and phalloidin
Supramolecule | Name: Complex of actin, myosin-1b, and calmodulin with ADP and phalloidin type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: unidentified (others) |
-Macromolecule #1: Actin, alpha skeletal muscle
Macromolecule | Name: Actin, alpha skeletal muscle / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: Rabbit (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 |
-Macromolecule #2: Unconventional myosin-Ib
Macromolecule | Name: Unconventional myosin-Ib / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Rat (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 |
-Macromolecule #3: Calmodulin
Macromolecule | Name: Calmodulin / type: protein_or_peptide / ID: 3 / 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 #4: Phalloidin
Macromolecule | Name: Phalloidin / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: death cap (death cap) |
Molecular weight | Theoretical: 808.899 Da |
Sequence | String: A(2TL)(DCY)(HYP)AW(EEP) |
-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: |
-Macromolecule #6: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 6 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-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: 3.2 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: 40400 |
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Final angle assignment | Type: NOT APPLICABLE |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
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Output model | PDB-6c1d: |