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- PDB-5v7x: Crystal Structure of Myosin 1b residues 1-728 with bound sulfate ... -

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Basic information

Entry
Database: PDB / ID: 5v7x
TitleCrystal Structure of Myosin 1b residues 1-728 with bound sulfate and Calmodulin
Components
  • Calmodulin-1
  • Unconventional myosin-Ib
KeywordsMOTOR PROTEIN / myosin / motor / calmodulin / unconventional / actin / force
Function / homology
Function and homology information


post-Golgi vesicle-mediated transport / actin filament-based movement / myosin complex / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde ...post-Golgi vesicle-mediated transport / actin filament-based movement / myosin complex / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / negative regulation of high voltage-gated calcium channel activity / PKA activation / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / CLEC7A (Dectin-1) induces NFAT activation / microfilament motor activity / Activation of RAC1 downstream of NMDARs / negative regulation of ryanodine-sensitive calcium-release channel activity / organelle localization by membrane tethering / : / autophagosome membrane docking / negative regulation of calcium ion export across plasma membrane / regulation of ryanodine-sensitive calcium-release channel activity / regulation of cardiac muscle cell action potential / presynaptic endocytosis / Synthesis of IP3 and IP4 in the cytosol / Phase 0 - rapid depolarisation / microvillus / Negative regulation of NMDA receptor-mediated neuronal transmission / phosphatidylinositol-3,4,5-trisphosphate binding / Unblocking of NMDA receptors, glutamate binding and activation / RHO GTPases activate PAKs / cytoskeletal motor activity / calcineurin-mediated signaling / regulation of cell communication by electrical coupling involved in cardiac conduction / Ion transport by P-type ATPases / brush border / actin filament bundle assembly / Uptake and function of anthrax toxins / protein phosphatase activator activity / Long-term potentiation / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / DARPP-32 events / Smooth Muscle Contraction / detection of calcium ion / regulation of cardiac muscle contraction / catalytic complex / RHO GTPases activate IQGAPs / calcium channel inhibitor activity / presynaptic cytosol / Activation of AMPK downstream of NMDARs / cellular response to interferon-beta / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Ion homeostasis / eNOS activation / Protein methylation / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / titin binding / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / phosphatidylinositol-4,5-bisphosphate binding / regulation of calcium-mediated signaling / voltage-gated potassium channel complex / FCERI mediated Ca+2 mobilization / calcium channel complex / substantia nigra development / FCGR3A-mediated IL10 synthesis / regulation of heart rate / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Ras activation upon Ca2+ influx through NMDA receptor / calyx of Held / adenylate cyclase activator activity / trans-Golgi network membrane / VEGFR2 mediated cell proliferation / VEGFR2 mediated vascular permeability / regulation of cytokinesis / actin filament organization / protein serine/threonine kinase activator activity / cell periphery / spindle microtubule / sarcomere / positive regulation of receptor signaling pathway via JAK-STAT / filopodium / Translocation of SLC2A4 (GLUT4) to the plasma membrane / actin filament / calcium channel regulator activity / transferrin transport / Transcriptional activation of mitochondrial biogenesis / RAF activation / response to calcium ion / cellular response to type II interferon / G2/M transition of mitotic cell cycle / Stimuli-sensing channels / endocytosis / spindle pole / apical part of cell / calcium-dependent protein binding / Signaling by RAF1 mutants
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #4820 / Class I myosin tail homology domain / Class I myosin, motor domain / Unconventional myosin tail, actin- and lipid-binding / Class I myosin tail homology (TH1) domain profile. / IQ calmodulin-binding motif / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site / Myosin motor domain profile. / Myosin head, motor domain ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #4820 / Class I myosin tail homology domain / Class I myosin, motor domain / Unconventional myosin tail, actin- and lipid-binding / Class I myosin tail homology (TH1) domain profile. / IQ calmodulin-binding motif / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site / Myosin motor domain profile. / Myosin head, motor domain / Myosin head (motor domain) / Myosin. Large ATPases. / IQ motif profile. / Kinesin motor domain superfamily / EF-hand / : / Recoverin; domain 1 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / 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 / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Calmodulin-1 / Unconventional myosin-Ib
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.141 Å
AuthorsZwolak, A. / Shuman, H. / Dominguez, R. / Ostap, E.M.
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.
#1: Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2014
Title: A vertebrate myosin-I structure reveals unique insights into myosin mechanochemical tuning.
Authors: Shuman, H. / Greenberg, M.J. / Zwolak, A. / Lin, T. / Sindelar, C.V. / Dominguez, R. / Ostap, E.M.
History
DepositionMar 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Unconventional myosin-Ib
B: Calmodulin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,9043
Polymers103,8082
Non-polymers961
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-39 kcal/mol
Surface area40190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.765, 48.730, 118.512
Angle α, β, γ (deg.)90.00, 89.95, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Unconventional myosin-Ib / Myosin I alpha / MMIa / Myosin heavy chain myr 1


Mass: 86954.969 Da / Num. of mol.: 1 / Fragment: UNP residues 1-728
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Myo1b, Myo1a, Myr1 / Cell (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q05096
#2: Protein Calmodulin-1


Mass: 16852.545 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CALM1, CALM, CAM, CAM1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P0DP23
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.05 Å3/Da / Density % sol: 59.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 10% PEG 3350, 100 mM LiOOCCH3, 100 mM HEPES, pH 7.0, 20 mM Mg2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 7, 2012
Details: Monochromator: Double silicon(111) crystal monochromator with cryogenically-cooled first crystal and sagittally-bent second crystal horizontally-focusing at 3.3:1 demagnification. Mirror: ...Details: Monochromator: Double silicon(111) crystal monochromator with cryogenically-cooled first crystal and sagittally-bent second crystal horizontally-focusing at 3.3:1 demagnification. Mirror: Meridionally-bent fused silica mirror with palladium and uncoated stripes vertically-focusing at 6.6:1 demagnification.
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.39
ReflectionResolution: 2.799→39.504 Å / Num. obs: 30781 / % possible obs: 95.8 % / Redundancy: 7.3 % / Net I/σ(I): 9.5

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 3.141→39.504 Å / Cross valid method: THROUGHOUT / σ(F): 37.84 / Phase error: 26.56 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2023 1094 4.97 %
Rwork0.1882 --
obs0.1928 22155 98.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.141→39.504 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7003 0 5 0 7008
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0127139
X-RAY DIFFRACTIONf_angle_d0.8349617
X-RAY DIFFRACTIONf_dihedral_angle_d8.2074349
X-RAY DIFFRACTIONf_chiral_restr0.0491053
X-RAY DIFFRACTIONf_plane_restr0.0051256
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1436-3.28650.3191420.22982399X-RAY DIFFRACTION87
3.2865-3.45940.28271270.21632619X-RAY DIFFRACTION95
3.4594-3.67560.22561340.20412641X-RAY DIFFRACTION95
3.6756-3.95860.21271280.18992628X-RAY DIFFRACTION95
3.9586-4.35550.18661510.17732635X-RAY DIFFRACTION95
4.3555-4.98220.17571350.16532661X-RAY DIFFRACTION95
4.9822-6.26390.17511360.19042674X-RAY DIFFRACTION95
6.2639-26.85640.19151410.19012771X-RAY DIFFRACTION95

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