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- PDB-4zlk: Crystal structure of mouse myosin-5a in complex with calcium-boun... -

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Basic information

Entry
Database: PDB / ID: 4zlk
TitleCrystal structure of mouse myosin-5a in complex with calcium-bound calmodulin
Components
  • Calmodulin
  • Unconventional myosin-Va
KeywordsMOTOR PROTEIN/METAL BINDING PROTEIN / myosin / calmodulin / molecular motor / IQ motif / MOTOR PROTEIN-METAL BINDING PROTEIN complex
Function / homology
Function and homology information


actomyosin, myosin complex part / establishment of endoplasmic reticulum localization to postsynapse / axo-dendritic protein transport / positive regulation of cellular response to insulin stimulus / endoplasmic reticulum localization / melanosome localization / CaMK IV-mediated phosphorylation of CREB / Cam-PDE 1 activation / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Glycogen breakdown (glycogenolysis) ...actomyosin, myosin complex part / establishment of endoplasmic reticulum localization to postsynapse / axo-dendritic protein transport / positive regulation of cellular response to insulin stimulus / endoplasmic reticulum localization / melanosome localization / CaMK IV-mediated phosphorylation of CREB / Cam-PDE 1 activation / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Glycogen breakdown (glycogenolysis) / Activation of RAC1 downstream of NMDARs / Reduction of cytosolic Ca++ levels / Sodium/Calcium exchangers / Activation of Ca-permeable Kainate Receptor / CLEC7A (Dectin-1) induces NFAT activation / Synthesis of IP3 and IP4 in the cytosol / RHO GTPases activate PAKs / Calmodulin induced events / Inactivation, recovery and regulation of the phototransduction cascade / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Calcineurin activates NFAT / eNOS activation / Ion transport by P-type ATPases / Unblocking of NMDA receptors, glutamate binding and activation / locomotion involved in locomotory behavior / Protein methylation / reactive gliosis / melanin metabolic process / RAF activation / VEGFR2 mediated vascular permeability / RAS processing / Smooth Muscle Contraction / Ca2+ pathway / negative regulation of calcium ion transmembrane transporter activity / unconventional myosin complex / FCERI mediated Ca+2 mobilization / post-Golgi vesicle-mediated transport / RAF/MAP kinase cascade / RHO GTPases activate IQGAPs / Extra-nuclear estrogen signaling / insulin-responsive compartment / negative regulation of dopamine secretion / developmental pigmentation / regulation of postsynaptic cytosolic calcium ion concentration / melanosome transport / actin filament-based movement / PKA activation / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / secretory granule localization / melanin biosynthetic process / Platelet degranulation / Regulation of actin dynamics for phagocytic cup formation / filopodium tip / hair follicle maturation / melanocyte differentiation / postsynaptic actin cytoskeleton / : / establishment of protein localization to mitochondrial membrane / Stimuli-sensing channels / actomyosin / regulation of exocytosis / Ion homeostasis / type 3 metabotropic glutamate receptor binding / negative regulation of synaptic transmission, glutamatergic / vesicle transport along actin filament / ATP-dependent protein binding / positive regulation of vascular associated smooth muscle cell migration / long-chain fatty acid biosynthetic process / syntaxin-1 binding / insulin secretion / myosin complex / intermediate filament / odontogenesis / pigmentation / regulation of synaptic vesicle endocytosis / microfilament motor activity / negative regulation of high voltage-gated calcium channel activity / regulation of synaptic vesicle exocytosis / negative regulation of calcium ion export across plasma membrane / organelle localization by membrane tethering / regulation of cardiac muscle cell action potential / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / dopamine metabolic process / response to corticosterone / positive regulation of ryanodine-sensitive calcium-release channel activity / nitric-oxide synthase binding / exocytosis / protein phosphatase activator activity / smooth endoplasmic reticulum / positive regulation of cyclic-nucleotide phosphodiesterase activity / cytoskeletal motor activity / positive regulation of phosphoprotein phosphatase activity / adenylate cyclase binding / catalytic complex / photoreceptor outer segment / detection of calcium ion / negative regulation of ryanodine-sensitive calcium-release channel activity
Similarity search - Function
Myosin 5a, cargo-binding domain / Class V myosin, motor domain / Dilute domain / DIL domain / Dilute domain profile. / DIL / IQ calmodulin-binding motif / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Short calmodulin-binding motif containing conserved Ile and Gln residues. ...Myosin 5a, cargo-binding domain / Class V myosin, motor domain / Dilute domain / DIL domain / Dilute domain profile. / DIL / IQ calmodulin-binding motif / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Short calmodulin-binding motif containing conserved Ile and Gln residues. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / IQ motif, EF-hand binding site / Kinesin motor domain superfamily / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Calmodulin-1 / Calmodulin-2 / Unconventional myosin-Va
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.502 Å
AuthorsShen, M. / Zhang, N. / Zheng, S. / Zhang, W.-B. / Zhang, H.-M. / Lu, Z. / Su, Q.P. / Sun, Y. / Ye, K. / Li, X.-D.
Funding support China, 5items
OrganizationGrant numberCountry
National Basic Research Program of China2013CB932802 China
National Basic Research Program of China2012CB114102 China
National Natural Science Foundation of China31171367 China
National Natural Science Foundation of China31470791 China
National Natural Science Foundation of China31325007 China
CitationJournal: To Be Published
Title: Structural basis for calcium regulation of myosin 5 motor function
Authors: Shen, M. / Zheng, S. / Zhang, W. / Lu, Z. / Ye, K. / Li, X.
History
DepositionMay 1, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2016Group: Structure summary
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Unconventional myosin-Va
B: Calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,8416
Polymers113,6802
Non-polymers1604
Water4,612256
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint-60 kcal/mol
Surface area40200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.079, 99.455, 248.159
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Unconventional myosin-Va / / myosin-5a / Dilute myosin heavy chain / non-muscle


Mass: 96827.820 Da / Num. of mol.: 1 / Fragment: UNP residues 1-791
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Myo5a, Dilute / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q99104
#2: Protein Calmodulin / / CaM


Mass: 16852.545 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
Gene: Calm1, Calm, Cam, Cam1, Calm2, Cam2, Camb, Calm3, Cam3, Camc
Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P62204, UniProt: P0DP26*PLUS
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 256 / Source method: isolated from a natural source / Formula: H2O

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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: 3.04 Å3/Da / Density % sol: 59.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM Tris-HCl, pH7.5, 2 mM CaCl2, 2 mM DTT, 2 mM NaN3, 10% glycerol, 6% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 47736 / % possible obs: 97.4 % / Redundancy: 9.8 % / Rmerge(I) obs: 0.106 / Net I/av σ(I): 22.9 / Net I/σ(I): 2

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OE9

1oe9


Resolution: 2.502→48.849 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.246 2410 5.06 %
Rwork0.1964 --
obs0.1989 47657 97.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.502→48.849 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7027 0 4 256 7287
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097171
X-RAY DIFFRACTIONf_angle_d1.1579650
X-RAY DIFFRACTIONf_dihedral_angle_d16.0982700
X-RAY DIFFRACTIONf_chiral_restr0.0471040
X-RAY DIFFRACTIONf_plane_restr0.0051245
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5017-2.55280.35771260.25032414X-RAY DIFFRACTION88
2.5528-2.60830.30791320.2522494X-RAY DIFFRACTION94
2.6083-2.6690.31811290.2252506X-RAY DIFFRACTION92
2.669-2.73570.28431470.21042513X-RAY DIFFRACTION95
2.7357-2.80970.25441340.21542583X-RAY DIFFRACTION94
2.8097-2.89230.28611400.21852578X-RAY DIFFRACTION97
2.8923-2.98570.28161330.22722633X-RAY DIFFRACTION97
2.9857-3.09240.29481430.21532669X-RAY DIFFRACTION98
3.0924-3.21620.3031460.21582654X-RAY DIFFRACTION99
3.2162-3.36250.23761440.20732692X-RAY DIFFRACTION99
3.3625-3.53980.26171520.19972722X-RAY DIFFRACTION100
3.5398-3.76150.24361480.1952731X-RAY DIFFRACTION100
3.7615-4.05170.25021490.18562742X-RAY DIFFRACTION100
4.0517-4.45920.20791570.16752729X-RAY DIFFRACTION100
4.4592-5.10390.21341470.16172792X-RAY DIFFRACTION100
5.1039-6.42810.26291340.20372817X-RAY DIFFRACTION100
6.4281-48.85790.18591490.1862978X-RAY DIFFRACTION100

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