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- PDB-4r8g: Crystal Structure of Myosin-1c tail in complex with Calmodulin -

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Basic information

Entry
Database: PDB / ID: 4r8g
TitleCrystal Structure of Myosin-1c tail in complex with Calmodulin
Components
  • Calmodulin
  • Unconventional myosin-Ic
KeywordsPROTEIN BINDING/CALCIUM-BINDING PROTEIN / EF hand / PH domain / IQ motif / Myosin / Ca2+ signaling / Force sensing / Calcium binding / lipid binding / plasma membrane / cytoskeleton / PROTEIN BINDING-CALCIUM-BINDING PROTEIN complex
Function / homology
Function and homology information


stereocilium membrane / small GTPase binding => GO:0031267 / positive regulation of cellular response to insulin stimulus / B-WICH complex positively regulates rRNA expression / microfilament motor activity => GO:0000146 / : / positive regulation of vascular endothelial growth factor signaling pathway / stereocilium bundle / positive regulation of cell migration by vascular endothelial growth factor signaling pathway / Regulation of actin dynamics for phagocytic cup formation ...stereocilium membrane / small GTPase binding => GO:0031267 / positive regulation of cellular response to insulin stimulus / B-WICH complex positively regulates rRNA expression / microfilament motor activity => GO:0000146 / : / positive regulation of vascular endothelial growth factor signaling pathway / stereocilium bundle / positive regulation of cell migration by vascular endothelial growth factor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / stereocilium / vesicle transport along actin filament / protein targeting to membrane / regulation of bicellular tight junction assembly / myosin complex / microfilament motor activity / positive regulation of actin filament polymerization / filamentous actin / microvillus / brush border / positive regulation of protein targeting to membrane / protein targeting / mRNA transport / lateral plasma membrane / phagocytic vesicle / nuclear pore / basal plasma membrane / actin filament organization / phospholipid binding / cytoplasmic vesicle membrane / ruffle membrane / cellular response to type II interferon / actin filament binding / actin cytoskeleton / actin binding / cytoplasmic vesicle / vesicle / nuclear body / calmodulin binding / positive regulation of cell migration / membrane raft / signaling receptor binding / calcium ion binding / nucleolus / ATP binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. ...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. / 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 B / Unconventional myosin-Ic
Similarity search - Component
Biological speciesMus musculus (house mouse)
Xenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.503 Å
AuthorsLu, Q. / Li, J. / Ye, F. / Zhang, M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2015
Title: Structure of myosin-1c tail bound to calmodulin provides insights into calcium-mediated conformational coupling.
Authors: Lu, Q. / Li, J. / Ye, F. / Zhang, M.
History
DepositionSep 2, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Database references / Category: citation / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_ref_seq_dif.details
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Unconventional myosin-Ic
B: Calmodulin
A: Calmodulin
H: Calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,5637
Polymers88,2754
Non-polymers2883
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12250 Å2
ΔGint-154 kcal/mol
Surface area37900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.447, 105.447, 288.068
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Unconventional myosin-Ic / Myosin I beta / MMI-beta / MMIb


Mass: 38111.070 Da / Num. of mol.: 1 / Fragment: UNP residues 733-1063
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Myo1c / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WTI7
#2: Protein Calmodulin / / CaM


Mass: 16721.350 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: calm1, calm2 / Production host: Escherichia coli (E. coli) / References: UniProt: P62155, UniProt: P0DP33*PLUS
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / 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: 4.54 Å3/Da / Density % sol: 72.88 %
Crystal growTemperature: 289.3 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2.0M ammonium sulfate, 5% 1,4-dioxane, MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289.3K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 30, 2012
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 21359 / Biso Wilson estimate: 107.11 Å2

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Processing

Software
NameVersionClassification
SHARPphasing
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 3.503→45.59 Å / SU ML: 0.47 / σ(F): 1.34 / Phase error: 31.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3044 1091 5.13 %Random
Rwork0.2425 ---
obs0.2455 21266 99.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.503→45.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5555 0 15 0 5570
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075652
X-RAY DIFFRACTIONf_angle_d1.3867678
X-RAY DIFFRACTIONf_dihedral_angle_d17.931985
X-RAY DIFFRACTIONf_chiral_restr0.052900
X-RAY DIFFRACTIONf_plane_restr0.0071008
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
3.5027-3.6620.35961310.28712452
3.662-3.8550.30271380.27872452
3.855-4.09640.30921550.24892457
4.0964-4.41240.32791470.22962479
4.4124-4.8560.31331360.22462479
4.856-5.55760.28881310.23932546
5.5576-6.99790.3211270.28132575
6.9979-45.59340.28131260.22322735

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