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- PDB-5ibw: Complex of MlcC bound to the tandem IQ motif of MyoC -

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Basic information

Entry
Database: PDB / ID: 5ibw
TitleComplex of MlcC bound to the tandem IQ motif of MyoC
Components
  • Calcium-binding EF-hand domain-containing protein
  • Myosin IC heavy chain
KeywordsMOTOR PROTEIN / Myosin IQ motif Complex
Function / homology
Function and homology information


phagocytic cup lip / actin wave / macropinocytic cup cytoskeleton / microfilament motor activity => GO:0000146 / myosin I binding / chemotaxis to cAMP / pinocytosis / mitotic actomyosin contractile ring assembly / macropinocytic cup / myosin light chain binding ...phagocytic cup lip / actin wave / macropinocytic cup cytoskeleton / microfilament motor activity => GO:0000146 / myosin I binding / chemotaxis to cAMP / pinocytosis / mitotic actomyosin contractile ring assembly / macropinocytic cup / myosin light chain binding / mitotic spindle microtubule / vesicle transport along actin filament / filopodium assembly / myosin complex / myosin II complex / microfilament motor activity / cell leading edge / myosin heavy chain binding / microvillus / phagocytosis / enzyme regulator activity / mitotic spindle organization / cell motility / actin filament organization / phospholipid binding / endocytosis / actin filament binding / actin cytoskeleton / lamellipodium / actin cytoskeleton organization / microtubule binding / vesicle / calcium ion binding / ATP binding / plasma membrane / cytoplasm / cytosol
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. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / Kinesin motor domain superfamily / EF-hand ...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. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / Kinesin motor domain superfamily / EF-hand / Recoverin; domain 1 / SH3 domain / EF-hand domain pair / EF-hand, calcium binding motif / Src homology 3 domains / EF-hand calcium-binding domain profile. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / EF-hand domain / EF-hand domain pair / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Myosin IC heavy chain / Calcium-binding EF-hand domain-containing protein
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLangelaan, D.N. / Smith, S.P.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structure of the Single-lobe Myosin Light Chain C in Complex with the Light Chain-binding Domains of Myosin-1C Provides Insights into Divergent IQ Motif Recognition.
Authors: Langelaan, D.N. / Liburd, J. / Yang, Y. / Miller, E. / Chitayat, S. / Crawley, S.W. / Cote, G.P. / Smith, S.P.
History
DepositionFeb 22, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Sep 21, 2016Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Calcium-binding EF-hand domain-containing protein
B: Calcium-binding EF-hand domain-containing protein
C: Myosin IC heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3234
Polymers23,3003
Non-polymers231
Water4,288238
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint-35 kcal/mol
Surface area11110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.680, 31.410, 56.410
Angle α, β, γ (deg.)75.790, 84.000, 67.060
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Calcium-binding EF-hand domain-containing protein


Mass: 8917.953 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Gene: DDB_G0289563 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): BL21(DE3) / References: UniProt: Q54HC2
#2: Protein/peptide Myosin IC heavy chain


Mass: 5464.219 Da / Num. of mol.: 1 / Fragment: UNP residues 699-739
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Gene: myoC, dmiC, DDB_G0276617 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): BL21(DE3) / References: UniProt: P42522
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 1.96 Å3/Da / Density % sol: 37.13 % / Description: Small triangular prisms
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: 0.7M NaH2PO4/K2HPO4 pH 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.7712 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7712 Å / Relative weight: 1
ReflectionResolution: 1.9→28.2 Å / Num. obs: 12613 / % possible obs: 90.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 26.9
Reflection shellResolution: 1.9→1.97 Å

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IX7

2ix7


Resolution: 1.9→28.2 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.19 631 -
Rwork0.14 --
obs-11982 90.9 %
Displacement parametersBiso max: 50.42 Å2 / Biso mean: 16.7145 Å2 / Biso min: 4.77 Å2
Refinement stepCycle: LAST / Resolution: 1.9→28.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1606 0 1 238 1845
LS refinement shellResolution: 1.9→2.05 Å / Rfactor Rfree: 0.19 / Rfactor Rwork: 0.12

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