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- PDB-5jcy: Spir2-GTBM bound to MyoVa-GTD -

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Basic information

Entry
Database: PDB / ID: 5jcy
TitleSpir2-GTBM bound to MyoVa-GTD
Components
  • Protein spire homolog 2
  • Unconventional myosin-Va
KeywordsMOTOR PROTEIN / myosin / complex / Spir actin nucleator
Function / homology
Function and homology information


formin-nucleated actin cable assembly / establishment of meiotic spindle localization / polar body extrusion after meiotic divisions / actin filament network formation / actin nucleation / post-Golgi vesicle-mediated transport / insulin-responsive compartment / Golgi vesicle transport / melanosome transport / actin filament-based movement ...formin-nucleated actin cable assembly / establishment of meiotic spindle localization / polar body extrusion after meiotic divisions / actin filament network formation / actin nucleation / post-Golgi vesicle-mediated transport / insulin-responsive compartment / Golgi vesicle transport / melanosome transport / actin filament-based movement / filopodium tip / cleavage furrow formation / vesicle transport along actin filament / myosin complex / positive regulation of double-strand break repair / microfilament motor activity / Insulin processing / cleavage furrow / intracellular transport / vesicle-mediated transport / ruffle / actin filament polymerization / actin filament organization / Translocation of SLC2A4 (GLUT4) to the plasma membrane / protein localization to plasma membrane / FCGR3A-mediated phagocytosis / cytoplasmic vesicle membrane / Regulation of actin dynamics for phagocytic cup formation / small GTPase binding / cellular response to insulin stimulus / melanosome / actin filament binding / actin cytoskeleton / protein transport / actin binding / cell cortex / growth cone / actin cytoskeleton organization / cytoskeleton / calmodulin binding / neuron projection / RNA binding / extracellular exosome / ATP binding / membrane / cytosol / cytoplasm
Similarity search - Function
Protein Spire2 / Protein Spire / Kinase non-catalytic C-lobe domain / KIND domain / KIND domain profile. / kinase non-catalytic C-lobe domain / WH2 domain / WH2 domain profile. / Myosin 5a, cargo-binding domain / Class V myosin, motor domain ...Protein Spire2 / Protein Spire / Kinase non-catalytic C-lobe domain / KIND domain / KIND domain profile. / kinase non-catalytic C-lobe domain / WH2 domain / WH2 domain profile. / 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 / Zinc finger, FYVE/PHD-type / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Protein spire homolog 2 / Unconventional myosin-Va
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPylypenko, O. / Malherbes, G. / Welz, T. / Kerkhoff, E. / Houdusse, A.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-13-BSV8-0019-01 France
CitationJournal: Elife / Year: 2016
Title: Coordinated recruitment of Spir actin nucleators and myosin V motors to Rab11 vesicle membranes.
Authors: Pylypenko, O. / Welz, T. / Tittel, J. / Kollmar, M. / Chardon, F. / Malherbe, G. / Weiss, S. / Michel, C.I. / Samol-Wolf, A. / Grasskamp, A.T. / Hume, A. / Goud, B. / Baron, B. / England, P. ...Authors: Pylypenko, O. / Welz, T. / Tittel, J. / Kollmar, M. / Chardon, F. / Malherbe, G. / Weiss, S. / Michel, C.I. / Samol-Wolf, A. / Grasskamp, A.T. / Hume, A. / Goud, B. / Baron, B. / England, P. / Titus, M.A. / Schwille, P. / Weidemann, T. / Houdusse, A. / Kerkhoff, E.
History
DepositionApr 15, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jan 10, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Unconventional myosin-Va
B: Protein spire homolog 2


Theoretical massNumber of molelcules
Total (without water)48,5392
Polymers48,5392
Non-polymers00
Water7,782432
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-11 kcal/mol
Surface area18370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.610, 41.220, 108.220
Angle α, β, γ (deg.)90.00, 115.89, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2165-

HOH

21A-2206-

HOH

31A-2245-

HOH

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Components

#1: Protein Unconventional myosin-Va / / Dilute myosin heavy chain / non-muscle / Myosin heavy chain 12 / Myosin-12 / Myoxin


Mass: 45350.605 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MYO5A, MYH12 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9Y4I1
#2: Protein/peptide Protein spire homolog 2 / Spir-2


Mass: 3188.585 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q8WWL2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 432 / 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: 2.06 Å3/Da / Density % sol: 40.26 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: 50 mM Hepes, 50 mM MOPS, 10% (w/v) PEG 1000, 10% (w/v) PEG 3350, 10% (v/v) MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97934 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.76→44.81 Å / Num. obs: 39553 / % possible obs: 99.1 % / Redundancy: 6.5 % / Rsym value: 0.074 / Net I/σ(I): 15.7
Reflection shellResolution: 1.76→1.86 Å / Num. unique all: 6165 / Rsym value: 0.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LX1

4lx1


Resolution: 1.8→44.806 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 20.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1913 1849 5 %
Rwork0.1513 --
obs0.1533 36963 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→44.806 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3077 0 0 432 3509
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013267
X-RAY DIFFRACTIONf_angle_d1.0924442
X-RAY DIFFRACTIONf_dihedral_angle_d14.4211262
X-RAY DIFFRACTIONf_chiral_restr0.046513
X-RAY DIFFRACTIONf_plane_restr0.006576
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.84870.35811400.2782652X-RAY DIFFRACTION100
1.8487-1.90310.30761410.21922677X-RAY DIFFRACTION100
1.9031-1.96450.24241410.18952678X-RAY DIFFRACTION100
1.9645-2.03470.19831410.18662685X-RAY DIFFRACTION100
2.0347-2.11620.21071400.15722664X-RAY DIFFRACTION100
2.1162-2.21250.19181430.14442702X-RAY DIFFRACTION100
2.2125-2.32910.16131410.1352680X-RAY DIFFRACTION100
2.3291-2.4750.21241420.13552704X-RAY DIFFRACTION100
2.475-2.66610.19941420.14362696X-RAY DIFFRACTION100
2.6661-2.93440.2171430.1522722X-RAY DIFFRACTION100
2.9344-3.35890.20411430.14862718X-RAY DIFFRACTION100
3.3589-4.23130.13911440.13492726X-RAY DIFFRACTION100
4.2313-44.82010.18121480.14842810X-RAY DIFFRACTION99

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