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- PDB-6a9c: Crystal Structure c-terminal SH3 domain of Myosin IB from Entamoe... -

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Basic information

Entry
Database: PDB / ID: 6a9c
TitleCrystal Structure c-terminal SH3 domain of Myosin IB from Entamoeba histolytica bound to EhFP10(GEF) peptide.
Components
  • Peptide from Rho guanine nucleotide exchange factor
  • Unconventional myosin IB
KeywordsCONTRACTILE PROTEIN / SH3 / MyosinI / Entamoeba histolytica / EhMySH3
Function / homology
Function and homology information


phagosome reneutralization / lateral pseudopodium retraction / phagocytic cup lip / regulation of post-lysosomal vacuole size / actin wave / macropinocytic cup cytoskeleton / myosin I complex / chemotaxis to cAMP / pinocytosis / leading edge of lamellipodium ...phagosome reneutralization / lateral pseudopodium retraction / phagocytic cup lip / regulation of post-lysosomal vacuole size / actin wave / macropinocytic cup cytoskeleton / myosin I complex / chemotaxis to cAMP / pinocytosis / leading edge of lamellipodium / myosin light chain binding / actin-myosin filament sliding / actomyosin / vesicle transport along actin filament / filopodium assembly / endosomal transport / microfilament motor activity / exocytosis / phagocytosis / guanyl-nucleotide exchange factor activity / filopodium / cell motility / actin filament organization / phospholipid binding / endocytosis / phagocytic vesicle membrane / cell-cell junction / actin filament binding / actin cytoskeleton / early endosome / cytoskeleton / intracellular signal transduction / ATP binding / metal ion 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. / FYVE zinc finger / FYVE zinc finger / Protein present in Fab1, YOTB, Vac1, and EEA1 / Zinc finger, FYVE-related / Zinc finger FYVE/FYVE-related type profile. / Guanine-nucleotide dissociation stimulator, CDC24, conserved site ...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. / FYVE zinc finger / FYVE zinc finger / Protein present in Fab1, YOTB, Vac1, and EEA1 / Zinc finger, FYVE-related / Zinc finger FYVE/FYVE-related type profile. / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / IQ motif, EF-hand binding site / SH3 Domains / Kinesin motor domain superfamily / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH3 domain / Zinc finger, FYVE/PHD-type / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily / Zinc finger, RING/FYVE/PHD-type / Roll / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Unconventional myosin IB / Rho guanine nucleotide exchange factor, putative
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsGautam, G. / Gourinath, S.
CitationJournal: Plos Pathog. / Year: 2019
Title: EhFP10: A FYVE family GEF interacts with myosin IB to regulate cytoskeletal dynamics during endocytosis in Entamoeba histolytica.
Authors: Gautam, G. / Ali, M.S. / Bhattacharya, A. / Gourinath, S.
History
DepositionJul 13, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
B: Unconventional myosin IB
A: Unconventional myosin IB
E: Peptide from Rho guanine nucleotide exchange factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7055
Polymers16,5133
Non-polymers1922
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-28 kcal/mol
Surface area8530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.008, 60.013, 95.305
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 IB


Mass: 7747.666 Da / Num. of mol.: 2 / Fragment: SH3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Gene: EHI_110810 / Production host: Escherichia coli (E. coli) / References: UniProt: C4LUC7
#2: Protein/peptide Peptide from Rho guanine nucleotide exchange factor / FP10(GEF) peptide


Mass: 1017.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Entamoeba histolytica (eukaryote) / References: UniProt: C4M4E9
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.66 Å3/Da / Density % sol: 53.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.2M Ammonium sulphate, 30% PEG 8000

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.98→50.78 Å / Num. obs: 12177 / % possible obs: 100 % / Redundancy: 14 % / CC1/2: 0.9 / Rmerge(I) obs: 0.103 / Rsym value: 0.103 / Net I/σ(I): 27.76
Reflection shellResolution: 1.98→2.01 Å / Mean I/σ(I) obs: 3.3 / Num. unique obs: 1153 / CC1/2: 0.98

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5xgg

5xgg


Resolution: 1.98→50.78 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.94 / SU B: 4.188 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.153 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24009 596 4.9 %RANDOM
Rwork0.20126 ---
obs0.20307 11543 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 38.87 Å2
Baniso -1Baniso -2Baniso -3
1-1.67 Å2-0 Å2-0 Å2
2--0.78 Å2-0 Å2
3----2.44 Å2
Refinement stepCycle: 1 / Resolution: 1.98→50.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1090 0 10 54 1154
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191131
X-RAY DIFFRACTIONr_bond_other_d0.0070.021046
X-RAY DIFFRACTIONr_angle_refined_deg1.871.9471539
X-RAY DIFFRACTIONr_angle_other_deg1.03532423
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1015131
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.65625.81855
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.52615187
X-RAY DIFFRACTIONr_dihedral_angle_4_deg36.996151
X-RAY DIFFRACTIONr_chiral_restr0.1260.2159
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211255
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02248
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.883.439533
X-RAY DIFFRACTIONr_mcbond_other3.8513.427532
X-RAY DIFFRACTIONr_mcangle_it5.4875.104661
X-RAY DIFFRACTIONr_mcangle_other5.4825.119662
X-RAY DIFFRACTIONr_scbond_it10.0684.11598
X-RAY DIFFRACTIONr_scbond_other10.0614.12599
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other14.0735.942879
X-RAY DIFFRACTIONr_long_range_B_refined12.74227.9351221
X-RAY DIFFRACTIONr_long_range_B_other12.73727.9951222
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.981→2.032 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 44 -
Rwork0.255 807 -
obs--96.38 %

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