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- PDB-2f6h: Myosin V cargo binding domain -

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Basic information

Entry
Database: PDB / ID: 2f6h
TitleMyosin V cargo binding domain
ComponentsMyosin-2
KeywordsSTRUCTURAL PROTEIN / mysoin V / Cargo binding / Cargo transport / Vacuole binding / Secreatory vescile binding
Function / homology
Function and homology information


peroxisome inheritance / RHOT2 GTPase cycle / RHOT1 GTPase cycle / Myo2p-Vac17p-Vac8p transport complex / membrane addition at site of cytokinesis / meiotic nuclear membrane microtubule tethering complex / myosin V complex / vacuole inheritance / Golgi inheritance / incipient cellular bud site ...peroxisome inheritance / RHOT2 GTPase cycle / RHOT1 GTPase cycle / Myo2p-Vac17p-Vac8p transport complex / membrane addition at site of cytokinesis / meiotic nuclear membrane microtubule tethering complex / myosin V complex / vacuole inheritance / Golgi inheritance / incipient cellular bud site / cellular bud tip / vesicle docking involved in exocytosis / cellular bud neck / mating projection tip / vesicle transport along actin filament / fungal-type vacuole membrane / microfilament motor activity / actin filament bundle / filamentous actin / establishment of mitotic spindle orientation / transport vesicle / vesicle-mediated transport / actin filament organization / actin filament binding / actin cytoskeleton / protein transport / vesicle / calmodulin binding / ATP binding / cytoplasm
Similarity search - Function
: / Class V myosin, motor domain / Dilute domain / DIL domain / Dilute domain profile. / DIL / 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 ...: / Class V myosin, motor domain / Dilute domain / DIL domain / Dilute domain profile. / DIL / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.25 Å
AuthorsPashkova, N. / Jin, Y. / Ramaswamy, S. / Weisman, L.S.
CitationJournal: Embo J. / Year: 2006
Title: Structural basis for myosin V discrimination between distinct cargoes
Authors: Pashkova, N. / Jin, Y. / Ramaswamy, S. / Weisman, L.S.
History
DepositionNov 29, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
X: Myosin-2


Theoretical massNumber of molelcules
Total (without water)47,9891
Polymers47,9891
Non-polymers00
Water4,089227
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.780, 72.673, 167.982
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 Myosin-2 / / Class V unconventional myosin MYO2 / Type V myosin heavy chain MYO2 / Myosin V MYO2 / Cell division ...Class V unconventional myosin MYO2 / Type V myosin heavy chain MYO2 / Myosin V MYO2 / Cell division control protein 66


Mass: 47988.750 Da / Num. of mol.: 1 / Fragment: Cargo binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: MYO2, CDC66 / Production host: Escherichia coli (E. coli) / References: UniProt: P19524
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 3

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Sample preparation

CrystalDensity Matthews: 3.23 Å3/Da / Density % sol: 61.9 %
Crystal growTemperature: 279 K / pH: 6.5
Details: 1.7 M Nacl, 6% PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 279K, pH 6.50

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
41
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1.009
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 27, 2004
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.009 Å / Relative weight: 1
Reflection

D res high: 2.7 Å

Redundancy (%)IDAv σ(I) over netINumberRmerge(I) obsΧ2D res low (Å)Num. obs% possible obsRejects
1.8616.371450.0970.9824.742901686.8409
2.0327.486430.0880.9724.522877987.8442
1.8736.372700.0910.9824.752909886.9412
2.0447.586040.0890.9624.512912889451
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRejects
5.7924.7489.910.0330.84185
4.615.7983.210.0440.8726
4.034.6181.810.0520.8935
3.664.0384.410.0940.9427
3.43.6685.410.1321.0441
3.23.485.910.1690.9718
3.043.287.810.2441.1113
2.913.0489.410.2681.1338
2.82.9189.810.3510.9911
2.72.890.110.361.0115
5.7924.5282.420.0290.86116
4.615.7985.920.0520.8739
4.034.6187.420.060.933
3.664.0386.720.0910.9565
3.43.6688.220.1361.0779
3.23.488.920.1770.9531
3.043.289.320.2461.0128
2.913.0489.820.2941.0339
2.82.9189.820.3521.058
2.72.889.720.4051.084
5.824.7592.730.030.85135
4.615.884.130.0440.8527
4.034.618130.0510.9130
3.664.0383.630.0870.9332
3.43.668530.1321.0237
3.23.485.730.1560.9728
3.043.288.130.231.0435
2.913.0489.230.2611.0336
2.82.9190.230.3251.0827
2.72.889.930.3451.0925
5.7924.518440.030.84111
4.615.7986.940.050.8635
4.034.6188.640.0590.8862
3.664.0388.540.0870.9567
3.43.6689.240.1351.0173
3.23.489.740.1921.0141
3.043.290.740.2431.0222
2.913.0490.840.3151.0514
2.82.919140.3370.9922
2.72.890.640.40814
ReflectionResolution: 2.2→20.82 Å / Num. obs: 28080 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 5.46 % / Biso Wilson estimate: 17 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 8.9
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.532 / Mean I/σ(I) obs: 4.1 / % possible all: 98.5

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Processing

Software
NameVersionClassification
d*TREKdata reduction
SOLVEphasing
REFMAC5.2refinement
d*TREKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.25→12 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.914 / SU B: 5.814 / SU ML: 0.145 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.258 / ESU R Free: 0.209
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1408 5 %RANDOM
Rwork0.217 ---
obs0.219 26672 93.2 %-
all-28080 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.63 Å2
Baniso -1Baniso -2Baniso -3
1-1.11 Å20 Å20 Å2
2--0.22 Å20 Å2
3----1.32 Å2
Refinement stepCycle: LAST / Resolution: 2.25→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3162 0 0 227 3389
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223223
X-RAY DIFFRACTIONr_bond_other_d0.0010.022978
X-RAY DIFFRACTIONr_angle_refined_deg1.3131.9664375
X-RAY DIFFRACTIONr_angle_other_deg0.82236933
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1655386
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.25325.068146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.07915585
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5731513
X-RAY DIFFRACTIONr_chiral_restr0.0810.2515
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023487
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02627
X-RAY DIFFRACTIONr_nbd_refined0.1950.2761
X-RAY DIFFRACTIONr_nbd_other0.1620.22979
X-RAY DIFFRACTIONr_nbtor_refined0.1830.21591
X-RAY DIFFRACTIONr_nbtor_other0.0870.21934
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.2178
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0910.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1930.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1610.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2331.52540
X-RAY DIFFRACTIONr_mcbond_other0.1541.5783
X-RAY DIFFRACTIONr_mcangle_it1.4223175
X-RAY DIFFRACTIONr_scbond_it1.8631493
X-RAY DIFFRACTIONr_scangle_it2.8414.51200
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.31 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 100 -
Rwork0.261 1928 -
obs--94.59 %

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