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- PDB-6ixq: Structure of Myo2-GTD in complex with Smy1 -

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Basic information

Entry
Database: PDB / ID: 6ixq
TitleStructure of Myo2-GTD in complex with Smy1
Components
  • Kinesin-related protein SMY1
  • Myosin-2
KeywordsPROTEIN BINDING / Cargo binding domain
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 / mitochondrion inheritance / RHOU GTPase cycle / meiotic nuclear membrane microtubule tethering complex / myosin V complex / vacuole inheritance ...peroxisome inheritance / RHOT2 GTPase cycle / RHOT1 GTPase cycle / Myo2p-Vac17p-Vac8p transport complex / membrane addition at site of cytokinesis / mitochondrion inheritance / RHOU GTPase cycle / meiotic nuclear membrane microtubule tethering complex / myosin V complex / vacuole inheritance / Golgi inheritance / incipient cellular bud site / cellular bud tip / cytoskeleton-dependent intracellular transport / vesicle transport along actin filament / cellular bud neck / mating projection tip / plus-end-directed microtubule motor activity / fungal-type vacuole membrane / vesicle docking involved in exocytosis / kinesin complex / microtubule-based movement / microfilament motor activity / intracellular distribution of mitochondria / filamentous actin / establishment of mitotic spindle orientation / actin filament bundle / cytoskeletal motor activity / transport vesicle / vesicle-mediated transport / actin filament organization / small GTPase binding / actin filament binding / actin cytoskeleton / protein transport / microtubule binding / vesicle / microtubule / calmodulin binding / ATP hydrolysis activity / ATP binding / membrane / cytoplasm
Similarity search - Function
: / Class V myosin, motor domain / Dilute domain / DIL domain / Dilute domain profile. / DIL / Kinesin-like protein / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Kinesin motor domain signature. ...: / Class V myosin, motor domain / Dilute domain / DIL domain / Dilute domain profile. / DIL / Kinesin-like protein / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / Kinesin motor domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Myosin-2 / Kinesin-related protein SMY1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.06 Å
AuthorsTang, K. / Wei, Z.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31770791 China
National Natural Science Foundation of China31570741 China
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Structural mechanism for versatile cargo recognition by the yeast class V myosin Myo2.
Authors: Tang, K. / Li, Y. / Yu, C. / Wei, Z.
History
DepositionDec 11, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 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

Downloads & links

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Assembly

Deposited unit
A: Myosin-2
B: Kinesin-related protein SMY1


Theoretical massNumber of molelcules
Total (without water)53,7702
Polymers53,7702
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-13 kcal/mol
Surface area20090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.510, 93.510, 204.136
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Myosin-2 / Cell division control protein 66 / Class V unconventional myosin MYO2 / Type V myosin heavy chain ...Cell division control protein 66 / Class V unconventional myosin MYO2 / Type V myosin heavy chain MYO2 / Myosin V MYO2


Mass: 48747.227 Da / Num. of mol.: 1 / Mutation: Deletions 1342-1347
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: MYO2, CDC66, YOR326W, O6167 / Plasmid: modified pET32a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P19524
#2: Protein/peptide Kinesin-related protein SMY1 / Suppressor protein SMY1


Mass: 5022.541 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: SMY1, YKL079W, YKL409 / Plasmid: modified pET32a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P32364

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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: 4.79 Å3/Da / Density % sol: 74.33 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 8% w/v PEG 8000, 0.1M sodium dihydrogen phosphate pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.06→75.28 Å / Num. obs: 20270 / % possible obs: 99.7 % / Redundancy: 18.7 % / Biso Wilson estimate: 125.48 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.017 / Rrim(I) all: 0.071 / Net I/σ(I): 20.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
3.06-3.2220.71.69329110.9780.3781.736100
9.66-75.2815.70.0437380.9970.0110.04599.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimless0.6.2data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2F6H

2f6h


Resolution: 3.06→39.717 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 35.1
RfactorNum. reflection% reflection
Rfree0.2233 976 4.87 %
Rwork0.2031 --
obs0.2041 20042 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 345.96 Å2 / Biso mean: 172.9546 Å2 / Biso min: 75.68 Å2
Refinement stepCycle: final / Resolution: 3.06→39.717 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3258 0 0 0 3258
Num. residues----406
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043321
X-RAY DIFFRACTIONf_angle_d0.6254510
X-RAY DIFFRACTIONf_chiral_restr0.023536
X-RAY DIFFRACTIONf_plane_restr0.003563
X-RAY DIFFRACTIONf_dihedral_angle_d12.6731206
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0556-3.21670.39351290.35742662279198
3.2167-3.41810.40041630.32862603276698
3.4181-3.68180.25461030.27772737284099
3.6818-4.0520.27761260.24112715284199
4.052-4.63760.23991540.19162693284799
4.6376-5.83990.21211550.20492746290199
5.8399-39.72060.18831460.171829103056100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.09320.50950.76724.30631.75562.9513-0.0197-0.094-0.25970.316-0.171-0.09990.4708-0.9368-01.4787-0.13210.11421.4827-0.08671.454379.938152.8928222.632
21.6144-2.38821.54890.59250.56930.7201-0.37020.42410.1033-0.89340.00180.0169-0.7120.30110.00061.5182-0.36680.22361.0884-0.21361.376988.809365.0336228.4236
31.67192.21531.15592.47340.08671.99010.1155-0.1049-0.38420.67480.0901-0.49780.7689-0.2583-1.00321.16940.2215-0.20941.025-0.08171.110895.205572.269255.6039
4-0.8618-0.10560.3212.58660.92191.70390.1763-0.3941-0.07550.2816-0.5799-0.15680.3997-0.5261-0.01531.3608-0.11410.10041.5808-0.13641.528494.312869.9593242.6787
55.56583.2142-3.89086.4842-4.98544.1198-0.79730.6792-0.1971-1.41911.4205-0.06272.9552-0.491-0.27732.396-0.1876-0.12081.561-0.18361.918283.682339.7059215.9284
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1152 through 1280 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1281 through 1326 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1327 through 1462 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1463 through 1572 )
5X-RAY DIFFRACTION5chain 'B' and (resid 633 through 647 )

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