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- PDB-6ixo: Apo structure of Myo2-GTD -

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Basic information

Entry
Database: PDB / ID: 6ixo
TitleApo structure of Myo2-GTD
ComponentsMyosin-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 / 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 / MOLECULAR REPLACEMENT / Resolution: 1.901 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3816
Polymers47,9621
Non-polymers4205
Water4,612256
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area350 Å2
ΔGint-27 kcal/mol
Surface area19030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.660, 72.164, 168.324
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: 47961.508 Da / Num. of mol.: 1 / Mutation: 1342-1347 deletions
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: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 3.21 Å3/Da / Density % sol: 61.65 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1 M potassium chloride, 1 M ammonium sulfate and 0.1 M HEPES pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 49545 / % possible obs: 100 % / Redundancy: 11.6 % / Biso Wilson estimate: 32.77 Å2 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.032 / Rrim(I) all: 0.111 / Χ2: 1.168 / Net I/σ(I): 5.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.9312.11.90524550.7640.5621.9881.115100
1.93-1.9711.91.57924110.7780.471.6491.137100
1.97-2.0111.81.29624730.8350.3891.3551.124100
2.01-2.0511.71.04524230.8910.3141.0921.146100
2.05-2.0911.60.87224280.9010.2640.9121.161100
2.09-2.1411.20.69224470.9280.2140.7251.18899.8
2.14-2.1910.30.52624500.9430.1710.5531.207100
2.19-2.2511.70.46824550.970.1410.4891.234100
2.25-2.3212.10.40824550.9750.1210.4251.209100
2.32-2.3912.10.31424430.9850.0930.3271.249100
2.39-2.4811.80.27124380.9880.0810.2841.273100
2.48-2.5811.80.21824770.9910.0650.2281.339100
2.58-2.711.60.18324600.9930.0560.1921.355100
2.7-2.8410.50.13924810.9950.0450.1471.329100
2.84-3.02120.11624840.9970.0350.1221.31799.9
3.02-3.2512.20.09324800.9980.0270.0971.244100
3.25-3.5811.80.07525040.9980.0220.0781.17999.9
3.58-4.0910.80.0625050.9980.0190.0630.95199.8
4.09-5.1611.50.05525800.9980.0170.0570.778100
5.16-5010.70.05326960.9980.0170.0560.83299.8

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Processing

Software
NameVersionClassification
HKL-3000data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2F6H

2f6h


Resolution: 1.901→42.081 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.52
RfactorNum. reflection% reflection
Rfree0.2063 1999 4.04 %
Rwork0.1738 --
obs0.1751 49421 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 188.77 Å2 / Biso mean: 48.8398 Å2 / Biso min: 19.49 Å2
Refinement stepCycle: final / Resolution: 1.901→42.081 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3112 0 21 256 3389
Biso mean--163.32 50.59 -
Num. residues----384
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143236
X-RAY DIFFRACTIONf_angle_d1.2594409
X-RAY DIFFRACTIONf_chiral_restr0.068517
X-RAY DIFFRACTIONf_plane_restr0.006548
X-RAY DIFFRACTIONf_dihedral_angle_d14.0221191
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9006-1.94810.36171380.3093312345098
1.9481-2.00080.311410.273933093450100
2.0008-2.05970.30831400.245533393479100
2.0597-2.12620.25791420.219633623504100
2.1262-2.20220.23931420.199133673509100
2.2022-2.29030.26641410.184833373478100
2.2903-2.39460.23371420.173433743516100
2.3946-2.52080.19721420.17433763518100
2.5208-2.67870.19841430.167133833526100
2.6787-2.88550.2131420.176833673509100
2.8855-3.17580.23141450.171334213566100
3.1758-3.63510.19051430.164434163559100
3.6351-4.57890.18441460.142734613607100
4.5789-42.09130.16951520.16733598375099
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)
10.8334-0.10110.00041.8599-0.5434.40770.0112-0.2107-0.06510.56810.0411-0.0760.20380.091-0.04570.3270.0169-0.0110.24060.0190.25242.818-24.25439.577
21.56320.36041.12170.8915-1.19325.99150.0097-0.0814-0.02160.05520.02020.11090.0019-0.5513-0.0150.15330.01040.00570.2768-0.00410.2944-9.966-18.6938.423
31.89740.40920.91931.28120.24381.7038-0.53120.54910.5345-0.26010.11960.1426-1.23830.49610.30070.5443-0.0965-0.10540.32720.11320.4149-5.39-4.665-7.027
40.2753-1.27180.82434.6016-3.1532.21-0.0632-0.0993-0.16550.45550.32680.6325-0.1569-0.373-0.31790.4560.0161-00.36780.04840.3792-4.403-28.63746.174
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1152:1326 )A1152 - 1326
2X-RAY DIFFRACTION2( CHAIN A AND RESID 1327:1445 )A1327 - 1445
3X-RAY DIFFRACTION3( CHAIN A AND RESID 1446:1532 )A1446 - 1532
4X-RAY DIFFRACTION4( CHAIN A AND RESID 1533:1569 )A1533 - 1569

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