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- PDB-5o2l: Myosin VI motor domain in the Pre-Transition State -

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Basic information

Entry
Database: PDB / ID: 5o2l
TitleMyosin VI motor domain in the Pre-Transition State
ComponentsUnconventional myosin-VI
KeywordsMOTOR PROTEIN / MYOSIN / MOTOR DOMAIN / Pre-Transition State
Function / homology
Function and homology information


regulation of secretion / actin filament-based movement / inner ear auditory receptor cell differentiation / vesicle transport along actin filament / myosin complex / clathrin-coated vesicle / microfilament motor activity / inner ear morphogenesis / filamentous actin / microvillus ...regulation of secretion / actin filament-based movement / inner ear auditory receptor cell differentiation / vesicle transport along actin filament / myosin complex / clathrin-coated vesicle / microfilament motor activity / inner ear morphogenesis / filamentous actin / microvillus / cytoskeletal motor activity / DNA damage response, signal transduction by p53 class mediator / clathrin-coated pit / ruffle / filopodium / actin filament organization / actin filament / ADP binding / sensory perception of sound / intracellular protein transport / ruffle membrane / endocytosis / actin filament binding / actin cytoskeleton / cell cortex / cytoplasmic vesicle / nuclear membrane / vesicle / calmodulin binding / perinuclear region of cytoplasm / Golgi apparatus / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Myosin VI head, motor domain, U50 subdomain / : / Myosin VI, lever arm / Myosin VI, cargo binding domain / Class VI myosin, motor domain / Myosin VI cargo binding domain / Myosin S1 fragment, N-terminal / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #530 / Kinesin motor domain / Kinesin ...Myosin VI head, motor domain, U50 subdomain / : / Myosin VI, lever arm / Myosin VI, cargo binding domain / Class VI myosin, motor domain / Myosin VI cargo binding domain / Myosin S1 fragment, N-terminal / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #530 / Kinesin motor domain / Kinesin / Myosin S1 fragment, N-terminal / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / Kinesin motor domain superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / SH3 type barrels. / Roll / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / Unconventional myosin-VI / Unconventional myosin-VI
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsIsabet, T. / Benisty, H. / Houdusse, A.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: An intermediate along the recovery stroke of myosin VI revealed by X-ray crystallography and molecular dynamics.
Authors: Blanc, F. / Isabet, T. / Benisty, H. / Sweeney, H.L. / Cecchini, M. / Houdusse, A.
History
DepositionMay 22, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2018Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 20, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Unconventional myosin-VI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,80012
Polymers89,5461
Non-polymers1,25411
Water4,306239
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-20 kcal/mol
Surface area33060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.340, 83.830, 177.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Unconventional myosin-VI /


Mass: 89545.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: MYO6 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: F1RQI7, UniProt: Q29122*PLUS

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Non-polymers , 5 types, 250 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 3.01 Å3/Da / Density % sol: 59.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 7% polyethylene glycol [PEG] 8000, 50 mM TRIS, pH 7.5, 1 mM TCEP, 15% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 3, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 55469 / % possible obs: 99.6 % / Redundancy: 5.1 % / Biso Wilson estimate: 49.48 Å2 / Net I/σ(I): 15.57
Reflection shellResolution: 2.2→2.26 Å / Mean I/σ(I) obs: 1.29

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
Cootmodel building
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2v26

2v26


Resolution: 2.2→22.18 Å / Cor.coef. Fo:Fc: 0.9593 / Cor.coef. Fo:Fc free: 0.9343 / SU R Cruickshank DPI: 0.185 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.186 / SU Rfree Blow DPI: 0.168 / SU Rfree Cruickshank DPI: 0.169
RfactorNum. reflection% reflectionSelection details
Rfree0.2268 2769 4.99 %RANDOM
Rwork0.1823 ---
obs0.1844 55469 99.78 %-
Displacement parametersBiso mean: 67.33 Å2
Baniso -1Baniso -2Baniso -3
1--2.0872 Å20 Å20 Å2
2---5.602 Å20 Å2
3---7.6892 Å2
Refine analyzeLuzzati coordinate error obs: 0.367 Å
Refinement stepCycle: 1 / Resolution: 2.2→22.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6065 0 80 239 6384
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016265HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.068457HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2926SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes165HARMONIC2
X-RAY DIFFRACTIONt_gen_planes919HARMONIC5
X-RAY DIFFRACTIONt_it6265HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.19
X-RAY DIFFRACTIONt_other_torsion3.01
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion801SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7456SEMIHARMONIC4
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3194 202 5 %
Rwork0.2605 3835 -
all0.2635 4037 -
obs--99.78 %
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)
11.4788-0.34590.46380.66330.06491.781-0.0407-0.18330.1246-0.15640.039-0.0518-0.3194-0.0250.0017-0.066-0.06150.0453-0.0329-0.0191-0.2999-3.51131.970324.9344
28.31552.9104-0.31448.31542.91043.4091-0.0202-0.0147-0.5442-0.5308-0.24610.5072-0.3337-0.46170.2663-0.296-0.1009-0.04080.192-0.0381-0.173231.471664.057734.946
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|5 - A|704 A|995 - A|1006 S|* }
2X-RAY DIFFRACTION2{ A|705 - A|789 T|* }

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