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- PDB-4dbr: Myosin VI D179Y (MD) pre-powerstroke state -

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Basic information

Entry
Database: PDB / ID: 4dbr
TitleMyosin VI D179Y (MD) pre-powerstroke state
ComponentsMyosin-VI
KeywordsMOTOR PROTEIN
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 / VANADATE ION / Unconventional myosin-VI / Unconventional myosin-VI
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsPylypenko, O. / Sweeney, H.L. / Houdusse, A.
CitationJournal: To be Published
Title: Mutations in myosin VI that cause a loss of coordination between heads provide insights into the structural changes underlying force generation and the importance of gating
Authors: Song, L. / Pylypenko, O. / Yang, Z. / Houdusse, A. / Sweeney, L.H.
History
DepositionJan 16, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Myosin-VI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,72812
Polymers89,6651
Non-polymers1,06311
Water13,097727
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.940, 93.530, 102.430
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 Myosin-VI /


Mass: 89665.078 Da / Num. of mol.: 1 / Fragment: MOTOR DOMAIN, UNP residues 5-788 / Mutation: D179Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: MYO6 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: F1RQI7, UniProt: Q29122*PLUS

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Non-polymers , 5 types, 738 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#3: 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
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-VO4 / VANADATE ION / Vanadate


Mass: 114.939 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: VO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 727 / 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: 2.46 Å3/Da / Density % sol: 49.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 50 mM TrisHCl pH 8, 5.5% PEG8K, 50 mM KSCN, 5% glycerol, 20 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 9, 2010
RadiationMonochromator: Si III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 1.9→29.361 Å / Num. all: 69738 / Num. obs: 69466 / % possible obs: 99.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shellResolution: 1.9→1.95 Å / % possible all: 98.1

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Processing

Software
NameVersionClassification
DNAdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→29.361 Å / SU ML: 0.52 / σ(F): 1.99 / Phase error: 22.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2159 3242 5 %RANDOM
Rwork0.1736 ---
obs0.1757 64845 99.77 %-
all-69738 --
Solvent computationShrinkage radii: 1.24 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.567 Å2 / ksol: 0.314 e/Å3
Refinement stepCycle: LAST / Resolution: 1.95→29.361 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6005 0 65 727 6797
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096270
X-RAY DIFFRACTIONf_angle_d1.2578473
X-RAY DIFFRACTIONf_dihedral_angle_d13.4192329
X-RAY DIFFRACTIONf_chiral_restr0.082930
X-RAY DIFFRACTIONf_plane_restr0.0051097
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.01970.29853210.23376093X-RAY DIFFRACTION100
2.0197-2.10050.27123200.2076071X-RAY DIFFRACTION100
2.1005-2.19610.25653200.19796099X-RAY DIFFRACTION100
2.1961-2.31180.24233200.18126094X-RAY DIFFRACTION100
2.3118-2.45660.25033210.18326108X-RAY DIFFRACTION100
2.4566-2.64620.23513220.17796120X-RAY DIFFRACTION100
2.6462-2.91220.24953230.17986127X-RAY DIFFRACTION100
2.9122-3.33320.23133260.17646193X-RAY DIFFRACTION100
3.3332-4.19750.18813280.15376238X-RAY DIFFRACTION100
4.1975-29.3610.17763410.16436460X-RAY DIFFRACTION100

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