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- PDB-4e7s: Myosin VI D23R I24R R569E (MD) pre-powerstroke state -

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Basic information

Entry
Database: PDB / ID: 4e7s
TitleMyosin VI D23R I24R R569E (MD) pre-powerstroke state
ComponentsMyosin-VI
KeywordsMOTOR PROTEIN / myosin / molecular motor
Function / homology
Function and homology information


myosin complex / clathrin-coated vesicle / microvillus / cytoskeletal motor activity / clathrin-coated pit / filopodium / sensory perception of sound / ruffle membrane / actin filament binding / Golgi apparatus / ATP binding
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 / PHOSPHATE ION / VANADATE ION / Unconventional myosin-VI
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsIsabet, T. / Sweeney, H.L. / Houdusse, A.
CitationJournal: Mol.Cell / Year: 2012
Title: Processive Steps in the Reverse Direction Require Uncoupling of the Lead Head Lever Arm of Myosin VI.
Authors: Menetrey, J. / Isabet, T. / Ropars, V. / Mukherjea, M. / Pylypenko, O. / Liu, X. / Perez, J. / Vachette, P. / Sweeney, H.L. / Houdusse, A.M.
History
DepositionMar 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2012Group: Database references
Revision 1.2Feb 26, 2020Group: Data collection / Database references / Category: reflns / struct_ref_seq_dif
Item: _reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_Rsym_value / _struct_ref_seq_dif.details
Revision 1.3Feb 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_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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_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_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
B: Myosin-VI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,96115
Polymers182,1812
Non-polymers1,78013
Water8,449469
1
A: Myosin-VI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,0258
Polymers91,0901
Non-polymers9357
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Myosin-VI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,9367
Polymers91,0901
Non-polymers8466
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.947, 135.140, 196.540
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, 2 molecules AB

#1: Protein Myosin-VI /


Mass: 91090.461 Da / Num. of mol.: 2 / Mutation: D23R, I24R, R569E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: MYO6 / Cell (production host): SF9 cells / Production host: unidentified baculovirus / References: UniProt: F1RQI7

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Non-polymers , 6 types, 482 molecules

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


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-VO4 / VANADATE ION / Vanadate


Mass: 114.939 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: VO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 469 / 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: 2.99 Å3/Da / Density % sol: 58.82 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.75
Details: 6.75% PEG 8000, 50mM MES, 1mM TCEP, 6% Glycerol, and a stock solution of the protein at 10 mg.ml-1 trapped in the pre-powerstroke state with 2mM Mg.ADP and VO4, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.0716 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 27, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0716 Å / Relative weight: 1
ReflectionResolution: 2.25→30 Å / Num. obs: 102983 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.83 % / Rmerge(I) obs: 0.092 / Rsym value: 0.101
Reflection shellResolution: 2.25→2.3 Å / % possible all: 98

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→29.767 Å / SU ML: 0.28 / σ(F): 1.99 / Phase error: 21.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2165 5150 5 %
Rwork0.1794 --
obs0.1813 102975 98.89 %
all-102975 -
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.946 Å2 / ksol: 0.326 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.9652 Å20 Å2-0 Å2
2--3.4245 Å20 Å2
3----8.3897 Å2
Refinement stepCycle: LAST / Resolution: 2.25→29.767 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11946 0 107 469 12522
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112316
X-RAY DIFFRACTIONf_angle_d1.21516646
X-RAY DIFFRACTIONf_dihedral_angle_d14.0664504
X-RAY DIFFRACTIONf_chiral_restr0.081833
X-RAY DIFFRACTIONf_plane_restr0.0052157
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.33040.2855040.22979588X-RAY DIFFRACTION98
2.3304-2.42370.27035070.21589622X-RAY DIFFRACTION98
2.4237-2.53390.2635080.20479662X-RAY DIFFRACTION99
2.5339-2.66740.26525090.20159662X-RAY DIFFRACTION98
2.6674-2.83440.26125120.20729734X-RAY DIFFRACTION99
2.8344-3.05310.25275110.20149712X-RAY DIFFRACTION99
3.0531-3.35990.22885160.19029798X-RAY DIFFRACTION99
3.3599-3.84520.21475190.17629867X-RAY DIFFRACTION99
3.8452-4.84120.18465250.14719974X-RAY DIFFRACTION100
4.8412-29.76970.18885390.174310206X-RAY DIFFRACTION99

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