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- PDB-4pk4: Myosin VI motor domain in the PPS state - from a Pi release state... -

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Basic information

Entry
Database: PDB / ID: 4pk4
TitleMyosin VI motor domain in the PPS state - from a Pi release state crystal, space group P212121 after long soaking with PO4
ComponentsUnconventional myosin-VI
KeywordsMOTOR PROTEIN / motor domain / Pre powerstroke state
Function / homology
Function and homology information


myosin complex / cytoskeletal motor activity / microvillus / clathrin-coated pit / sensory perception of sound / ruffle membrane / actin filament binding / calmodulin binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Myosin VI, cargo binding domain / Class VI myosin, motor domain / : / Myosin VI cargo binding domain / Myosin VI, lever arm / Myosin VI head, motor domain, U50 subdomain / Myosin S1 fragment, N-terminal / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #530 / Kinesin motor domain / Kinesin ...Myosin VI, cargo binding domain / Class VI myosin, motor domain / : / Myosin VI cargo binding domain / Myosin VI, lever arm / Myosin VI head, motor domain, U50 subdomain / 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 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Four Helix Bundle (Hemerythrin (Met), subunit A) / 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 / Unconventional myosin-VI
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 Å
AuthorsIsabet, T. / Benisty, H. / Llinas, P. / Sweeney, H.L. / Houdusse, A.
Funding support France, United States, 3items
OrganizationGrant numberCountry
French National Research AgencyBLAN07 France
French National Research AgencyBLAN10 France
National Institutes of HealthRO01DC009100 United States
CitationJournal: Dev.Cell / Year: 2015
Title: How actin initiates the motor activity of Myosin.
Authors: Llinas, P. / Isabet, T. / Song, L. / Ropars, V. / Zong, B. / Benisty, H. / Sirigu, S. / Morris, C. / Kikuti, C. / Safer, D. / Sweeney, H.L. / Houdusse, A.
History
DepositionMay 13, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 29, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2016Group: Database references
Revision 2.0Aug 30, 2017Group: Atomic model / Author supporting evidence / Derived calculations
Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / pdbx_struct_conn_angle / struct_conn / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_site_gen.auth_seq_id
Revision 2.1Dec 20, 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

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Assembly

Deposited unit
A: Unconventional myosin-VI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,3944
Polymers89,8471
Non-polymers5463
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-28 kcal/mol
Surface area32070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.590, 94.790, 101.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Unconventional myosin-VI


Mass: 89847.180 Da / Num. of mol.: 1 / Fragment: residues 2-789
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
#2: Chemical ChemComp-ADP / ADENOSINE-5'-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-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.12 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 6,6% PEG8k, 50mM Tris pH8,5, 1mM TCEP, 3% Glycerol then soaked during 45 minutes with 100mM NaH2PO4 pH7,5
PH range: 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 6, 2011
RadiationMonochromator: Si III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.78→50 Å / Num. obs: 23205 / % possible obs: 99.3 % / Redundancy: 7.23 % / Biso Wilson estimate: 84.54 Å2 / Rmerge(I) obs: 0.127 / Net I/σ(I): 16.53
Reflection shellResolution: 2.78→2.85 Å / Redundancy: 4.9 % / Rmerge(I) obs: 1.125 / Mean I/σ(I) obs: 1.35 / % possible all: 98.1

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Processing

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

2v26


Resolution: 2.78→31 Å / Cor.coef. Fo:Fc: 0.9477 / Cor.coef. Fo:Fc free: 0.8992 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.361
RfactorNum. reflection% reflectionSelection details
Rfree0.2591 1161 5 %RANDOM
Rwork0.1871 ---
obs0.1908 23205 99.08 %-
Displacement parametersBiso mean: 104.44 Å2
Baniso -1Baniso -2Baniso -3
1--16.6649 Å20 Å20 Å2
2---5.5072 Å20 Å2
3---22.1721 Å2
Refine analyzeLuzzati coordinate error obs: 0.53 Å
Refinement stepCycle: 1 / Resolution: 2.78→31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6004 0 33 15 6052
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016168HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.178353HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2159SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes166HARMONIC2
X-RAY DIFFRACTIONt_gen_planes914HARMONIC5
X-RAY DIFFRACTIONt_it6168HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.66
X-RAY DIFFRACTIONt_other_torsion20.99
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion800SEMIHARMONIC5
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_contact7117SEMIHARMONIC4
LS refinement shellResolution: 2.78→2.9 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.2955 140 5.03 %
Rwork0.2414 2641 -
all0.244 2781 -
obs--99.08 %
Refinement TLS params.Method: refined / Origin x: 18.9055 Å / Origin y: -21.9872 Å / Origin z: -10.6339 Å
111213212223313233
T-0.3792 Å2-0.1094 Å2-0.1112 Å2--0.2942 Å20.0455 Å2---0.3149 Å2
L1.5168 °2-0.2438 °20.4323 °2-2.3935 °2-1.0327 °2--3.7703 °2
S0.3069 Å °0.0195 Å °-0.0345 Å °-0.0511 Å °-0.2108 Å °0.3129 Å °0.2652 Å °0.2458 Å °-0.0961 Å °
Refinement TLS groupSelection details: { A|* }

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