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- PDB-4pjm: Myosin VI motor domain in the Pi release state, space group P2121... -

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Basic information

Entry
Database: PDB / ID: 4pjm
TitleMyosin VI motor domain in the Pi release state, space group P212121 - soaked with PO4 - located in the active site
ComponentsUnconventional myosin-VI
KeywordsMOTOR PROTEIN / myosin VI / motor domain / Pi release state
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 / ISOPROPYL ALCOHOL / PHOSPHATE ION / Unconventional myosin-VI
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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 12, 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 / _atom_site.occupancy / _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

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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)91,15913
Polymers89,8471
Non-polymers1,31112
Water10,845602
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-24 kcal/mol
Surface area31510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.490, 95.330, 103.340
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: 89847.180 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

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Non-polymers , 6 types, 614 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: 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
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 602 / 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: 2.51 Å3/Da / Density % sol: 50.95 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.75
Details: 4,5%PEG8k, 50mM MES pH 6,75, 1mM TCEP, 3% Isopropanol, 3% TertButanol, 50mM KSCN, 3% Glyc?rol then soaked with 150mM NaH2PO4 pH 7,5 and 25% Glyc?rol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.984 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 18, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 57304 / % possible obs: 99.9 % / Redundancy: 14.92 % / Biso Wilson estimate: 27.86 Å2 / Rmerge(I) obs: 0.108 / Net I/σ(I): 17.63
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 14.75 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 6.38 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
Cootmodel building
PHASERphasing
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→45.74 Å / Cor.coef. Fo:Fc: 0.9518 / Cor.coef. Fo:Fc free: 0.9314 / SU R Cruickshank DPI: 0.152 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.161 / SU Rfree Blow DPI: 0.139 / SU Rfree Cruickshank DPI: 0.136
RfactorNum. reflection% reflectionSelection details
Rfree0.1959 2866 5 %RANDOM
Rwork0.1605 ---
obs0.1622 57304 99.87 %-
Displacement parametersBiso mean: 32.08 Å2
Baniso -1Baniso -2Baniso -3
1--2.1705 Å20 Å20 Å2
2---3.0109 Å20 Å2
3---5.1814 Å2
Refine analyzeLuzzati coordinate error obs: 0.217 Å
Refinement stepCycle: 1 / Resolution: 2.05→45.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5907 0 83 602 6592
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016115HARMONIC2
X-RAY DIFFRACTIONt_angle_deg18274HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2104SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes148HARMONIC2
X-RAY DIFFRACTIONt_gen_planes909HARMONIC5
X-RAY DIFFRACTIONt_it6115HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.24
X-RAY DIFFRACTIONt_other_torsion16.46
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion793SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies7HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7890SEMIHARMONIC4
LS refinement shellResolution: 2.05→2.1 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2175 210 5 %
Rwork0.161 3993 -
all0.1638 4203 -
obs--99.87 %
Refinement TLS params.Method: refined / Origin x: 1.2677 Å / Origin y: -3.8907 Å / Origin z: -13.7702 Å
111213212223313233
T-0.07 Å20.0092 Å20.0037 Å2--0.0769 Å20.0054 Å2---0.0609 Å2
L0.4056 °20.0574 °20.1261 °2-0.3086 °2-0.0576 °2--1.0533 °2
S-0.0424 Å °-0.0257 Å °-0.0492 Å °-0.001 Å °0.0367 Å °0.0421 Å °-0.0305 Å °-0.1048 Å °0.0057 Å °
Refinement TLS groupSelection details: { A|* }

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