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- PDB-4pfp: Myosin VI motor domain in the Pi release state (with Pi) space gr... -

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Basic information

Entry
Database: PDB / ID: 4pfp
TitleMyosin VI motor domain in the Pi release state (with Pi) space group P21
ComponentsUnconventional myosin-VI
KeywordsMOTOR PROTEIN / Pi release state / Motor domain
Function / homology
Function and homology information


inner ear auditory receptor cell differentiation / vesicle transport along actin filament / myosin complex / clathrin-coated vesicle / inner ear morphogenesis / microfilament motor activity / microvillus / endocytic vesicle / clathrin-coated pit / filopodium ...inner ear auditory receptor cell differentiation / vesicle transport along actin filament / myosin complex / clathrin-coated vesicle / inner ear morphogenesis / microfilament motor activity / microvillus / endocytic vesicle / clathrin-coated pit / filopodium / actin filament organization / sensory perception of sound / ruffle membrane / endocytosis / actin filament binding / Golgi apparatus / ATP binding / metal ion 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 / S-1,2-PROPANEDIOL / PHOSPHATE ION / Unconventional myosin-VI
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.32 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
DepositionApr 30, 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 2.1May 8, 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
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.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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Unconventional myosin-VI
C: Unconventional myosin-VI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,95810
Polymers179,6942
Non-polymers1,2648
Water7,404411
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-69 kcal/mol
Surface area65230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.650, 94.890, 97.300
Angle α, β, γ (deg.)90.00, 99.55, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AC

#1: Protein Unconventional myosin-VI


Mass: 89847.180 Da / Num. of mol.: 2 / 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

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Non-polymers , 5 types, 419 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-PGO / S-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 411 / 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: 2.55 Å3/Da / Density % sol: 51.76 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 4,5% PEG8k, 50mM MES pH 6,5, 1mM TCEP, 10mM NaH2PO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 19, 2011
RadiationMonochromator: SI III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.32→45 Å / Num. obs: 78052 / % possible obs: 99.8 % / Redundancy: 6.67 % / Biso Wilson estimate: 50.6 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 14.44
Reflection shellResolution: 2.32→2.38 Å / Redundancy: 3.78 % / Rmerge(I) obs: 0.648 / Mean I/σ(I) obs: 2.27 / % possible all: 99.2

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
Cootmodel building
PHASERphasing
XDSdata reduction
RefinementResolution: 2.32→23.39 Å / Cor.coef. Fo:Fc: 0.9496 / Cor.coef. Fo:Fc free: 0.93 / SU R Cruickshank DPI: 0.293 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.283 / SU Rfree Blow DPI: 0.207 / SU Rfree Cruickshank DPI: 0.212
RfactorNum. reflection% reflectionSelection details
Rfree0.229 3899 5 %RANDOM
Rwork0.1891 ---
obs0.1911 78052 99.84 %-
Displacement parametersBiso mean: 54.25 Å2
Baniso -1Baniso -2Baniso -3
1-9.9293 Å20 Å2-0.4695 Å2
2---6.7259 Å20 Å2
3----3.2034 Å2
Refine analyzeLuzzati coordinate error obs: 0.329 Å
Refinement stepCycle: 1 / Resolution: 2.32→23.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12037 0 76 411 12524
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0112369HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0916737HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4321SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes315HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1836HARMONIC5
X-RAY DIFFRACTIONt_it12369HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.91
X-RAY DIFFRACTIONt_other_torsion17.74
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1602SEMIHARMONIC5
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_contact14477SEMIHARMONIC4
LS refinement shellResolution: 2.32→2.38 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2659 286 5 %
Rwork0.2198 5433 -
all0.2221 5719 -
obs--99.84 %
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)
12.40610.3307-0.79440.5129-0.06650.727-0.1045-0.0837-0.2248-0.03870.0361-0.01340.077-0.02180.0684-0.21590.0003-0.0232-0.05670.0308-0.183739.8232-3.0560.9227
21.1185-0.1921-0.22540.6755-0.04180.5109-0.03110.00670.01360.03490.1333-0.00260.0836-0.0309-0.1022-0.1519-0.0201-0.0146-0.1440.0092-0.140118.1486-5.7292-49.7002
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ C|* }

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