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- PDB-4pjj: MYOSIN VI (MD-INSERT2-CAM, DELTA-INSERT1) post-rigor state - long... -

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Basic information

Entry
Database: PDB / ID: 4pjj
TitleMYOSIN VI (MD-INSERT2-CAM, DELTA-INSERT1) post-rigor state - long soaking with PO4
Components
  • Calmodulin
  • Unconventional myosin-VI
KeywordsMOTOR PROTEIN / MYOSIN VI / POST-RIGOR STATE / MG.ADP.BEFX / CALMODULIN / MOLECULAR MOTOR
Function / homology
Function and homology information


negative regulation of phospholipase C-activating phototransduction signaling pathway / myosin VI complex / myosin VI head/neck binding / myosin VII complex / negative regulation of opsin-mediated signaling pathway / photoreceptor cell axon guidance / rhabdomere development / rhabdomere / detection of chemical stimulus involved in sensory perception of smell / myosin V complex ...negative regulation of phospholipase C-activating phototransduction signaling pathway / myosin VI complex / myosin VI head/neck binding / myosin VII complex / negative regulation of opsin-mediated signaling pathway / photoreceptor cell axon guidance / rhabdomere development / rhabdomere / detection of chemical stimulus involved in sensory perception of smell / myosin V complex / kinetochore organization / autophagic cell death / G protein-coupled opsin signaling pathway / actin filament-based movement / myosin V binding / cellular response to ethanol / myosin complex / clathrin-coated vesicle / muscle cell cellular homeostasis / myosin heavy chain binding / mitotic spindle pole / channel regulator activity / centriole replication / cytoskeletal motor activity / microvillus / enzyme regulator activity / clathrin-coated pit / centriole / filopodium / sensory perception of sound / mitotic spindle / ruffle membrane / spindle / actin filament binding / sensory perception of smell / cell cortex / midbody / centrosome / calcium ion binding / Golgi apparatus / nucleoplasm / ATP binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2980 / Arc Repressor Mutant, subunit A - #820 / Myosin VI head, motor domain, U50 subdomain / Myosin VI, cargo binding domain / Class VI myosin, motor domain / : / Myosin VI cargo binding domain / Myosin VI, lever arm / Myosin S1 fragment, N-terminal / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #530 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2980 / Arc Repressor Mutant, subunit A - #820 / Myosin VI head, motor domain, U50 subdomain / Myosin VI, cargo binding domain / Class VI myosin, motor domain / : / Myosin VI cargo binding domain / Myosin VI, lever arm / 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. / : / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Kinesin motor domain superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Helix non-globular / EF-hand domain pair / EF-hand, calcium binding motif / Special / SH3 type barrels. / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Arc Repressor Mutant, subunit A / Roll / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / Unconventional myosin-VI / Calmodulin
Similarity search - Component
Biological speciesSus scrofa (pig)
Drosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Derived calculations
Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / pdbx_distant_solvent_atoms / 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_distant_solvent_atoms.auth_seq_id / _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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
B: Calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,62110
Polymers106,7152
Non-polymers9068
Water6,377354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6720 Å2
ΔGint-90 kcal/mol
Surface area38820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.010, 109.240, 180.360
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 , 2 types, 2 molecules AB

#1: Protein Unconventional myosin-VI


Mass: 89873.477 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
#2: Protein Calmodulin / CaM


Mass: 16841.520 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Cam, CG8472 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P62152

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Non-polymers , 6 types, 362 molecules

#3: 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
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / 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: 3.37 Å3/Da / Density % sol: 63.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 9% PEG8k, 50mM Hepes pH 7,5, 1mM TCEP, 3% EG, 3% MPD
PH range: 7.5

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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: Apr 5, 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: 2.4→45 Å / Num. obs: 57130 / % possible obs: 99.8 % / Redundancy: 9.57 % / Biso Wilson estimate: 57.71 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.23
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 9.69 % / Rmerge(I) obs: 1.076 / Mean I/σ(I) obs: 2.31 / % possible all: 98.9

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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: 2VAS

2vas


Resolution: 2.4→43.74 Å / Cor.coef. Fo:Fc: 0.9524 / Cor.coef. Fo:Fc free: 0.9387 / SU R Cruickshank DPI: 0.217 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.222 / SU Rfree Blow DPI: 0.179 / SU Rfree Cruickshank DPI: 0.179
RfactorNum. reflection% reflectionSelection details
Rfree0.2067 2855 5 %RANDOM
Rwork0.1723 ---
obs0.1741 57130 99.86 %-
Displacement parametersBiso mean: 59.36 Å2
Baniso -1Baniso -2Baniso -3
1-3.6418 Å20 Å20 Å2
2---7.7911 Å20 Å2
3---4.1492 Å2
Refine analyzeLuzzati coordinate error obs: 0.293 Å
Refinement stepCycle: 1 / Resolution: 2.4→43.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7090 0 52 354 7496
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017275HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.069815HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2591SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes207HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1058HARMONIC5
X-RAY DIFFRACTIONt_it7275HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.93
X-RAY DIFFRACTIONt_other_torsion18.45
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion936SEMIHARMONIC5
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_contact8710SEMIHARMONIC4
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2494 208 5.03 %
Rwork0.2059 3927 -
all0.2081 4135 -
obs--99.86 %
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)
10.7177-0.04210.07390.7443-0.42520.7943-0.0071-0.08220.15120.12670.00670.0075-0.115-0.02080.0004-0.20740.0174-0.0153-0.139-0.029-0.2005-9.0009-25.552819.1011
21.52270.31540.57984.2015-2.23341.9782-0.15490.24090.2898-0.1805-0.1832-0.428-0.08870.35020.338-0.0562-0.00050.0259-0.03350.1478-0.176717.872-63.763435.6755
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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