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- PDB-2bki: Myosin VI nucleotide-free (MDinsert2-IQ) crystal structure -

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Basic information

Entry
Database: PDB / ID: 2bki
TitleMyosin VI nucleotide-free (MDinsert2-IQ) crystal structure
Components
  • CALMODULIN
  • UNCONVENTIONAL MYOSIN
KeywordsMOTOR PROTEIN/METAL-BINDING PROTEIN / MOTOR PROTEIN-METAL-BINDING PROTEIN COMPLEX / COMPLEX (MOTOR PROTEIN-CALMODULIN) / MYOSIN VI / REVERSE MYOSIN / CALMODULIN / IQ MOTIF / NON- CONVENTIONAL MYOSIN / NUCLEOTIDE-FREE CONFORMATION / MUSCLE PROTEIN
Function / homology
Function and homology information


CH domain binding / regulation of secretion / inner ear auditory receptor cell differentiation / actin filament-based movement / myosin complex / clathrin-coated vesicle / inner ear morphogenesis / microfilament motor activity / myosin binding / filamentous actin ...CH domain binding / regulation of secretion / inner ear auditory receptor cell differentiation / actin filament-based movement / myosin complex / clathrin-coated vesicle / inner ear morphogenesis / microfilament motor activity / myosin binding / filamentous actin / microvillus / cytoskeletal motor activity / ruffle / actin filament organization / actin filament / filopodium / DNA damage response, signal transduction by p53 class mediator / intracellular protein transport / sensory perception of sound / ADP binding / ruffle membrane / endocytosis / disordered domain specific binding / actin filament binding / intracellular protein localization / myelin sheath / actin cytoskeleton / cytoplasmic vesicle / cell cortex / nuclear membrane / calmodulin binding / calcium ion binding / centrosome / perinuclear region of cytoplasm / Golgi apparatus / protein-containing complex / nucleoplasm / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Myosin VI, cargo binding domain / Class VI myosin, motor domain / : / Myosin VI cargo binding domain / Myosin VI, lever arm / 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 VI, cargo binding domain / Class VI myosin, motor domain / : / Myosin VI cargo binding domain / Myosin VI, lever arm / 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 / EF-hand / : / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Calmodulin / Unconventional myosin-VI
Similarity search - Component
Biological speciesSUS SCROFA (pig)
GALLUS GALLUS (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsMenetrey, J. / Bahloul, A. / Yengo, C. / Wells, A. / Morris, C. / Sweeney, H.L. / Houdusse, A.
CitationJournal: Nature / Year: 2005
Title: The Structure of the Myosin Vi Motor Reveals the Mechanism of Directionality Reversal
Authors: Menetrey, J. / Bahloul, A. / Wells, A. / Yengo, C. / Morris, C. / Sweeney, H.L. / Houdusse, A.
History
DepositionFeb 16, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 7, 2005Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2015Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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_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_conn.ptnr2_label_seq_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: UNCONVENTIONAL MYOSIN
B: CALMODULIN
D: CALMODULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,2478
Polymers131,9913
Non-polymers2565
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)104.781, 250.167, 67.274
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein UNCONVENTIONAL MYOSIN / MYOSIN VI


Mass: 98285.633 Da / Num. of mol.: 1 / Fragment: DOMAIN LONG-S1, RESIDUES 1-858
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SUS SCROFA (pig) / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q29122
#2: Protein CALMODULIN / CAM


Mass: 16852.545 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GALLUS GALLUS (chicken) / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P62149
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE AUTHORS STATE THAT THE ORIGINAL SEQUENCE (UNIPROT Q29122) OF MYOSIN VI FROM PIG WAS MOST LIKELY ...THE AUTHORS STATE THAT THE ORIGINAL SEQUENCE (UNIPROT Q29122) OF MYOSIN VI FROM PIG WAS MOST LIKELY INCORRECT BECAUSE THE CHANGES THAT ARE IN THEIR CLONE (LYS DELETION AND THE 6 MUTATIONS) ARE CONSERVED ACROSS THE MYOSIN VI FAMILY.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.91 Å3/Da / Density % sol: 68.31 %
Crystal growDetails: 8-10% PEG 8000, 50MM MES PH 6.7, 150MM NH4.SO4, 3% ISO-PROPANOL, 3% TERT-BUTANOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.96115
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96115 Å / Relative weight: 1
ReflectionResolution: 2.9→40 Å / Num. obs: 38961 / % possible obs: 97 % / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 16.3
Reflection shellResolution: 2.9→3.06 Å / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.7 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OE9

1oe9


Resolution: 2.9→40 Å / Cor.coef. Fo:Fc: 0.86 / Cor.coef. Fo:Fc free: 0.809 / SU B: 17.988 / SU ML: 0.339 / Cross valid method: THROUGHOUT / ESU R: 1.125 / ESU R Free: 0.43 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. CAM BOUND TO THE IQ MOTIF IS POORLY DEFINED IN THE DENSITY, ONLY POLY-ALA CHAINS HAVE BEEN MODELED FOR IT.
RfactorNum. reflection% reflectionSelection details
Rfree0.304 1948 5.1 %RANDOM
Rwork0.264 ---
obs0.266 36191 95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 43.74 Å2
Baniso -1Baniso -2Baniso -3
1--2.74 Å20 Å20 Å2
2--2.65 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7991 0 9 49 8049
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0218138
X-RAY DIFFRACTIONr_bond_other_d0.0020.027293
X-RAY DIFFRACTIONr_angle_refined_deg1.1491.94610997
X-RAY DIFFRACTIONr_angle_other_deg2.037316926
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.23851042
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0640.21229
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.029247
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021662
X-RAY DIFFRACTIONr_nbd_refined0.1740.21835
X-RAY DIFFRACTIONr_nbd_other0.2070.27914
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0810.24801
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2101
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1640.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2260.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2020.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5171.55197
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.96528235
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.12932941
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.9874.52762
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.98 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.343 118
Rwork0.293 2389

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