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- PDB-2vb6: Myosin VI (MD-insert2-CaM, Delta Insert1) Post-rigor state (cryst... -

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Basic information

Entry
Database: PDB / ID: 2vb6
TitleMyosin VI (MD-insert2-CaM, Delta Insert1) Post-rigor state (crystal form 2)
Components
  • CALMODULIN
  • MYOSIN VI
KeywordsMOTOR PROTEIN / MYOSIN VI / POST-RIGOR STATE / MG.ADP.BEFX / CALMODULIN / CAM / MOLECULAR MOTOR
Function / homology
Function and homology information


CH domain binding / regulation of secretion / actin filament-based movement / inner ear auditory receptor cell differentiation / myosin complex / clathrin-coated vesicle / inner ear morphogenesis / microfilament motor activity / myosin binding / filamentous actin ...CH domain binding / regulation of secretion / actin filament-based movement / inner ear auditory receptor cell differentiation / myosin complex / clathrin-coated vesicle / inner ear morphogenesis / microfilament motor activity / myosin binding / filamentous actin / cytoskeletal motor activity / microvillus / DNA damage response, signal transduction by p53 class mediator / ruffle / filopodium / actin filament organization / actin filament / intracellular protein transport / sensory perception of sound / ADP binding / ruffle membrane / endocytosis / disordered domain specific binding / actin filament binding / protein localization / actin cytoskeleton / cell cortex / cytoplasmic vesicle / nuclear membrane / calmodulin binding / calcium ion binding / perinuclear region of cytoplasm / Golgi apparatus / protein-containing complex / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2980 / Alpha-Beta Plaits - #1590 / 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 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2980 / Alpha-Beta Plaits - #1590 / 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 / Alpha-Beta Plaits / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / Calmodulin / Unconventional myosin-VI
Similarity search - Component
Biological speciesSUS SCROFA (pig)
GALLUS GALLUS (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIRECT METHODS / Resolution: 2.3 Å
AuthorsMenetrey, J. / Llinas, P. / Cicolari, J. / Squires, G. / Liu, X. / Li, A. / Sweeney, H.L. / Houdusse, A.
CitationJournal: Embo J. / Year: 2008
Title: The Post-Rigor Structure of Myosin Vi and Implications for the Recovery Stroke.
Authors: Menetrey, J. / Llinas, P. / Cicolari, J. / Squires, G. / Liu, X. / Li, A. / Sweeney, H.L. / Houdusse, A.
History
DepositionSep 6, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_asym_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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_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.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: MYOSIN VI
B: CALMODULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,4199
Polymers106,7412
Non-polymers6787
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-32.9 kcal/mol
Surface area47740 Å2
MethodPQS
Unit cell
Length a, b, c (Å)73.310, 107.590, 178.300
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 MYOSIN VI / UNCONVENTIONAL MYOSIN VI


Mass: 89899.477 Da / Num. of mol.: 1
Fragment: MOTOR DOMAIN-INSERT2,RESIDUES 2-277,304-377,379-816
Source method: isolated from a genetically manipulated source
Details: INSERT1 DELETION (C278-A303) / Source: (gene. exp.) SUS SCROFA (pig) / Plasmid: SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q29122
#2: Protein CALMODULIN


Mass: 16841.520 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GALLUS GALLUS (chicken) / Plasmid: SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P62149

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Non-polymers , 5 types, 244 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-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 237 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.45 Å3/Da / Density % sol: 54.9 % / Description: NONE
Crystal growDetails: 10% PEG 8000, 50MM GLYCINE PH 9.5, 6% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 1.008
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 18, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 2.3→46.18 Å / Num. obs: 62924 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 8 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 21.1
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 5.8 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: DIRECT METHODS
Starting model: NONE

Resolution: 2.3→46.18 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.9 / SU B: 5.696 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.238 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.253 3215 5.1 %RANDOM
Rwork0.21 ---
obs0.212 59653 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.36 Å2
Baniso -1Baniso -2Baniso -3
1--0.87 Å20 Å20 Å2
2--1.44 Å20 Å2
3----0.57 Å2
Refinement stepCycle: LAST / Resolution: 2.3→46.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6998 0 36 237 7271
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0227091
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3341.969547
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6755862
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.61424.423355
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.048151264
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9751543
X-RAY DIFFRACTIONr_chiral_restr0.1440.21033
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025368
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1950.23264
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.24865
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2339
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.170.235
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1550.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6861.54443
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.11426904
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.54632965
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.4954.52643
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: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.307 224
Rwork0.234 4318

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