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- PDB-1oe9: Crystal structure of Myosin V motor with essential light chain-nu... -

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Basic information

Entry
Database: PDB / ID: 1oe9
TitleCrystal structure of Myosin V motor with essential light chain-nucleotide-free
Components
  • MYOSIN LIGHT CHAIN 1, SLOW-TWITCH MUSCLE A ISOFORM
  • MYOSIN VA
KeywordsATPASE/MYOSIN / ATPASE-MYOSIN COMPLEX / UNCONVENTIONAL MYOSIN / MYOSIN V / CHICKEN / MOLECULAR MOTOR / ATPASE / ELC / IQ MOTIF / MUSCLE PROTEIN / ATP-BINDING
Function / homology
Function and homology information


minus-end directed microfilament motor activity / unconventional myosin complex / insulin-responsive compartment / muscle myosin complex / muscle filament sliding / myosin II complex / vesicle transport along actin filament / myosin complex / structural constituent of muscle / microfilament motor activity ...minus-end directed microfilament motor activity / unconventional myosin complex / insulin-responsive compartment / muscle myosin complex / muscle filament sliding / myosin II complex / vesicle transport along actin filament / myosin complex / structural constituent of muscle / microfilament motor activity / filamentous actin / cytoskeletal motor activity / Smooth Muscle Contraction / skeletal muscle tissue development / vesicle-mediated transport / muscle contraction / actin filament organization / protein localization to plasma membrane / cellular response to insulin stimulus / actin filament binding / actin cytoskeleton / vesicle / calmodulin binding / Golgi membrane / calcium ion binding / extracellular exosome / ATP binding / cytosol / cytoplasm
Similarity search - Function
Myosin 5a, cargo-binding domain / Class V myosin, motor domain / Dilute domain / DIL domain / Dilute domain profile. / DIL / IQ calmodulin-binding motif / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Short calmodulin-binding motif containing conserved Ile and Gln residues. ...Myosin 5a, cargo-binding domain / Class V myosin, motor domain / Dilute domain / DIL domain / Dilute domain profile. / DIL / IQ calmodulin-binding motif / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Short calmodulin-binding motif containing conserved Ile and Gln residues. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / IQ motif, EF-hand binding site / Kinesin motor domain superfamily / EF-hand / Recoverin; domain 1 / EF-hand, calcium binding motif / 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
Myosin light chain 6B / Unconventional myosin-Va
Similarity search - Component
Biological speciesGALLUS GALLUS (chicken)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsCoureux, P.-D. / Wells, A.L. / Menetrey, J. / Yengo, C.M. / Morris, C.A. / Sweeney, H.L. / Houdusse, A.
CitationJournal: Nature / Year: 2003
Title: A Structural State of the Myosin V Motor without Bound Nucleotide
Authors: Coureux, P.-D. / Wells, A.L. / Menetrey, J. / Yengo, C.M. / Morris, C.A. / Sweeney, H.L. / Houdusse, A.
History
DepositionMar 21, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 26, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MYOSIN VA
B: MYOSIN LIGHT CHAIN 1, SLOW-TWITCH MUSCLE A ISOFORM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,7943
Polymers108,6972
Non-polymers961
Water5,999333
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)53.933, 98.247, 111.378
Angle α, β, γ (deg.)90.00, 101.43, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein MYOSIN VA / MYOSIN 5A / DILUTE MYOSIN HEAVY CHAIN / NON-MUSCLE / MYOSIN HEAVY CHAIN P190 / MYOSIN-V


Mass: 91607.172 Da / Num. of mol.: 1 / Fragment: MOTOR DOMAIN, RESIDUES 1-792
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GALLUS GALLUS (chicken) / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q02440
#2: Protein MYOSIN LIGHT CHAIN 1, SLOW-TWITCH MUSCLE A ISOFORM / / MLC1SA


Mass: 17090.277 Da / Num. of mol.: 1 / Fragment: RESIDUES 59-208
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P14649
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 333 / Source method: isolated from a natural source / Formula: H2O
Compound detailsMYOSIN VA: PROCESSIVE ACTIN-BASED MOTOR THAT CAN MOVE IN LARGE STEPS. POSSIBLY INVOLVED IN ...MYOSIN VA: PROCESSIVE ACTIN-BASED MOTOR THAT CAN MOVE IN LARGE STEPS. POSSIBLY INVOLVED IN MELANOSOME TRANSPORT. USUALLYASSOCIATED WITH MYOSIN LIGHT-CHAINS. MYOSIN LIGHT-CHAIN: THIS PROTEIN IS SIMILAR TO OTHER EF-HAND CALCIUM-BINDING PROTEINS BUT DOES NOT BIND CALCIUM.
Sequence detailsTHE LAST THREE RESIDUES AT THE C-TERMINUS FOR CHAIN A DERIVE FROM THE EXPRESSION VECTOR USED IN THE ...THE LAST THREE RESIDUES AT THE C-TERMINUS FOR CHAIN A DERIVE FROM THE EXPRESSION VECTOR USED IN THE EXPERIMENT.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 47.8 %
Crystal growpH: 6.5
Details: 6% PEG8000 (W/V), 50MM MOPS PH 6.5, 2MM DTT, 2MM NAN3
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
16 %PEG80001reservoir
250 mMMOPS1reservoirpH6.5
32 mMdithiothreitol1reservoir
42 mM1reservoirNaN3
58 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9756
DetectorDate: Nov 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9756 Å / Relative weight: 1
ReflectionResolution: 2.05→40 Å / Num. obs: 69115 / % possible obs: 96.8 % / Observed criterion σ(I): 3 / Redundancy: 2.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 14
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 2 % / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 2.34 / % possible all: 88.4
Reflection
*PLUS
Highest resolution: 2 Å / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
% possible obs: 88.4 % / Rmerge(I) obs: 0.335

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2MYS

2mys


Resolution: 2.05→40 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.912 / SU B: 4.969 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.206 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.DISORDERED REGIONS WERE NOT MODELED.DISORDERED SIDE-CHAINS WERE NOT MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.264 3474 5 %RANDOM
Rwork0.22 ---
obs0.222 65624 96.8 %-
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: 39.16 Å2
Baniso -1Baniso -2Baniso -3
1-1.12 Å20 Å20.22 Å2
2---0.91 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 2.05→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6919 0 5 333 7257
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0227077
X-RAY DIFFRACTIONr_bond_other_d0.0020.026387
X-RAY DIFFRACTIONr_angle_refined_deg1.31.959557
X-RAY DIFFRACTIONr_angle_other_deg0.791314860
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3885860
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_restr0.080.21049
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027832
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021470
X-RAY DIFFRACTIONr_nbd_refined0.2030.21626
X-RAY DIFFRACTIONr_nbd_other0.2370.27596
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0850.24141
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.2370
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1350.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2560.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1810.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8231.54327
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.50926928
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.06732750
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.4164.52624
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: 2.05→2.1 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.324 218
Rwork0.282 4338
Refinement
*PLUS
Highest resolution: 2 Å / Rfactor Rfree: 0.263 / Rfactor Rwork: 0.219
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.014
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.296

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