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- PDB-3gn4: Myosin lever arm -

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Basic information

Entry
Database: PDB / ID: 3gn4
TitleMyosin lever arm
Components
  • Calmodulin
  • Myosin-VI
KeywordsMOTOR PROTEIN / unconventional myosin / motility / lever arm / 3-helix bundle / Actin-binding / ATP-binding / Calmodulin-binding / Coiled coil / Cytoplasm / Endocytosis / Golgi apparatus / Hearing / Membrane / Myosin / Nucleotide-binding / Nucleus / Phosphoprotein / Protein transport / Transport / Acetylation / Calcium / MOTOR PROTEIN-METAL BINDING PROTEIN COMPLEX
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 / regulation of secretion / kinetochore organization / autophagic cell death / G protein-coupled opsin signaling pathway / actin filament-based movement / inner ear auditory receptor cell differentiation / myosin V binding / cellular response to ethanol / myosin complex / clathrin-coated vesicle / inner ear morphogenesis / microfilament motor activity / muscle cell cellular homeostasis / myosin heavy chain binding / mitotic spindle pole / channel regulator activity / filamentous actin / centriole replication / cytoskeletal motor activity / microvillus / DNA damage response, signal transduction by p53 class mediator / enzyme regulator activity / ruffle / centriole / filopodium / actin filament organization / actin filament / intracellular protein transport / sensory perception of sound / ADP binding / mitotic spindle / ruffle membrane / spindle / endocytosis / actin filament binding / sensory perception of smell / protein localization / actin cytoskeleton / cell cortex / midbody / cytoplasmic vesicle / nuclear membrane / calmodulin binding / centrosome / calcium ion binding / perinuclear region of cytoplasm / Golgi apparatus / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Helical scaffold and wing domains of SecA / Helical scaffold and wing domains of SecA - #10 / 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. ...Helical scaffold and wing domains of SecA / Helical scaffold and wing domains of SecA - #10 / 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 / Helix non-globular / EF-hand domain pair / EF-hand, calcium binding motif / Special / 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
Similarity search - Domain/homology
Calmodulin / Unconventional myosin-VI
Similarity search - Component
Biological speciesSus scrofa (pig)
Drosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMukherjea, M. / Llinas, P. / Kim, H. / Travaglia, M. / Safer, D. / Zong, A.B. / Menetrey, J. / Franzini-Armstrong, C. / Selvin, P.R. / Houdusse, A. / Sweeney, H.L.
CitationJournal: Mol.Cell / Year: 2009
Title: Myosin VI dimerization triggers an unfolding of a three-helix bundle in order to extend its reach
Authors: Mukherjea, M. / Llinas, P. / Kim, H. / Travaglia, M. / Safer, D. / Menetrey, J. / Franzini-Armstrong, C. / Selvin, P.R. / Houdusse, A. / Sweeney, H.L.
History
DepositionMar 16, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / pdbx_struct_conn_angle / struct_conn / struct_sheet / struct_site
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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 / _struct_sheet.number_strands / _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
D: Calmodulin
E: Myosin-VI
F: Calmodulin
H: Calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,51322
Polymers101,9986
Non-polymers51516
Water1,26170
1
A: Myosin-VI
B: Calmodulin
D: Calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,25711
Polymers50,9993
Non-polymers2588
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8250 Å2
ΔGint-145 kcal/mol
Surface area21220 Å2
MethodPISA
2
E: Myosin-VI
F: Calmodulin
H: Calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,25711
Polymers50,9993
Non-polymers2588
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7930 Å2
ΔGint-136 kcal/mol
Surface area20770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.790, 118.390, 182.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Myosin-VI / Unconventional myosin VI


Mass: 17347.979 Da / Num. of mol.: 2 / Fragment: sequence database residues 771-918
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: MYO6 / Plasmid: SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q29122
#2: Protein
Calmodulin / CaM


Mass: 16825.520 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Cam, CG8472 / Plasmid: SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P62152
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O

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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: 2.73 Å3/Da / Density % sol: 55.02 %
Crystal growTemperature: 277 K / pH: 8.5
Details: 16 % PEG 2K, 100 mM MgCl2, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9537
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 29, 2007
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.7→49.63 Å / Num. obs: 31647 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 7.2 % / Biso Wilson estimate: 55.75 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.077
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.447 / Mean I/σ(I) obs: 4.8 / Rsym value: 0.447 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2BKH

2bkh


Resolution: 2.7→45.515 Å / SU ML: 0.38 / σ(F): 1.55 / Phase error: 26.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2638 1603 5.07 %
Rwork0.2083 --
obs0.2111 31630 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.486 Å2 / ksol: 0.336 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.5399 Å20 Å2-0 Å2
2--19.7142 Å20 Å2
3----17.1743 Å2
Refinement stepCycle: LAST / Resolution: 2.7→45.515 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6261 0 16 70 6347
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066334
X-RAY DIFFRACTIONf_angle_d0.9618539
X-RAY DIFFRACTIONf_dihedral_angle_d17.0492299
X-RAY DIFFRACTIONf_chiral_restr0.063976
X-RAY DIFFRACTIONf_plane_restr0.0041129
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.78720.30171440.25472659X-RAY DIFFRACTION100
2.7872-2.88680.34511320.23562727X-RAY DIFFRACTION100
2.8868-3.00230.26071470.22022661X-RAY DIFFRACTION100
3.0023-3.1390.29161580.21662681X-RAY DIFFRACTION100
3.139-3.30440.30421280.22012711X-RAY DIFFRACTION100
3.3044-3.51140.3021550.21242697X-RAY DIFFRACTION100
3.5114-3.78230.24121620.19812697X-RAY DIFFRACTION100
3.7823-4.16270.23521440.17412730X-RAY DIFFRACTION100
4.1627-4.76460.23111760.16342735X-RAY DIFFRACTION100
4.7646-6.00070.25571240.19992788X-RAY DIFFRACTION100
6.0007-45.52140.23461330.21122941X-RAY DIFFRACTION100

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