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- PDB-3l9i: Myosin VI nucleotide-free (mdinsert2) L310G mutant crystal structure -

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Basic information

Entry
Database: PDB / ID: 3l9i
TitleMyosin VI nucleotide-free (mdinsert2) L310G mutant crystal structure
Components
  • Calmodulin
  • Myosin-VI
KeywordsMOTOR PROTEIN / myosin VI / unconventional myosin / directionality / motility / gating / Actin-binding / ATP-binding / Calmodulin-binding / Endocytosis / Golgi apparatus / Hearing / Membrane / Myosin / Nucleotide-binding / Nucleus / Phosphoprotein / Protein transport / Transport
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 / photoreceptor cell axon guidance / negative regulation of opsin-mediated signaling pathway / rhabdomere development / rhabdomere / detection of chemical stimulus involved in sensory perception of smell / regulation of secretion ...negative regulation of phospholipase C-activating phototransduction signaling pathway / myosin VI complex / myosin VI head/neck binding / myosin VII complex / photoreceptor cell axon guidance / negative regulation of opsin-mediated signaling pathway / rhabdomere development / rhabdomere / detection of chemical stimulus involved in sensory perception of smell / regulation of secretion / myosin V complex / kinetochore organization / autophagic cell death / G protein-coupled opsin signaling pathway / inner ear auditory receptor cell differentiation / actin filament-based movement / myosin V binding / channel regulator activity / myosin complex / clathrin-coated vesicle / inner ear morphogenesis / myosin heavy chain binding / muscle cell cellular homeostasis / microfilament motor activity / mitotic spindle pole / filamentous actin / microvillus / centriole replication / cellular response to ethanol / cytoskeletal motor activity / enzyme regulator activity / ruffle / centriole / actin filament organization / filopodium / actin filament / DNA damage response, signal transduction by p53 class mediator / intracellular protein transport / sensory perception of sound / ADP binding / microtubule cytoskeleton organization / ruffle membrane / spindle / endocytosis / actin filament binding / mitotic spindle / sensory perception of smell / intracellular protein localization / actin cytoskeleton / cytoplasmic vesicle / midbody / cell cortex / nuclear membrane / calmodulin binding / calcium ion binding / centrosome / perinuclear region of cytoplasm / Golgi apparatus / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
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 motor domain profile. / 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 motor domain profile. / Myosin head, motor domain / Myosin head (motor domain) / Myosin. Large ATPases. / Kinesin motor domain superfamily / : / 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
Similarity search - Domain/homology
ACETATE ION / PHOSPHATE ION / TERTIARY-BUTYL ALCOHOL / Calmodulin / Unconventional myosin-VI
Similarity search - Component
Biological speciesSus scrofa (pig)
Drosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsPylypenko, O. / Song, L. / Sweeney, L.H. / Houdusse, A.
CitationJournal: To be Published
Title: Role of insert i of myosin VI in modulating nucleotide affinity
Authors: Pylypenko, O. / Song, L. / Squires, G. / Liu, X. / Zong, A.B. / Houdusse, A. / Sweeney, L.H.
History
DepositionJan 5, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Myosin-VI
C: Calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,53513
Polymers109,8022
Non-polymers73211
Water14,934829
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-37 kcal/mol
Surface area42260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.540, 104.400, 90.330
Angle α, β, γ (deg.)90.00, 91.09, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules AC

#1: Protein Myosin-VI / Unconventional myosin VI


Mass: 92976.969 Da / Num. of mol.: 1 / Fragment: MOTOR DOMAIN-INSERT2, RESIDUES 2-816 / Mutation: L310G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: MYO6 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q29122
#2: Protein Calmodulin / CaM


Mass: 16825.520 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Cam, CG8472 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P62152

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Non-polymers , 5 types, 840 molecules

#3: Chemical ChemComp-TBU / TERTIARY-BUTYL ALCOHOL / 2-METHYL-2-PROPANOL


Mass: 74.122 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#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.: 829 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.94 Å3/Da / Density % sol: 58.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 4% PEG 8000, 50mM Glycine pH9, 3% iso-propanol, 3% tert-butanol, 1mM TCEP , VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.1271 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 30, 2008
RadiationMonochromator: Kirkpatrick-Baez pair of bi-morph mirrors plus channel cut cryogenically cooled monochromator crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1271 Å / Relative weight: 1
ReflectionResolution: 2.2→19.97 Å / Num. all: 64550 / Num. obs: 64176 / % possible obs: 99.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 41.5 Å2 / Rsym value: 0.061 / Net I/σ(I): 14.25
Reflection shellResolution: 2.2→2.25 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 3.77 / Num. unique all: 4157 / Rsym value: 0.38 / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0088refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BKH

2bkh


Resolution: 2.2→19.97 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.923 / SU B: 5.744 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.234 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23471 3209 5 %RANDOM
Rwork0.18463 ---
all0.18711 60958 --
obs0.18711 60958 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 40.942 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7482 0 37 829 8348
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0227936
X-RAY DIFFRACTIONr_bond_other_d0.0010.025497
X-RAY DIFFRACTIONr_angle_refined_deg1.3591.96310719
X-RAY DIFFRACTIONr_angle_other_deg0.898313443
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.85451011
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.43324.591403
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.553151478
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7261551
X-RAY DIFFRACTIONr_chiral_restr0.0820.21172
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028864
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021619
X-RAY DIFFRACTIONr_mcbond_it0.7851.54797
X-RAY DIFFRACTIONr_mcbond_other0.1621.51943
X-RAY DIFFRACTIONr_mcangle_it1.4627732
X-RAY DIFFRACTIONr_scbond_it2.06633139
X-RAY DIFFRACTIONr_scangle_it3.3734.52946
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 233 -
Rwork0.218 4426 -
obs--100 %

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