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- PDB-1w8j: Crystal Structure Of Myosin V Motor Domain - Nucleotide-Free -

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Basic information

Entry
Database: PDB / ID: 1w8j
TitleCrystal Structure Of Myosin V Motor Domain - Nucleotide-Free
ComponentsMYOSIN VA
KeywordsMOTOR PROTEIN / UNCONVENTIONAL MYOSIN / MYOSIN V / CHICKEN / MOLECULAR MOTOR / ATPASE / ELC / IQ MOTIF / MUSCLE PROTEIN / ATP-BINDING MOTOR PROTEIN
Function / homology
Function and homology information


minus-end directed microfilament motor activity / insulin-responsive compartment / vesicle transport along actin filament / myosin complex / microfilament motor activity / filamentous actin / vesicle-mediated transport / actin filament organization / protein localization to plasma membrane / cellular response to insulin stimulus ...minus-end directed microfilament motor activity / insulin-responsive compartment / vesicle transport along actin filament / myosin complex / microfilament motor activity / filamentous actin / vesicle-mediated transport / actin filament organization / protein localization to plasma membrane / cellular response to insulin stimulus / actin filament binding / actin cytoskeleton / vesicle / calmodulin binding / Golgi membrane / ATP binding / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Unconventional myosin-Va
Similarity search - Component
Biological speciesGALLUS GALLUS (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsCoureux, P.-D. / Sweeney, H.L. / Houdusse, A.
CitationJournal: Embo J. / Year: 2004
Title: Three Myosin V Structures Delineate Essential Features of Chemo-Mechanical Transduction
Authors: Coureux, P.-D. / Sweeney, H.L. / Houdusse, A.
History
DepositionSep 22, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2005Provider: 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
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MYOSIN VA
B: MYOSIN VA
C: MYOSIN VA
D: MYOSIN VA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)352,4317
Polymers352,1434
Non-polymers2883
Water72140
1
A: MYOSIN VA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,1322
Polymers88,0361
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: MYOSIN VA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,1322
Polymers88,0361
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: MYOSIN VA


Theoretical massNumber of molelcules
Total (without water)88,0361
Polymers88,0361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: MYOSIN VA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,1322
Polymers88,0361
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)134.476, 162.308, 174.696
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 VA / MYOSIN 5A / MYOSIN-V / MYOSIN HEAVY CHAIN P190


Mass: 88035.711 Da / Num. of mol.: 4 / Fragment: MOTOR DOMAIN, RESIDUES 1-766
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: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.8 Å3/Da / Density % sol: 56.2 %
Crystal growpH: 6.3
Details: 10% PEG 8000, 50 MM MES PH 6.3, 100 MM AMMONIUM SULPHATE, 2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.7→40 Å / Num. obs: 99891 / % possible obs: 99.9 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 4.56
Reflection shellResolution: 2.7→2.84 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 3.8 / % possible all: 99.9

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OE9

1oe9


Resolution: 2.7→119.52 Å / SU B: 14.856 / SU ML: 0.303 / ESU R: 1.119 / ESU R Free: 0.404 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.3083 5308 5 %RANDOM
Rwork0.2547 ---
obs0.2574 99928 99.9 %-
Displacement parametersBiso mean: 46.669 Å2
Baniso -1Baniso -2Baniso -3
1-1.01 Å20 Å20 Å2
2--0.09 Å20 Å2
3----1.1 Å2
Refinement stepCycle: LAST / Resolution: 2.7→119.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22701 0 15 40 22756

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