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- PDB-1w7i: Crystal Structure Of Myosin V Motor Without nucleotide soaked in ... -

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Basic information

Entry
Database: PDB / ID: 1w7i
TitleCrystal Structure Of Myosin V Motor Without nucleotide soaked in 10 mM MgADP
Components
  • MYOSIN LIGHT CHAIN 1, SLOW-TWITCH MUSCLE A ISOFORM
  • MYOSIN VA
KeywordsMOTOR PROTEIN / UNCONVENTIONAL MYOSIN / MYOSIN V / CHICKEN / MOLECULAR MOTOR / ATPASE / ELC / IQ MOTIF / MUSCLE PROTEIN / MGADP
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
ADENOSINE-5'-DIPHOSPHATE / Myosin light chain 6B / Unconventional myosin-Va
Similarity search - Component
Biological speciesGALLUS GALLUS (chicken)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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 3, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2005Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2015Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / 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 / _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 VA
B: MYOSIN LIGHT CHAIN 1, SLOW-TWITCH MUSCLE A ISOFORM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,1253
Polymers108,6972
Non-polymers4271
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)54.926, 99.253, 112.513
Angle α, β, γ (deg.)90.00, 101.78, 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
Details: SOAKED MGADP / 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-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / 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.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 56.7 %
Crystal growpH: 6.3
Details: 6% PEG 8000, 50 MM MOPS PH 6.5, 2 MM DTT AND 2 MM NAN3

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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: 3→111.8 Å / Num. obs: 21972 / % possible obs: 97.3 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 18.1
Reflection shellResolution: 3→3.07 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.284 / Mean I/σ(I) obs: 3.1 / % possible all: 88.3

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Processing

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

1oe9


Resolution: 3→111.8 Å / SU B: 21.824 / SU ML: 0.411 / ESU R Free: 0.55
RfactorNum. reflection% reflection
Rfree0.318 1176 5.1 %
Rwork0.248 --
obs0.252 21972 97.22 %
Displacement parametersBiso mean: 56.7 Å2
Baniso -1Baniso -2Baniso -3
1-2.56 Å20 Å21.23 Å2
2---1.71 Å20 Å2
3----0.35 Å2
Refinement stepCycle: LAST / Resolution: 3→111.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6872 0 27 11 6910

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