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- PDB-5wst: Crystal structure of Myo7a SAH -

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Basic information

Entry
Database: PDB / ID: 5wst
TitleCrystal structure of Myo7a SAH
ComponentsUnconventional myosin-VIIa
KeywordsMOTOR PROTEIN / Molecular motor
Function / homology
Function and homology information


pigment granule localization / upper tip-link density / pigment granule transport / The canonical retinoid cycle in rods (twilight vision) / myosin VII complex / phagolysosome assembly / stereocilium base / inner ear receptor cell differentiation / equilibrioception / sensory perception of light stimulus ...pigment granule localization / upper tip-link density / pigment granule transport / The canonical retinoid cycle in rods (twilight vision) / myosin VII complex / phagolysosome assembly / stereocilium base / inner ear receptor cell differentiation / equilibrioception / sensory perception of light stimulus / mechanoreceptor differentiation / photoreceptor connecting cilium / inner ear receptor cell stereocilium organization / sensory organ development / actin filament-based movement / inner ear auditory receptor cell differentiation / sensory perception / stereocilium / cell projection organization / myosin complex / auditory receptor cell stereocilium organization / inner ear morphogenesis / spectrin binding / microfilament motor activity / cochlea development / lysosome organization / cytoskeletal motor activity / microvillus / inner ear development / photoreceptor outer segment / phagocytosis / visual perception / photoreceptor inner segment / actin filament organization / sensory perception of sound / intracellular protein transport / protein localization / ADP binding / endocytosis / actin filament binding / melanosome / actin cytoskeleton / actin binding / cell cortex / calmodulin binding / apical plasma membrane / protein domain specific binding / lysosomal membrane / synapse / protein-containing complex binding / ATP binding / identical protein binding / membrane / cytoplasm / cytosol
Similarity search - Function
Class VII myosin, motor domain / Myosin VII, FERM domain C-lobe, repeat 1 / Myosin VII, FERM domain C-lobe, repeat 2 / MyTH4 domain / MyTH4 domain superfamily / MyTH4 domain / MyTH4 domain profile. / Domain in Myosin and Kinesin Tails / IQ calmodulin-binding motif / FERM central domain ...Class VII myosin, motor domain / Myosin VII, FERM domain C-lobe, repeat 1 / Myosin VII, FERM domain C-lobe, repeat 2 / MyTH4 domain / MyTH4 domain superfamily / MyTH4 domain / MyTH4 domain profile. / Domain in Myosin and Kinesin Tails / IQ calmodulin-binding motif / FERM central domain / FERM/acyl-CoA-binding protein superfamily / 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 / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Kinesin motor domain superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily / Ubiquitin-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Unconventional myosin-VIIa
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsLi, J. / Chen, Y. / Deng, Y. / Lu, Q. / Zhang, M.
CitationJournal: Structure / Year: 2017
Title: Ca(2+)-Induced Rigidity Change of the Myosin VIIa IQ Motif-Single alpha Helix Lever Arm Extension
Authors: Li, J. / Chen, Y. / Deng, Y. / Unarta, I.C. / Lu, Q. / Huang, X. / Zhang, M.
History
DepositionDec 8, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Unconventional myosin-VIIa
B: Unconventional myosin-VIIa


Theoretical massNumber of molelcules
Total (without water)17,2382
Polymers17,2382
Non-polymers00
Water1267
1
A: Unconventional myosin-VIIa


Theoretical massNumber of molelcules
Total (without water)8,6191
Polymers8,6191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Unconventional myosin-VIIa


Theoretical massNumber of molelcules
Total (without water)8,6191
Polymers8,6191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.810, 42.610, 59.680
Angle α, β, γ (deg.)90.000, 90.070, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Unconventional myosin-VIIa


Mass: 8618.834 Da / Num. of mol.: 2 / Fragment: UNP residues 866-932
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Myo7a, Myo7 / Production host: Escherichia coli (E. coli) / References: UniProt: P97479
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.86 Å3/Da / Density % sol: 57.03 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 4.6
Details: 0.2M ammonium acetate, 0.1M sodium acetate (pH 4.6), 30%(w/v) PEG 4,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97928 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97928 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.46
ReflectionResolution: 2.1→50 Å / Num. obs: 11455 / % possible obs: 99 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 8.3
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.618 / Mean I/σ(I) obs: 2 / Rsym value: 0.618 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→32.554 Å / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.67
RfactorNum. reflection% reflection
Rfree0.2388 551 4.81 %
Rwork0.1945 --
obs0.201 11446 98.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 103.47 Å2 / Biso mean: 40.3804 Å2 / Biso min: 18.16 Å2
Refinement stepCycle: final / Resolution: 2.1→32.554 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1182 0 0 7 1189
Biso mean---36.81 -
Num. residues----141
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011195
X-RAY DIFFRACTIONf_angle_d1.0671568
X-RAY DIFFRACTIONf_chiral_restr0.037158
X-RAY DIFFRACTIONf_plane_restr0.004211
X-RAY DIFFRACTIONf_dihedral_angle_d19.141814
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1009-2.31190.29961310.27872724285595
2.3119-2.64550.28061290.25232705283495
2.6455-3.32940.23031410.20952708284994
3.3294-17.6950.22671470.15992731287893

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