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- PDB-3h8d: Crystal structure of Myosin VI in complex with Dab2 peptide -

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Basic information

Entry
Database: PDB / ID: 3h8d
TitleCrystal structure of Myosin VI in complex with Dab2 peptide
Components
  • Disabled homolog 2
  • Myosin-VI
KeywordsMOTOR PROTEIN/SIGNALING PROTEIN / Myosin VI / Myosin 6 / Dab2 / Cargo binding / Protein-peptide complex / Actin-binding / ATP-binding / Calmodulin-binding / Cell projection / Coated pit / Coiled coil / Cytoplasm / Cytoplasmic vesicle / Deafness / Disease mutation / Endocytosis / Golgi apparatus / Hearing / Membrane / Motor protein / Myosin / Nucleotide-binding / Nucleus / Phosphoprotein / Protein transport / Transport / Alternative splicing / MOTOR PROTEIN-SIGNALING PROTEIN COMPLEX
Function / homology
Function and homology information


: / leading edge cell differentiation / RHOBTB1 GTPase cycle / positive regulation of aldosterone biosynthetic process / positive regulation of aldosterone secretion / presynaptic endocytic zone / RHOU GTPase cycle / RHOBTB2 GTPase cycle / pinocytosis / Gap junction degradation ...: / leading edge cell differentiation / RHOBTB1 GTPase cycle / positive regulation of aldosterone biosynthetic process / positive regulation of aldosterone secretion / presynaptic endocytic zone / RHOU GTPase cycle / RHOBTB2 GTPase cycle / pinocytosis / Gap junction degradation / regulation of secretion / Gap junction degradation / Formation of annular gap junctions / positive regulation of clathrin-dependent endocytosis / endoderm development / positive regulation of Wnt signaling pathway, planar cell polarity pathway / cochlear hair cell ribbon synapse / positive regulation of early endosome to late endosome transport / cellular response to electrical stimulus / renal protein absorption / positive regulation of integrin-mediated signaling pathway / AP-2 adaptor complex binding / Trafficking of AMPA receptors / clathrin coat of coated pit / inner ear auditory receptor cell differentiation / postsynaptic neurotransmitter receptor internalization / Cargo recognition for clathrin-mediated endocytosis / myeloid cell differentiation / clathrin coat assembly / Clathrin-mediated endocytosis / actin filament-based movement / clathrin-coated vesicle membrane / response to salt / clathrin-cargo adaptor activity / negative regulation of androgen receptor signaling pathway / glutamate secretion / postsynaptic actin cytoskeleton / inner ear morphogenesis / response to steroid hormone / hematopoietic stem cell proliferation / vesicle membrane / clathrin-coated vesicle / myosin complex / cargo receptor activity / low-density lipoprotein particle receptor binding / clathrin binding / inner ear development / microfilament motor activity / dendrite development / SMAD binding / filamentous actin / microvillus / positive regulation of receptor recycling / positive regulation of SMAD protein signal transduction / brush border / positive regulation of receptor internalization / cellular response to transforming growth factor beta stimulus / protein targeting / positive regulation of endocytosis / endocytic vesicle / negative regulation of protein localization to plasma membrane / positive regulation of epithelial to mesenchymal transition / ruffle / positive regulation of substrate adhesion-dependent cell spreading / transforming growth factor beta receptor signaling pathway / phosphatidylinositol-4,5-bisphosphate binding / presynaptic modulation of chemical synaptic transmission / clathrin-coated pit / synapse assembly / sensory perception of sound / positive regulation of cell adhesion / phosphatidylinositol binding / receptor-mediated endocytosis / cellular response to epidermal growth factor stimulus / negative regulation of extrinsic apoptotic signaling pathway / actin filament organization / DNA damage response, signal transduction by p53 class mediator / locomotory behavior / filopodium / positive regulation of transcription elongation by RNA polymerase II / negative regulation of canonical Wnt signaling pathway / negative regulation of ERK1 and ERK2 cascade / cell morphogenesis / negative regulation of cell growth / regulation of synaptic plasticity / negative regulation of epithelial cell proliferation / positive regulation of JNK cascade / integrin binding / Wnt signaling pathway / Schaffer collateral - CA1 synapse / ruffle membrane / endocytosis / in utero embryonic development / apical part of cell / intracellular protein localization / actin filament binding / actin cytoskeleton / negative regulation of neuron projection development / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / protein transport
Similarity search - Function
: / : / Disabled homolog 2-like, sulfatide-binding motifs / Myosin VI, cargo binding domain / Class VI myosin, motor domain / : / Myosin VI cargo binding domain / Myosin VI, lever arm / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. ...: / : / Disabled homolog 2-like, sulfatide-binding motifs / Myosin VI, cargo binding domain / Class VI myosin, motor domain / : / Myosin VI cargo binding domain / Myosin VI, lever arm / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / 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 / PH-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
2,3-DIHYDROXY-1,4-DITHIOBUTANE / THIOCYANATE ION / Disabled homolog 2 / Unconventional myosin-VI
Similarity search - Component
Biological speciesMus musculus (house mouse)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SIRAS / MAD / Resolution: 2.2 Å
AuthorsYu, C. / Feng, W. / Wei, Z. / Zhang, M.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2009
Title: Myosin VI undergoes cargo-mediated dimerization
Authors: Yu, C. / Feng, W. / Wei, Z. / Miyanoiri, Y. / Wen, W. / Zhao, Y. / Zhang, M.
History
DepositionApr 29, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_ref_seq_dif.details / _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: Myosin-VI
C: Myosin-VI
D: Myosin-VI
E: Disabled homolog 2
F: Disabled homolog 2
G: Disabled homolog 2
H: Disabled homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,99213
Polymers85,6288
Non-polymers3645
Water4,792266
1
A: Myosin-VI
B: Myosin-VI
E: Disabled homolog 2
F: Disabled homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9306
Polymers42,8144
Non-polymers1162
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6780 Å2
ΔGint-35 kcal/mol
Surface area15710 Å2
MethodPISA
2
C: Myosin-VI
D: Myosin-VI
G: Disabled homolog 2
H: Disabled homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0627
Polymers42,8144
Non-polymers2483
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7140 Å2
ΔGint-45 kcal/mol
Surface area17000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.177, 69.952, 78.537
Angle α, β, γ (deg.)90.000, 98.020, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Protein/peptide , 2 types, 8 molecules ABCDEFGH

#1: Protein
Myosin-VI


Mass: 16412.789 Da / Num. of mol.: 4
Fragment: Myosin VI Cargo Binding Domain, residues 1137-1265
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Myo6, Sv / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q64331
#2: Protein/peptide
Disabled homolog 2 / DOC-2 / Mitogen-responsive phosphoprotein / C9


Mass: 4994.147 Da / Num. of mol.: 4 / Fragment: Dab2's Myosin VI binding motif, residues 675-713
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Dab2, Doc2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O88797

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Non-polymers , 4 types, 271 molecules

#3: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CNS
#4: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / 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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.244.03
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2891vapor diffusion, hanging drop720% PEG3350, 0.2M potassium thiocyanate for Myosin VI and 20% PEG3350, 0.2M sodium iodide for Dab2, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
2892vapor diffusion, hanging drop720% PEG3350, 0.2M sodium iodide, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 6, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→77.85 Å / Num. obs: 36631 / % possible obs: 97 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 8.893 / Num. measured all: 135314
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.2-2.323.60.5481.41894852170.54895.3
2.32-2.463.70.39321845549940.39395.9
2.46-2.633.70.2992.61748746920.29996.5
2.63-2.843.70.1973.91639443980.19797
2.84-3.113.70.1276.11523440920.12797.4
3.11-3.483.70.07410.41383937160.07497.8
3.48-4.023.70.04516.71225732930.04598.2
4.02-4.923.70.03241039228130.0398.5
4.92-6.963.70.03421803621980.03498.9
6.96-34.993.50.02619.8427212180.02698

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
SHARPphasing
RESOLVEphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
CrystalCleardata collection
RefinementMethod to determine structure: SIRAS / Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.916 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 5.701 / SU ML: 0.147 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.272 / ESU R Free: 0.223 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.251 1833 5 %RANDOM
Rwork0.189 ---
obs0.192 36631 96.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 82.48 Å2 / Biso mean: 31.984 Å2 / Biso min: 6.59 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å20 Å2-0.11 Å2
2--0.73 Å20 Å2
3----0.44 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5087 0 18 266 5371
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0225235
X-RAY DIFFRACTIONr_angle_refined_deg1.0921.9457068
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4015616
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.5424.184294
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.9715911
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4881544
X-RAY DIFFRACTIONr_chiral_restr0.0750.2703
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024136
X-RAY DIFFRACTIONr_nbd_refined0.1930.22233
X-RAY DIFFRACTIONr_nbtor_refined0.2970.23455
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2329
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1480.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1690.211
X-RAY DIFFRACTIONr_mcbond_it1.63223090
X-RAY DIFFRACTIONr_mcangle_it2.86334963
X-RAY DIFFRACTIONr_scbond_it3.98342145
X-RAY DIFFRACTIONr_scangle_it5.83362100
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 146 -
Rwork0.25 2480 -
all-2626 -
obs--94.8 %

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