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- PDB-3au4: Structure of the human myosin-X MyTH4-FERM cassette bound to its ... -

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Basic information

Entry
Database: PDB / ID: 3au4
TitleStructure of the human myosin-X MyTH4-FERM cassette bound to its specific cargo, DCC
Components
  • Myosin-X
  • Netrin receptor DCC
KeywordsMOTOR PROTEIN/APOPTOSIS / protein-protein complex / motor protein cargo transportation / MOTOR PROTEIN-APOPTOSIS complex
Function / homology
Function and homology information


plus-end directed microfilament motor activity / dorsal/ventral axon guidance / DSCAM interactions / spinal cord ventral commissure morphogenesis / anterior/posterior axon guidance / negative regulation of collateral sprouting / Role of second messengers in netrin-1 signaling / negative regulation of dendrite development / Netrin-1 signaling / Regulation of commissural axon pathfinding by SLIT and ROBO ...plus-end directed microfilament motor activity / dorsal/ventral axon guidance / DSCAM interactions / spinal cord ventral commissure morphogenesis / anterior/posterior axon guidance / negative regulation of collateral sprouting / Role of second messengers in netrin-1 signaling / negative regulation of dendrite development / Netrin-1 signaling / Regulation of commissural axon pathfinding by SLIT and ROBO / positive regulation of cell-cell adhesion / cytoskeleton-dependent intracellular transport / filopodium tip / regulation of filopodium assembly / Netrin mediated repulsion signals / Caspase activation via Dependence Receptors in the absence of ligand / filopodium membrane / DCC mediated attractive signaling / myosin complex / spectrin binding / microfilament motor activity / phosphatidylinositol-3,4,5-trisphosphate binding / postsynaptic modulation of chemical synaptic transmission / ruffle / axonogenesis / axon guidance / filopodium / FCGR3A-mediated phagocytosis / postsynaptic density membrane / Schaffer collateral - CA1 synapse / cell-cell adhesion / Regulation of actin dynamics for phagocytic cup formation / neuron migration / actin filament binding / transmembrane signaling receptor activity / lamellipodium / regulation of cell shape / negative regulation of neuron projection development / cell cortex / calmodulin binding / neuron projection / axon / neuronal cell body / apoptotic process / nucleolus / cell surface / signal transduction / ATP binding / plasma membrane / cytosol
Similarity search - Function
MyTH4 domain / Unconventional myosin-X, coiled coil domain / Class X myosin, motor domain / Myosin X, N-terminal SH3 domain / Myosin X, FERM domain C-lobe / Unconventional myosin-X coiled coil domain / Myosin X N-terminal SH3 domain / : / Neogenin, C-terminal / Neogenin C-terminus ...MyTH4 domain / Unconventional myosin-X, coiled coil domain / Class X myosin, motor domain / Myosin X, N-terminal SH3 domain / Myosin X, FERM domain C-lobe / Unconventional myosin-X coiled coil domain / Myosin X N-terminal SH3 domain / : / Neogenin, C-terminal / Neogenin C-terminus / MyTH4 domain / MyTH4 domain superfamily / MyTH4 domain / MyTH4 domain profile. / Domain in Myosin and Kinesin Tails / RA like domain / Acyl-CoA Binding Protein - #10 / Ras association (RalGDS/AF-6) domain / Acyl-CoA Binding Protein / Ras-associating (RA) domain / IQ calmodulin-binding motif / FERM central domain / FERM/acyl-CoA-binding protein superfamily / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / PH-domain like / PH domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Kinesin motor domain superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Ubiquitin-like (UB roll) / Alpha Horseshoe / Immunoglobulin subtype / Immunoglobulin / PH-like domain superfamily / Roll / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Roll / Immunoglobulin-like fold / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Netrin receptor DCC / Unconventional myosin-X
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsHirano, Y. / Hatano, T. / Hakoshima, T.
CitationJournal: Embo J. / Year: 2011
Title: Structural basis of cargo recognition by the myosin-X MyTH4-FERM domain
Authors: Hirano, Y. / Hatano, T. / Takahashi, A. / Toriyama, M. / Inagaki, N. / Hakoshima, T.
History
DepositionJan 28, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2014Group: Database references
Revision 1.2Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Myosin-X
B: Netrin receptor DCC


Theoretical massNumber of molelcules
Total (without water)70,1492
Polymers70,1492
Non-polymers00
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-16 kcal/mol
Surface area28500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.221, 49.564, 93.978
Angle α, β, γ (deg.)90.00, 116.71, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Myosin-X / Unconventional myosin-10


Mass: 63425.477 Da / Num. of mol.: 1 / Fragment: MyTH4-FERM cassette, UNP residues 1486-2058
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MYO10, KIAA0799 / Plasmid: pET47b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 star (DE3) / References: UniProt: Q9HD67
#2: Protein Netrin receptor DCC / Colorectal cancer suppressor / Immunoglobulin superfamily DCC subclass member 1 / Tumor suppressor protein DCC


Mass: 6723.331 Da / Num. of mol.: 1 / Fragment: P3 domain, UNP residues 1390-1447
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DCC, IGDCC1 / Plasmid: pET49b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 star (DE3) / References: UniProt: P43146
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUE SER1663THR IS NATURAL VARIANT ACCORDING TO DATABASE Q9HD67 (MYO10_HUMAN).

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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: 2.53 Å3/Da / Density % sol: 51.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100mM maric acid-MES-Tris (MMT) buffer, 2% PEG 1500, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Feb 18, 2010 / Details: mirrors
RadiationMonochromator: Rotated-inclined double-crystal monochromator , Si (111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 55849 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 24.5 Å2
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.574 / Mean I/σ(I) obs: 2.6 / % possible all: 99.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
SnBphasing
CNS1.3refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.9→34.06 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 156618.39 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.233 2685 5 %RANDOM
Rwork0.215 ---
obs0.215 53297 95.7 %-
all-53297 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.5739 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 39.7 Å2
Baniso -1Baniso -2Baniso -3
1--6.13 Å20 Å20.2 Å2
2--0.41 Å20 Å2
3---5.72 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.9→34.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4434 0 0 243 4677
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.471.5
X-RAY DIFFRACTIONc_mcangle_it2.312
X-RAY DIFFRACTIONc_scbond_it2.112
X-RAY DIFFRACTIONc_scangle_it3.192.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.299 396 4.9 %
Rwork0.269 7705 -
obs-7705 88.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top

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