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- PDB-3pzd: Structure of the myosin X MyTH4-FERM/DCC complex -

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Basic information

Entry
Database: PDB / ID: 3pzd
TitleStructure of the myosin X MyTH4-FERM/DCC complex
Components
  • Myosin-X
  • Netrin receptor DCC
KeywordsMOTOR PROTEIN/APOPTOSIS / protein-protein complex / MyTH4 domain / FERM domain / Cargo Binding / MOTOR PROTEIN-APOPTOSIS complex
Function / homology
Function and homology information


Caspase activation via Dependence Receptors in the absence of ligand / Netrin-1 signaling / DCC mediated attractive signaling / plus-end directed microfilament motor activity / netrin receptor activity / dorsal/ventral axon guidance / spinal cord ventral commissure morphogenesis / anterior/posterior axon guidance / Netrin-1 signaling / growth cone membrane ...Caspase activation via Dependence Receptors in the absence of ligand / Netrin-1 signaling / DCC mediated attractive signaling / plus-end directed microfilament motor activity / netrin receptor activity / dorsal/ventral axon guidance / spinal cord ventral commissure morphogenesis / anterior/posterior axon guidance / Netrin-1 signaling / growth cone membrane / positive regulation of cell-cell adhesion / filopodium tip / cytoskeleton-dependent intracellular transport / regulation of filopodium assembly / filopodium membrane / myosin complex / microfilament motor activity / spectrin binding / postsynaptic modulation of chemical synaptic transmission / phosphatidylinositol-3,4,5-trisphosphate binding / axonal growth cone / ruffle / filopodium / axon guidance / FCGR3A-mediated phagocytosis / neuron migration / postsynaptic density membrane / Schaffer collateral - CA1 synapse / Regulation of actin dynamics for phagocytic cup formation / positive regulation of neuron projection development / cell-cell adhesion / actin filament binding / lamellipodium / regulation of cell shape / cell cortex / transcription coactivator activity / positive regulation of ERK1 and ERK2 cascade / calmodulin binding / neuron projection / axon / neuronal cell body / nucleolus / apoptotic process / cell surface / signal transduction / ATP binding / identical protein 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 / Immunoglobulin domain / FERM central domain / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site / FERM/acyl-CoA-binding protein superfamily / 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) / PH-domain like / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Immunoglobulin I-set / Kinesin motor domain superfamily / PH domain / Immunoglobulin I-set domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / PH domain profile. / Pleckstrin homology domain. / Fibronectin type III domain / Pleckstrin homology 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)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 2.5 Å
AuthorsWei, Z. / Yan, J. / Pan, L. / Zhang, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Cargo recognition mechanism of myosin X revealed by the structure of its tail MyTH4-FERM tandem in complex with the DCC P3 domain
Authors: Wei, Z. / Yan, J. / Lu, Q. / Pan, L. / Zhang, M.
History
DepositionDec 14, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 4, 2013Group: Database references
Revision 1.3Mar 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-X
B: Netrin receptor DCC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,7013
Polymers62,6092
Non-polymers921
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-16 kcal/mol
Surface area27720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.167, 49.528, 92.814
Angle α, β, γ (deg.)90.000, 112.580, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 58671.219 Da / Num. of mol.: 1 / Fragment: MyTH4-FERM tandem
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIAA0799, MYO10 / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HD67
#2: Protein/peptide Netrin receptor DCC / Tumor suppressor protein DCC


Mass: 3937.300 Da / Num. of mol.: 1 / Fragment: P3 motif
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dcc / Production host: Escherichia coli (E. coli) / References: UniProt: P70211
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.89 Å3/Da / Density % sol: 57.39 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 8% PEG 8000, 10% glycerol, HEPES buffer, pH 7.5, vapor diffusion, hanging drop, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jan 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionRedundancy: 10.6 % / Av σ(I) over netI: 6.9 / Number: 153693 / Rmerge(I) obs: 0.108 / Rsym value: 0.108 / D res high: 3 Å / D res low: 82.479 Å / Num. obs: 14470 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
9.4949.6999.610.0380.0389.6
6.719.4910010.0460.04610.6
5.486.7110010.0820.08210.7
4.745.4810010.070.0710.8
4.244.7410010.070.0710.8
3.874.2410010.0960.09610.8
3.593.8710010.1330.13310.8
3.353.5910010.1830.18310.7
3.163.3510010.2960.29610.6
33.1610010.4470.44710.3
ReflectionResolution: 2.5→29.58 Å / Num. all: 24981 / Num. obs: 24981 / % possible obs: 99.5 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 16.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.5-2.643.70.5470.4682.71321435890.2810.5470.4682.799.1
2.64-2.83.70.390.3343.81250233900.20.390.3343.899.1
2.8-2.993.70.2610.2245.91188532170.1340.2610.2245.999.5
2.99-3.233.70.1730.14891103229940.0890.1730.148999.7
3.23-3.543.70.1030.08815.61042528100.0530.1030.08815.699.7
3.54-3.953.70.0690.05923.7921525010.0360.0690.05923.799.9
3.95-4.563.70.0490.04232.7825422440.0250.0490.04232.7100
4.56-5.593.70.0430.03737.6697619050.0220.0430.03737.6100
5.59-7.913.60.0390.03339.2541214930.020.0390.03339.2100
7.91-29.5793.40.0320.02752.728168380.0180.0320.02752.797.6

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Phasing

PhasingMethod: SIRAS

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
SHARPphasing
RESOLVEphasing
REFMAC5.5.0072refinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
RefinementMethod to determine structure: SIRAS / Resolution: 2.5→29.58 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.917 / Occupancy max: 1 / Occupancy min: 1 / SU B: 19.778 / SU ML: 0.202 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.282 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.2589 1243 5 %RANDOM
Rwork0.2028 ---
obs0.2056 23737 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 134.66 Å2 / Biso mean: 50.5504 Å2 / Biso min: 4.83 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20 Å21.09 Å2
2--0.69 Å2-0 Å2
3----0.23 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4220 0 6 101 4327
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0224319
X-RAY DIFFRACTIONr_angle_refined_deg1.1451.9695849
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6255530
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.71424.56193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.66815750
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7721519
X-RAY DIFFRACTIONr_chiral_restr0.0750.2653
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213239
X-RAY DIFFRACTIONr_mcbond_it1.45622666
X-RAY DIFFRACTIONr_mcangle_it2.55234294
X-RAY DIFFRACTIONr_scbond_it4.01741653
X-RAY DIFFRACTIONr_scangle_it5.87261555
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 121 -
Rwork0.264 1694 -
all-1815 -
obs--98.69 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.3376-0.51450.26613.42580.33661.9144-0.07290.06760.1283-0.26810.03360.1248-0.10530.0090.03930.067-0.0048-0.02210.00860.00390.01062.92240.199713.4541
27.17631.60052.34071.43161.75383.5511-0.1910.38730.2002-0.06220.1695-0.1386-0.25380.38070.02140.1254-0.03390.03690.1933-0.03210.10734.04844.724717.3242
35.2404-0.1729-2.58831.12610.79794.93490.43330.05290.64590.073-0.1098-0.1168-0.6564-0.1139-0.32340.1340.02750.01470.1462-0.00530.141458.582113.565315.1523
45.1364-0.438-1.26876.48480.82375.79880.4062-0.20021.04850.1962-0.00840.0346-1.1786-0.3321-0.39790.42620.00250.13920.3676-0.15450.343240.82221.898434.4471
53.84011.71135.2761.81640.78429.73330.438-0.082-0.56020.09970.1027-0.30420.6193-0.4536-0.54080.4472-0.05390.040.5376-0.16950.354341.659713.408447.7273
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1501 - 1696
2X-RAY DIFFRACTION2A1697 - 1789
3X-RAY DIFFRACTION3A1790 - 1952
4X-RAY DIFFRACTION4A1953 - 2047
5X-RAY DIFFRACTION5B1407 - 1443

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