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- PDB-6j56: Crystal structure of Myosin VI CBD in complex with Tom1 MBM -

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Basic information

Entry
Database: PDB / ID: 6j56
TitleCrystal structure of Myosin VI CBD in complex with Tom1 MBM
Components
  • Peptide from Target of Myb protein 1
  • Unconventional myosin-VI
KeywordsPROTEIN BINDING / Myosin VI / Tom1 / complex / autophagy
Function / homology
Function and homology information


myosin VI binding / substrate localization to autophagosome / regulation of endosome organization / regulation of secretion / minus-end directed microfilament motor activity / unconventional myosin complex / clathrin heavy chain binding / phosphatidylinositol-5-phosphate binding / autophagosome-lysosome fusion / inner ear auditory receptor cell differentiation ...myosin VI binding / substrate localization to autophagosome / regulation of endosome organization / regulation of secretion / minus-end directed microfilament motor activity / unconventional myosin complex / clathrin heavy chain binding / phosphatidylinositol-5-phosphate binding / autophagosome-lysosome fusion / inner ear auditory receptor cell differentiation / actin filament-based movement / clathrin-coated vesicle membrane / Gap junction degradation / Trafficking of AMPA receptors / positive regulation of autophagosome maturation / RHOBTB1 GTPase cycle / endosomal transport / azurophil granule membrane / inner ear morphogenesis / clathrin binding / microfilament motor activity / filamentous actin / microvillus / RHOU GTPase cycle / cytoskeletal motor activity / polyubiquitin modification-dependent protein binding / endocytic vesicle / RHOBTB2 GTPase cycle / specific granule membrane / ruffle / clathrin-coated pit / autophagosome / actin filament organization / ubiquitin binding / actin filament / filopodium / DNA damage response, signal transduction by p53 class mediator / intracellular protein transport / sensory perception of sound / ADP binding / ruffle membrane / endocytosis / apical part of cell / actin filament binding / intracellular protein localization / protein transport / actin cytoskeleton / actin binding / cytoplasmic vesicle / early endosome membrane / cell cortex / nuclear membrane / early endosome / calmodulin binding / endosome / endosome membrane / response to xenobiotic stimulus / lysosomal membrane / Neutrophil degranulation / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / extracellular exosome / nucleoplasm / ATP binding / identical protein binding / nucleus / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Target of Myb protein 1 / GAT domain / GAT domain superfamily / GAT domain / GAT domain profile. / Myosin VI, cargo binding domain / Class VI myosin, motor domain / : / Myosin VI cargo binding domain / Myosin VI, lever arm ...Target of Myb protein 1 / GAT domain / GAT domain superfamily / GAT domain / GAT domain profile. / Myosin VI, cargo binding domain / Class VI myosin, motor domain / : / Myosin VI cargo binding domain / Myosin VI, lever arm / VHS domain / VHS domain / VHS domain profile. / Domain present in VPS-27, Hrs and STAM / ENTH/VHS / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Target of Myb1 membrane trafficking protein / Unconventional myosin-VI
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.798 Å
AuthorsHu, S. / Pan, L.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31800646 China
National Natural Science Foundation of China21822705 China
CitationJournal: Nat Commun / Year: 2019
Title: Structure of Myosin VI/Tom1 complex reveals a cargo recognition mode of Myosin VI for tethering.
Authors: Hu, S. / Guo, Y. / Wang, Y. / Li, Y. / Fu, T. / Zhou, Z. / Wang, Y. / Liu, J. / Pan, L.
History
DepositionJan 10, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Unconventional myosin-VI
C: Peptide from Target of Myb protein 1
B: Unconventional myosin-VI
D: Peptide from Target of Myb protein 1


Theoretical massNumber of molelcules
Total (without water)36,6844
Polymers36,6844
Non-polymers00
Water4,486249
1
A: Unconventional myosin-VI
C: Peptide from Target of Myb protein 1


Theoretical massNumber of molelcules
Total (without water)18,3422
Polymers18,3422
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-10 kcal/mol
Surface area8960 Å2
MethodPISA
2
B: Unconventional myosin-VI
D: Peptide from Target of Myb protein 1


Theoretical massNumber of molelcules
Total (without water)18,3422
Polymers18,3422
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-11 kcal/mol
Surface area8110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.733, 74.875, 50.873
Angle α, β, γ (deg.)90.00, 106.34, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Unconventional myosin-VI / Unconventional myosin-6


Mass: 15370.664 Da / Num. of mol.: 2 / Fragment: CBD domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MYO6, KIAA0389
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9UM54
#2: Protein/peptide Peptide from Target of Myb protein 1


Mass: 2971.303 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TOM1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: O60784
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 2.03 Å3/Da / Density % sol: 39.39 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: PEG 4000, sodium acetate trihydrate, TRIS hydrochloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97774 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97774 Å / Relative weight: 1
ReflectionResolution: 1.798→50 Å / Num. obs: 26915 / % possible obs: 98.5 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 28.14
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 6.2 % / Num. unique obs: 1342 / CC1/2: 0.976 / Rpim(I) all: 0.149 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H8D

3h8d


Resolution: 1.798→37.438 Å / SU ML: 0.17 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 22.55
RfactorNum. reflection% reflection
Rfree0.2335 1252 4.97 %
Rwork0.1766 --
obs0.1794 25194 92.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.798→37.438 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2281 0 0 249 2530
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012331
X-RAY DIFFRACTIONf_angle_d1.1633126
X-RAY DIFFRACTIONf_dihedral_angle_d15.418910
X-RAY DIFFRACTIONf_chiral_restr0.061313
X-RAY DIFFRACTIONf_plane_restr0.005410
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7984-1.87040.26251080.1922064X-RAY DIFFRACTION72
1.8704-1.95550.29121350.22092255X-RAY DIFFRACTION79
1.9555-2.05860.21761380.17762603X-RAY DIFFRACTION90
2.0586-2.18760.21971390.17912847X-RAY DIFFRACTION99
2.1876-2.35650.28171380.19872837X-RAY DIFFRACTION99
2.3565-2.59350.22211600.17932822X-RAY DIFFRACTION98
2.5935-2.96870.23831340.18512873X-RAY DIFFRACTION99
2.9687-3.73970.22441450.16822857X-RAY DIFFRACTION98
3.7397-37.44560.2211550.15932784X-RAY DIFFRACTION95
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)
12.00074.6382-7.04155.8664-4.57537.3959-0.00260.55642.56730.08711.1237-0.9143-2.57850.2121-0.77181.6923-0.2841-0.00430.6943-0.01541.020765.398521.720671.8482
26.0937-3.3459-4.19453.90944.7376.88180.1512-0.12510.2390.2618-0.1249-0.1204-0.0072-0.1216-0.07740.1557-0.023-0.01030.06250.01160.086171.97429.333762.4413
33.3214-0.3951-0.88495.92830.56650.26940.05091.274-1.1343-0.5581-0.0382-0.20251.57830.83560.09280.51820.11040.04740.3826-0.180.381171.6482-7.938650.3053
43.45130.84191.06112.10431.44323.81010.0521-0.2429-0.26420.037-0.0345-0.01840.1789-0.07290.00440.1305-0.0043-0.00660.07020.02180.084964.90521.090363.4476
53.6988-0.0379-2.03974.4059-1.19082.9211-0.0309-0.18330.02320.0001-0.1098-0.398-0.06681.13940.15610.1085-0.01690.00010.26340.00450.137178.58996.048362.261
63.940.5753-0.8573.34410.19294.7255-0.0124-0.13770.22280.02530.05480.2129-0.226-0.5053-0.07630.10750.0369-0.01890.14050.00590.112656.97968.593162.7226
75.6525-0.01272.28086.8858-1.46094.14540.18660.15291.4613-0.1583-0.5320.091-1.2433-0.5908-0.19920.34380.09320.00450.1899-0.03760.278157.782316.269967.6016
82.51.0946-0.9247.01460.4445.72670.5569-0.0194-1.2650.3280.0615-1.03631.40281.2137-0.16980.51250.1964-0.07350.26210.01150.397672.1689-7.955263.7499
94.8177-1.8045-1.71762.4925-0.20013.97980.18530.4787-0.5532-0.6480.3736-0.22580.9106-0.0148-0.35170.4186-0.0704-0.05510.1019-0.04010.280655.4546-9.476648.676
104.8354-0.2291-0.38813.09123.09325.86820.0468-0.16580.3517-0.367-0.1232-0.1271-0.6019-0.1071-0.13970.16910.0414-0.02680.11340.00540.154777.86667.576295.1634
114.0315-0.6418-0.24911.66210.19142.7255-0.02280.3860.27410.0406-0.0208-0.0318-0.04930.02020.00460.10780.0134-0.00130.12630.01370.093973.34288.361288.5816
126.4289-0.50760.95391.4565-0.35783.43450.0139-0.1913-0.30910.14450.10230.05790.178-0.2075-0.16420.1437-0.0030.01670.06620.0020.089968.05261.048293.8432
135.2397-1.56530.61795.94941.46555.18520.24750.4824-0.3644-0.43740.09150.37990.3032-0.0942-0.31590.0996-0.069-0.04910.2396-0.01890.161462.779-1.821782.4014
142.8933-2.0916-0.6864.73960.19552.88520.49810.81231.2246-0.1305-0.1251-0.5653-0.3781-0.0387-0.40350.2395-0.01850.04760.19590.05690.340778.365817.78188.5528
157.9994-1.51852.11049.196-0.9866.1839-0.1361-0.78390.4230.98120.75110.2873-0.0759-0.17790.47770.47560.03910.10840.1842-0.0780.381961.763519.6612104.1423
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1158 through 1165 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1166 through 1174 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1175 through 1191 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1192 through 1230 )
5X-RAY DIFFRACTION5chain 'A' and (resid 1231 through 1245 )
6X-RAY DIFFRACTION6chain 'A' and (resid 1246 through 1274 )
7X-RAY DIFFRACTION7chain 'A' and (resid 1275 through 1282 )
8X-RAY DIFFRACTION8chain 'C' and (resid 437 through 457 )
9X-RAY DIFFRACTION9chain 'C' and (resid 458 through 463 )
10X-RAY DIFFRACTION10chain 'B' and (resid 1166 through 1191 )
11X-RAY DIFFRACTION11chain 'B' and (resid 1192 through 1238 )
12X-RAY DIFFRACTION12chain 'B' and (resid 1239 through 1267 )
13X-RAY DIFFRACTION13chain 'B' and (resid 1268 through 1282 )
14X-RAY DIFFRACTION14chain 'D' and (resid 437 through 457 )
15X-RAY DIFFRACTION15chain 'D' and (resid 458 through 463 )

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