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- PDB-5hmp: Myosin Vc pre-powerstroke state -

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Basic information

Entry
Database: PDB / ID: 5hmp
TitleMyosin Vc pre-powerstroke state
ComponentsUnconventional myosin-Vc
KeywordsMOTOR PROTEIN / motor domain / Myosin
Function / homology
Function and homology information


vesicle transport along actin filament / myosin complex / microfilament motor activity / actin filament organization / actin filament binding / actin cytoskeleton / vesicle / calmodulin binding / extracellular exosome / ATP binding ...vesicle transport along actin filament / myosin complex / microfilament motor activity / actin filament organization / actin filament binding / actin cytoskeleton / vesicle / calmodulin binding / extracellular exosome / ATP binding / membrane / cytoplasm
Similarity search - Function
Myosin 5c, cargo-binding domain / Class V myosin, motor domain / Dilute domain / DIL domain / Dilute domain profile. / DIL / IQ calmodulin-binding motif / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Short calmodulin-binding motif containing conserved Ile and Gln residues. ...Myosin 5c, cargo-binding domain / Class V myosin, motor domain / Dilute domain / DIL domain / Dilute domain profile. / DIL / IQ calmodulin-binding motif / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / 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. / Kinesin motor domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / VANADATE ION / Unconventional myosin-Vc
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.397 Å
AuthorsRopars, V. / Pylypenko, O. / Sweeney, H.L. / Houdusse, A.
CitationJournal: Nat Commun / Year: 2016
Title: The myosin X motor is optimized for movement on actin bundles.
Authors: Virginie Ropars / Zhaohui Yang / Tatiana Isabet / Florian Blanc / Kaifeng Zhou / Tianming Lin / Xiaoyan Liu / Pascale Hissier / Frédéric Samazan / Béatrice Amigues / Eric D Yang / Hyokeun ...Authors: Virginie Ropars / Zhaohui Yang / Tatiana Isabet / Florian Blanc / Kaifeng Zhou / Tianming Lin / Xiaoyan Liu / Pascale Hissier / Frédéric Samazan / Béatrice Amigues / Eric D Yang / Hyokeun Park / Olena Pylypenko / Marco Cecchini / Charles V Sindelar / H Lee Sweeney / Anne Houdusse /
Abstract: Myosin X has features not found in other myosins. Its structure must underlie its unique ability to generate filopodia, which are essential for neuritogenesis, wound healing, cancer metastasis and ...Myosin X has features not found in other myosins. Its structure must underlie its unique ability to generate filopodia, which are essential for neuritogenesis, wound healing, cancer metastasis and some pathogenic infections. By determining high-resolution structures of key components of this motor, and characterizing the in vitro behaviour of the native dimer, we identify the features that explain the myosin X dimer behaviour. Single-molecule studies demonstrate that a native myosin X dimer moves on actin bundles with higher velocities and takes larger steps than on single actin filaments. The largest steps on actin bundles are larger than previously reported for artificially dimerized myosin X constructs or any other myosin. Our model and kinetic data explain why these large steps and high velocities can only occur on bundled filaments. Thus, myosin X functions as an antiparallel dimer in cells with a unique geometry optimized for movement on actin bundles.
History
DepositionJan 16, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Unconventional myosin-Vc
B: Unconventional myosin-Vc
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,11312
Polymers172,7162
Non-polymers1,39710
Water6,702372
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A: Unconventional myosin-Vc
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,0656
Polymers86,3581
Non-polymers7075
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Unconventional myosin-Vc
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,0496
Polymers86,3581
Non-polymers6915
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.780, 66.740, 131.260
Angle α, β, γ (deg.)90.000, 104.450, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Unconventional myosin-Vc


Mass: 86357.938 Da / Num. of mol.: 2 / Fragment: UNP resideus 5-754
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MYO5C / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9NQX4

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Non-polymers , 6 types, 382 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-VO4 / VANADATE ION


Mass: 114.939 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: VO4
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 372 / 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: 2.55 Å3/Da / Density % sol: 51.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG 8000, MES, DMSO

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2.39→48.5 Å / Num. obs: 67573 / % possible obs: 98.3 % / Redundancy: 3 % / Rsym value: 0.049 / Net I/σ(I): 13.47
Reflection shellResolution: 2.39→2.54 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 1.85 / Rsym value: 0.612 / % possible all: 96.4

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VOM

1vom


Resolution: 2.397→48.5 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2265 3380 5 %
Rwork0.2049 64193 -
obs0.206 67573 98.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 230.64 Å2 / Biso mean: 88.8356 Å2 / Biso min: 32.96 Å2
Refinement stepCycle: final / Resolution: 2.397→48.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11060 0 130 372 11562
Biso mean--67.8 65.43 -
Num. residues----1409
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711387
X-RAY DIFFRACTIONf_angle_d0.99815440
X-RAY DIFFRACTIONf_chiral_restr0.1351707
X-RAY DIFFRACTIONf_plane_restr0.0022000
X-RAY DIFFRACTIONf_dihedral_angle_d17.7594084
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3973-2.43160.35431240.30072359248388
2.4316-2.46780.31941450.280727592904100
2.4678-2.50640.3051390.2712626276599
2.5064-2.54750.28871410.266326872828100
2.5475-2.59140.31410.25526712812100
2.5914-2.63850.29751420.249127012843100
2.6385-2.68930.29221400.26542657279798
2.6893-2.74420.28641410.25612682282399
2.7442-2.80380.31061430.256227202863100
2.8038-2.86910.30831410.258826822823100
2.8691-2.94080.31841410.25732671281299
2.9408-3.02030.27531430.244327142857100
3.0203-3.10920.24271400.22862660280099
3.1092-3.20950.23551430.22652712285599
3.2095-3.32420.25551420.22092702284499
3.3242-3.45720.21971400.21922661280198
3.4572-3.61450.2421400.19552655279599
3.6145-3.8050.1971410.19082689283098
3.805-4.04330.22651390.19752640277997
4.0433-4.35530.2061420.17312702284498
4.3553-4.79330.17551420.16142699284198
4.7933-5.4860.20251420.1782684282698
5.486-6.90870.22921420.21252706284898
6.9087-48.53230.1751460.18212754290097
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)
12.05620.5050.911.14940.67971.33550.00550.26790.5107-0.08110.0994-0.215-0.43940.3333-0.03860.6476-0.17210.05760.69570.10120.770632.084324.545313.1528
22.5451-0.0889-0.66051.5781-0.03081.1787-0.00590.63110.0228-0.3173-0.0314-0.19950.02460.2423-0.04370.53110.03460.01030.73010.0390.473621.83340.6857-0.3632
31.72370.4859-0.63691.3599-0.16872.06660.03950.3409-0.12030.1459-0.05390.15680.252-0.21130.01580.4833-0.0249-0.00520.3631-0.0680.4076-0.3302-9.136915.8204
42.12810.1363-0.49461.27090.24382.32340.1342-0.0902-0.14070.328-0.0799-0.23680.2110.4993-0.05730.51170.0746-0.07710.40370.03280.454723.6106-5.848823.685
52.26520.5482-0.31460.6266-0.80661.20410.06510.0068-0.5080.2209-0.0799-0.27580.26830.1233-0.00560.73930.0759-0.01580.4176-0.03250.531614.0313-13.814923.0557
61.35620.9707-0.06511.76390.0941.940.1593-0.11060.43440.07610.0467-0.2643-0.42970.5615-0.11860.5701-0.05140.00750.64850.07670.570726.967513.190715.4722
72.33441.69130.29133.75271.47812.58860.2002-0.7098-0.4087-1.14940.1825-0.4235-1.37081.3062-0.24430.9589-0.19360.56071.7231-0.36841.603756.36949.7836-0.3652
82.09140.4334-0.10973.1059-0.21323.09210.09990.3453-0.03790.41610.27370.3070.5818-0.5977-0.34470.5525-0.1448-0.06070.80230.15750.6959-40.3701-32.17564.7565
90.44340.9007-0.11862.4068-1.27741.5972-0.01180.17280.1427-0.04630.64740.7866-0.0902-1.0091-0.34390.41460.0709-0.01970.9570.30360.7239-39.6399-3.72137.1344
101.76150.6819-0.85612.5161-0.75681.81640.10750.28030.3221-0.13630.1711-0.0561-0.5416-0.4192-0.13790.7180.12680.04890.47960.10780.5797-17.805816.077627.0161
110.32130.571-0.17361.4441-0.76280.97820.0377-0.14870.19260.49730.33780.5018-0.5586-0.669-0.15370.70560.29780.16780.83520.18930.7205-36.02314.304849.5394
121.71050.7234-0.96882.5725-1.66252.30850.0932-0.17320.30620.86020.2550.2085-0.9697-0.4516-0.27740.77920.18980.04250.5579-0.01320.5413-26.50443.483852.5126
132.3761-0.1658-0.78621.603-0.09820.77350.46280.0097-0.5423-0.7681-0.00360.5761-0.35640.3344-0.17781.0870.37180.0531.59740.10361.362-70.7235-8.141466.3846
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 136 )
2X-RAY DIFFRACTION2chain 'A' and (resid 137 through 205 )
3X-RAY DIFFRACTION3chain 'A' and (resid 206 through 390 )
4X-RAY DIFFRACTION4chain 'A' and (resid 391 through 544 )
5X-RAY DIFFRACTION5chain 'A' and (resid 545 through 640 )
6X-RAY DIFFRACTION6chain 'A' and (resid 641 through 684 )
7X-RAY DIFFRACTION7chain 'A' and (resid 685 through 750 )
8X-RAY DIFFRACTION8chain 'B' and (resid 5 through 79 )
9X-RAY DIFFRACTION9chain 'B' and (resid 80 through 298 )
10X-RAY DIFFRACTION10chain 'B' and (resid 299 through 390 )
11X-RAY DIFFRACTION11chain 'B' and (resid 391 through 490 )
12X-RAY DIFFRACTION12chain 'B' and (resid 491 through 687 )
13X-RAY DIFFRACTION13chain 'B' and (resid 688 through 754 )

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