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- PDB-5i0i: Crystal structure of myosin X motor domain with 2IQ motifs in pre... -

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Basic information

Entry
Database: PDB / ID: 5i0i
TitleCrystal structure of myosin X motor domain with 2IQ motifs in pre-powerstroke state
Components
  • (Calmodulin) x 4
  • Unconventional myosin-X
KeywordsMOTOR PROTEIN / myosin / motor domain / molecular motor / pre-powerstrocke state / motility
Function / homology
Function and homology information


plus-end directed microfilament motor activity / Netrin-1 signaling / cytoskeleton-dependent intracellular transport / : / : / : / : / filopodium tip / : / positive regulation of protein autophosphorylation ...plus-end directed microfilament motor activity / Netrin-1 signaling / cytoskeleton-dependent intracellular transport / : / : / : / : / filopodium tip / : / positive regulation of protein autophosphorylation / regulation of filopodium assembly / negative regulation of peptidyl-threonine phosphorylation / : / type 3 metabotropic glutamate receptor binding / filopodium membrane / myosin complex / positive regulation of peptidyl-threonine phosphorylation / positive regulation of DNA binding / CaM pathway / Cam-PDE 1 activation / positive regulation of protein serine/threonine kinase activity / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / CaMK IV-mediated phosphorylation of CREB / CASP4 inflammasome assembly / response to corticosterone / Glycogen breakdown (glycogenolysis) / spectrin binding / microfilament motor activity / negative regulation of ryanodine-sensitive calcium-release channel activity / Activation of RAC1 downstream of NMDARs / organelle localization by membrane tethering / CLEC7A (Dectin-1) induces NFAT activation / : / negative regulation of high voltage-gated calcium channel activity / autophagosome membrane docking / negative regulation of calcium ion export across plasma membrane / regulation of cardiac muscle cell action potential / presynaptic endocytosis / regulation of synaptic vesicle exocytosis / Synthesis of IP3 and IP4 in the cytosol / Phase 0 - rapid depolarisation / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / phosphatidylinositol-3,4,5-trisphosphate binding / calcineurin-mediated signaling / RHO GTPases activate PAKs / nitric-oxide synthase binding / regulation of cell communication by electrical coupling involved in cardiac conduction / adenylate cyclase binding / Uptake and function of anthrax toxins / Ion transport by P-type ATPases / protein phosphatase activator activity / Long-term potentiation / Calcineurin activates NFAT / regulation of ryanodine-sensitive calcium-release channel activity / regulation of calcium-mediated signaling / Regulation of MECP2 expression and activity / DARPP-32 events / Smooth Muscle Contraction / regulation of synaptic vesicle endocytosis / detection of calcium ion / regulation of cardiac muscle contraction / cellular response to interferon-beta / catalytic complex / RHO GTPases activate IQGAPs / phosphatidylinositol 3-kinase binding / activation of adenylate cyclase activity / calcium channel inhibitor activity / positive regulation of nitric-oxide synthase activity / presynaptic cytosol / ruffle / enzyme regulator activity / eNOS activation / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Activation of AMPK downstream of NMDARs / Ion homeostasis / regulation of heart rate / Protein methylation / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / response to amphetamine / titin binding / voltage-gated potassium channel complex / calcium channel complex / FCERI mediated Ca+2 mobilization / substantia nigra development / FCGR3A-mediated IL10 synthesis / protein serine/threonine kinase activator activity / sperm midpiece / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / calyx of Held / positive regulation of receptor signaling pathway via JAK-STAT / Ras activation upon Ca2+ influx through NMDA receptor
Similarity search - Function
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 / : / MyTH4 domain / MyTH4 domain superfamily / 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 / : / MyTH4 domain / MyTH4 domain superfamily / MyTH4 domain / MyTH4 domain profile. / Domain in Myosin and Kinesin Tails / RA like domain / 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 motor domain profile. / Myosin head, motor domain / Myosin head (motor domain) / Myosin. Large ATPases. / IQ motif profile. / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / PH domain / Kinesin motor domain superfamily / : / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / PH-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / VANADATE ION / Calmodulin-1 / Calmodulin-3 / Unconventional myosin-X
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsIsabet, T. / Sweeney, H.L. / Houdusse, A.
Funding support France, United States, 6items
OrganizationGrant numberCountry
French National Research AgencyANR blanche BLAN10 France
French National Research AgencyANR-13-BSV8-0019-01 France
Ligue contre le cancer France
ARC France
National Institutes of HealthDC009100 United States
National Institutes of HealthHL110869 United States
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
DepositionFeb 4, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2016Group: Database references
Revision 1.2Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 22, 2017Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_id
Revision 1.4May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Revision 2.0Aug 26, 2026Group: Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / pdbx_entry_details ...chem_comp / pdbx_entry_details / pdbx_nonpoly_atom_coordination / pdbx_nonpoly_atom_coordination_sphere / pdbx_nonpoly_atom_coordination_sphere_order
Item: _chem_comp.formula / Description: Metalloprotein remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Unconventional myosin-X
B: Unconventional myosin-X
C: Calmodulin
E: Calmodulin
G: Calmodulin
I: Calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,63022
Polymers228,3106
Non-polymers2,32016
Water28816
1
A: Unconventional myosin-X
C: Calmodulin
G: Calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,33013
Polymers112,9783
Non-polymers1,35210
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6590 Å2
ΔGint-131 kcal/mol
Surface area44380 Å2
MethodPISA
2
B: Unconventional myosin-X
E: Calmodulin
I: Calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,3009
Polymers115,3323
Non-polymers9686
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5570 Å2
ΔGint-88 kcal/mol
Surface area45180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.950, 173.410, 178.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 4 types, 5 molecules ABCEI

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


Mass: 91550.148 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MYO10, KIAA0799 / Production host: unidentified baculovirus / References: UniProt: Q9HD67
#2: Protein Calmodulin / CaM


Mass: 16450.014 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: CALM1, CALM, CAM, CAM1, CALM2, CAM2, CAMB, CALM3, CALML2, CAM3, CAMC, CAMIII
Production host: unidentified baculovirus / References: UniProt: P62158, UniProt: P0DP23*PLUS
#3: Protein Calmodulin / CaM


Mass: 16373.917 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: CALM1, CALM, CAM, CAM1, CALM2, CAM2, CAMB, CALM3, CALML2, CAM3, CAMC, CAMIII
Production host: unidentified baculovirus / References: UniProt: P62158, UniProt: P0DP23*PLUS
#5: Protein Calmodulin / CaM


Mass: 7408.098 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: CALM1, CALM, CAM, CAM1, CALM2, CAM2, CAMB, CALM3, CALML2, CAM3, CAMC, CAMIII
Production host: unidentified baculovirus / References: UniProt: P62158, UniProt: P0DP23*PLUS

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Protein/peptide , 1 types, 1 molecules G

#4: Protein/peptide Calmodulin / CaM


Mass: 4977.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: CALM1, CALM, CAM, CAM1, CALM2, CAM2, CAMB, CALM3, CALML2, CAM3, CAMC, CAMIII
Production host: unidentified baculovirus / References: UniProt: P62158, UniProt: P0DP23*PLUS

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Non-polymers , 6 types, 32 molecules

#6: Chemical ChemComp-MPO / 3[N-MORPHOLINO]PROPANE SULFONIC ACID


Mass: 209.263 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H15NO4S / Comment: pH buffer*YM
#7: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 114.939 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O4V
#9: 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
#10: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: SO4
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationN

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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: 3.84 Å3/Da / Density % sol: 68 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 7.5% PEG 10000, 100mM MOPS pH 7.0, 1mM TCEP and 50mM Magnesium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 3.15→50 Å / Num. obs: 61853 / % possible obs: 99.9 % / Redundancy: 16.9 % / Biso Wilson estimate: 118.26 Å2 / Net I/σ(I): 14.48
Reflection shellResolution: 3.15→3.23 Å / Redundancy: 16.8 % / Mean I/σ(I) obs: 1.15 / % possible all: 99.7

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.15→49.53 Å / Cor.coef. Fo:Fc: 0.9356 / Cor.coef. Fo:Fc free: 0.9334 / SU R Cruickshank DPI: 3.519 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.802 / SU Rfree Blow DPI: 0.333 / SU Rfree Cruickshank DPI: 0.342
RfactorNum. reflection% reflectionSelection details
Rfree0.2185 3073 4.97 %RANDOM
Rwork0.1916 ---
obs0.193 61853 99.92 %-
Displacement parametersBiso mean: 126.34 Å2
Baniso -1Baniso -2Baniso -3
1--4.4938 Å20 Å20 Å2
2---4.5664 Å20 Å2
3---9.0602 Å2
Refine analyzeLuzzati coordinate error obs: 0.383 Å
Refinement stepCycle: LAST / Resolution: 3.15→49.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15203 0 132 16 15351
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0115604HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2221163HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5390SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes460HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2300HARMONIC5
X-RAY DIFFRACTIONt_it15604HARMONIC20
X-RAY DIFFRACTIONt_nbd6SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.92
X-RAY DIFFRACTIONt_other_torsion19.78
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2061SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact17862SEMIHARMONIC4
LS refinement shellResolution: 3.15→3.23 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 224 5 %
Rwork0.2556 4254 -
all0.2573 4478 -
obs--99.96 %
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)
10.83760.03850.41861.31860.64751.35230.1118-0.07230.07970.1052-0.02470.0629-0.0225-0.1143-0.0871-0.23360.02560.1214-0.24570.0127-0.1605-16.278-30.42241.773
21.58310.18690.66390.80730.3171.77620.16220.63390.2812-0.21780.1109-0.1777-0.31090.4503-0.2731-0.16960.11430.3198-0.17480.1852-0.24781.9964-14.3879-30.2084
36.8069-3.028-2.65775.03161.95454.84980.11460.52860.2501-1.077-0.2193-0.40790.0961-0.14150.10480.47150.36480.0945-0.3248-0.0261-0.4575-20.066118.315117.6871
44.0158-2.98142.64345.7419-4.45234.9817-0.2278-0.622-0.1210.46610.34570.5035-0.13920.1232-0.11780.07980.2660.1032-0.11510.217-0.3119-47.6254-6.1245-46.7336
53.5775-3.75923.76261.5824-2.65644.2984-0.02220.1250.1167-0.00430.07240.10670.0414-0.0574-0.05030.16180.4484-0.0873-0.31610.37220.3616-37.724336.57377.699
60-4.79470.63340.11031.90940.46620.0596-0.10220.35960.0979-0.0054-0.039-0.25820.3831-0.05410.24020.31470.4396-0.18090.21680.0044-60.937317.0339-33.3798
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ E|* }
5X-RAY DIFFRACTION5{ G|* }
6X-RAY DIFFRACTION6{ I|* }

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