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5i0h

Crystal structure of myosin X motor domain in pre-powerstroke state

Method: X-RAY DIFFRACTION Dmax: 127.2 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Unconventional myosin-X

Homo sapiens

UniProt Q9HD67

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–741 Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 EDO 1,2-ETHANEDIOL × 8 SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；10% PEG 8000, 50mM Tris pH 7.5, 1mM TCEP and 125mM Lithium sulfate Resolution 1.80 Å R-free 0.190
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 1–741 Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 EDO 1,2-ETHANEDIOL × 10 SO4 SULFATE ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；10% PEG 8000, 50mM Tris pH 7.5, 1mM TCEP and 125mM Lithium sulfate Resolution 1.80 Å R-free 0.190

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 5I0H Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2LW9 NMR solution structure of Myo10 anti-CC Deposited 2012-07-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 883–933（51 aa）
Chain B 883–933（51 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；303 K；Ionic strength (raw mmCIF value) 100
NMR sample composition 0.8 mM [U-100% 13C; U-100% 15N] entity-1, 100% D2O | 100% D2O
Resolution not provided
3AU4 Structure of the human myosin-X MyTH4-FERM cassette bound to its specific cargo, DCC Deposited 2011-01-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1486–2058（573 aa） Fragment：MyTH4-FERM cassette, UNP residues 1486-2058
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；100mM maric acid-MES-Tris (MMT) buffer, 2% PEG 1500, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.90 Å R-free 0.233
3AU5 Structure of the human myosin-X MyTH4-FERM cassette Deposited 2011-01-28 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1486–2058（573 aa） Fragment：MyTH4-FERM cassette, UNP residues 1486-2058
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；10% PEG 8000, 5% MPD, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.55 Å R-free 0.281
3AU5 Structure of the human myosin-X MyTH4-FERM cassette Deposited 2011-01-28 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1486–2058（573 aa） Fragment：MyTH4-FERM cassette, UNP residues 1486-2058
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；10% PEG 8000, 5% MPD, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.55 Å R-free 0.281
3PZD Structure of the myosin X MyTH4-FERM/DCC complex Deposited 2010-12-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1503–2047（545 aa） Fragment：MyTH4-FERM tandem
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；8% PEG 8000, 10% glycerol, HEPES buffer, pH 7.5, vapor diffusion, hanging drop, temperature 289K
Resolution 2.50 Å R-free 0.259
5I0I Crystal structure of myosin X motor domain with 2IQ motifs in pre-powerstroke state Deposited 2016-02-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 3–793（791 aa）
Not recorded MPO 3[N-MORPHOLINO]PROPANE SULFONIC ACID × 1 MG MAGNESIUM ION × 1 VO4 VANADATE ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 SO4 SULFATE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；7.5% PEG 10000, 100mM MOPS pH 7.0, 1mM TCEP and 50mM Magnesium acetate
Resolution 3.15 Å R-free 0.218
5I0I Crystal structure of myosin X motor domain with 2IQ motifs in pre-powerstroke state Deposited 2016-02-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 3–793（791 aa）
Not recorded MPO 3[N-MORPHOLINO]PROPANE SULFONIC ACID × 1 MG MAGNESIUM ION × 1 VO4 VANADATE ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；7.5% PEG 10000, 100mM MOPS pH 7.0, 1mM TCEP and 50mM Magnesium acetate
Resolution 3.15 Å R-free 0.218
5KG8 Rigor myosin X co-complexed with an actin filament Deposited 2016-06-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 3–741（739 aa） Fragment：motor domain (UNP residues 3-741)
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.10 Å

6 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MYO10_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–741； UniProt 1–741 Author chain B； PDBConstruct 1–741； UniProt 1–741

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 5i0h

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5i0h
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5i0h
Deposition date deposition_date2016-02-04
Structure title titleCrystal structure of myosin X motor domain in pre-powerstroke state
Keywords keywordsmyosin, motor domain, molecular motor, pre-powerstroke state, motility, motor protein; MOTOR PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier36.43 Å
Radius of gyration Rg (electron density) rg_electron35.71 Å
Forward intensity I(0) i0439700000.00
Molecular weight molecular_weight167030.0 kDa
Excluded volume excluded_volume207750 ų
Envelope volume envelope_volume268820 ų
Hydration-shell volume shell_volume60815 ų
Envelope diameter envelope_diameter138.5 Å
Shell Rg shell_rg43.57 Å
Envelope Rg envelope_rg35.47 Å
Shape Rg shape_rg35.71 Å
Total Rg total_rg36.21 Å
Total atoms total_atoms11750
Residues n_residues1454
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax127.2 Å
Rg (real space) rg_real36.28 Å
Rg uncertainty (real space) rg_real_error1.07 Å
I(0) (real space) i0_real4.3970e+08
I(0) uncertainty (real space) i0_real_error7.3630e+06
Rg (reciprocal space) rg_reciprocal36.37 Å
I(0) (reciprocal space) i0_reciprocal439700000.0000
Solution quality estimate total_estimate0.7867
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary47.3 Å
Skewness Skewness skewness0.240
Kurtosis Kurtosis kurtosis-0.256
Angular range angular_range— – 0.2150 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha72300000.0000
Real-space data points n_real_points44
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.742; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id5i0hA01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily530 —
Domain ID domain_id5i0hA02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily4820 —
Domain ID domain_id5i0hB01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily530 —
Domain ID domain_id5i0hB02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily4820 —
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8. Citations (1)

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9. Files and Curves (10)