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3au4

Structure of the human myosin-X MyTH4-FERM cassette bound to its specific cargo, DCC

Method: X-RAY DIFFRACTION Dmax: 97.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1486–2058 Fragment：MyTH4-FERM cassette, UNP residues 1486-2058 Netrin receptor DCC × 1 （P43146） 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

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 3AU4 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 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
3AU5 Structure of the human myosin-X MyTH4-FERM cassette Deposited 2011-01-28 Different oligomeric state 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 oligomeric state 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 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
5I0H Crystal structure of myosin X motor domain 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 monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–741（741 aa）
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
5I0H Crystal structure of myosin X motor domain 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 monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–741（741 aa）
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
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 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 9 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 3–555； UniProt 1486–2058

Netrin receptor DCC

Homo sapiens

UniProt P43146

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 1390–1447 Fragment：P3 domain, UNP residues 1390-1447 Myosin-X × 1 （Q9HD67） 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

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 3AU4 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2ED7 Solution structure of the first fibronectin type III domain of human Netrin receptor DCC Deposited 2007-02-14 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 419–524（106 aa） Fragment：first fn3 domain, Fibronectin type-III 1
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient
NMR sample composition 1.3mM sample U-15N,13C; 20mM d-Tris-HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O, 90% H2O | 90% H2O/10% D2O
Resolution not provided
2ED8 Solution structure of the second fibronectin type III domain of human Netrin receptor DCC Deposited 2007-02-14 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 528–620（93 aa） Fragment：second fn3 domain, Fibronectin type-III 2
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；296 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient
NMR sample composition 1.2mM sample U-15N,13C; 20mM d-Tris-HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O, 90% H2O | 90% H2O/10% D2O
Resolution not provided
2ED9 Solution structure of the third fibronectin type III domain of human Netrin receptor DCC Deposited 2007-02-14 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 602–718（117 aa） Fragment：third fn3 domain
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；296 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient
NMR sample composition 0.5mM sample U-15N,13C; 20mM d-Tris-HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O' | 90% H2O/10% D2O
Resolution not provided
2EDB Solution structure of the fourth fibronectin type III domain of human Netrin receptor DCC Deposited 2007-02-14 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 716–818（103 aa） Fragment：fourth fn3 domain
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；296 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient
NMR sample composition 1.2mM sample U-15N,13C; 20mM d-Tris-HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O' | 90% H2O/10% D2O
Resolution not provided
2EDD Solution structure of the fifth fibronectin type III domain of human Netrin receptor DCC Deposited 2007-02-14 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 833–942（110 aa） Fragment：fifth fn3 domain
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；296 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient
NMR sample composition 1.2mM sample U-15N, 13C; 20mM d-Tris-HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O | 90% H2O/10% D2O
Resolution not provided
2EDE Solution structure of the sixth fibronectin type III domain of human Netrin receptor DCC Deposited 2007-02-14 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 944–1044（101 aa） Fragment：sixth fn3 domain
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；296 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient
NMR sample composition 1.3mM sample U-15N,13C; 20mM d-Tris-HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O | 90% H2O/10% D2O
Resolution not provided
4URT The crystal structure of a fragment of netrin-1 in complex with FN5- FN6 of DCC Deposited 2014-07-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 844–1043（200 aa） Fragment：FN5-FN6, RESIDUES 844-1043
Not recorded CA CALCIUM ION × 1 CL CHLORIDE ION × 1 SO4 SULFATE ION × 18 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；0.1M MES PH 6.0, 0.15M AMMONIUM SULFATE AND 15% (W/V) PEG 4000
Resolution 3.10 Å R-free 0.265
5X83 Structure of DCC FN456 domains Deposited 2017-02-28 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 721–815（95 aa） Fragment：UNP residues 721-815
Chain B 844–1043（200 aa） Fragment：UNP residues 844-1043
Chain C 721–815（95 aa） Fragment：UNP residues 721-815
Chain D 844–1043（200 aa） Fragment：UNP residues 844-1043
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；291 K；0.1M Sodium Phosphate Monobasic Monohydrate, 0.1M Potassium Phosphate Monobasic, 0.1M MES Monohydrate pH 6.5, 2.0M Sodium Chloride
Resolution 3.00 Å R-free 0.278

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

View Construct and Data Evidence
UniProt name DCC_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 6–63； UniProt 1390–1447

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 3au4

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3au4
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3au4
Deposition date deposition_date2011-01-28
Structure title titleStructure of the human myosin-X MyTH4-FERM cassette bound to its specific cargo, DCC
Keywords keywordsprotein-protein complex, motor protein cargo transportation, MOTOR PROTEIN-APOPTOSIS complex; MOTOR PROTEIN/APOPTOSIS
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_guinier30.05 Å
Radius of gyration Rg (electron density) rg_electron29.42 Å
Forward intensity I(0) i062399300.00
Molecular weight molecular_weight62977.0 kDa
Excluded volume excluded_volume79308 ų
Envelope volume envelope_volume104660 ų
Hydration-shell volume shell_volume30840 ų
Envelope diameter envelope_diameter102.6 Å
Shell Rg shell_rg35.19 Å
Envelope Rg envelope_rg29.13 Å
Shape Rg shape_rg29.42 Å
Total Rg total_rg29.98 Å
Total atoms total_atoms4434
Residues n_residues556
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 dmax97.7 Å
Rg (real space) rg_real30.12 Å
Rg uncertainty (real space) rg_real_error0.81 Å
I(0) (real space) i0_real6.2400e+07
I(0) uncertainty (real space) i0_real_error9.9530e+05
Rg (reciprocal space) rg_reciprocal30.09 Å
I(0) (reciprocal space) i0_reciprocal62400000.0000
Solution quality estimate total_estimate0.8880
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary29.5 Å
Skewness Skewness skewness0.367
Kurtosis Kurtosis kurtosis-0.495
Angular range angular_range— – 0.2650 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha13460000.0000
Real-space data points n_real_points54
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.908; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.955; Smooth: 0.862
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id3au4A01
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily530 — MyTH4 domain
Domain ID domain_id3au4A02
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Domain ID domain_id3au4A03
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology80 — Acyl-CoA Binding Protein
Homologous superfamily homologous superfamily10 —
Domain ID domain_id3au4A04
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology29 — PH-domain like
Homologous superfamily homologous superfamily30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)
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8. Citations (1)

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9. Files and Curves (10)