SAXSdb — 3wb8

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Unconventional myosin-Va

Mus musculus

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 1469–1853	Fragment：Globular Tail Domain (GTD), UNP residues 1469-1853	EDO 1,2-ETHANEDIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；20-30%(w/v) ethylene glycol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.50 Å R-free 0.225
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1469–1853	Fragment：Globular Tail Domain (GTD), UNP residues 1469-1853	EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；20-30%(w/v) ethylene glycol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.50 Å R-free 0.225
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 1469–1853	Fragment：Globular Tail Domain (GTD), UNP residues 1469-1853	EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；20-30%(w/v) ethylene glycol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.50 Å R-free 0.225
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 1469–1853	Fragment：Globular Tail Domain (GTD), UNP residues 1469-1853	EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；20-30%(w/v) ethylene glycol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.50 Å R-free 0.225
5	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain E； UniProt 1469–1853	Fragment：Globular Tail Domain (GTD), UNP residues 1469-1853	EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；20-30%(w/v) ethylene glycol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.50 Å R-free 0.225
6	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain F； UniProt 1469–1853	Fragment：Globular Tail Domain (GTD), UNP residues 1469-1853	EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；20-30%(w/v) ethylene glycol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.50 Å R-free 0.225
7	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain G； UniProt 1469–1853	Fragment：Globular Tail Domain (GTD), UNP residues 1469-1853	EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；20-30%(w/v) ethylene glycol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.50 Å R-free 0.225
8	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain H； UniProt 1469–1853	Fragment：Globular Tail Domain (GTD), UNP residues 1469-1853	EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；20-30%(w/v) ethylene glycol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.50 Å R-free 0.225

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 3WB8	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2IX7 Structure of apo-calmodulin bound to unconventional myosin V Deposited 2006-07-07	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 C 763–820（58 aa） Fragment：RESIDUES 763-820	Not recorded	SO4 SULFATE ION × 5 CYS CYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5；277 K；VAPOR DIFFUSION METHOD (4 C) PROTEIN SOLUTION; 10MG/ML IN 10MM IMIDAZOL PH7.0, 20MM NACL. RESERVOIR; 1.8M SA, 50MM MES PH5.0, 5% MPD, 5MM EGTA, 2MM NAN3, pH 5.00	Resolution 2.50 Å R-free 0.259
4KP3 Crystal Structure of MyoVa-GTD in Complex with Two Cargos Deposited 2013-05-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1469–1853（385 aa） Fragment：Globular Tail Domain (GTD), UNP residues 1469-1853 Chain B 1469–1853（385 aa） Fragment：Globular Tail Domain (GTD), UNP residues 1469-1853	Mutation：C1674S Mutation：C1674S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；289 K；12-16%(w/v) PEG3350, 2-4% tacsimate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.40 Å R-free 0.241
4ZLK Crystal structure of mouse myosin-5a in complex with calcium-bound calmodulin Deposited 2015-05-01	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 1–791（791 aa） Fragment：UNP residues 1-791	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；100 mM Tris-HCl, pH7.5, 2 mM CaCl2, 2 mM DTT, 2 mM NaN3, 10% glycerol, 6% PEG 8000	Resolution 2.50 Å R-free 0.246
6KU0 Crystal structure of MyoVa-GTD in complex with MICAL1-GTBM Deposited 2019-08-29	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1469–1853（385 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；1% w/v Tryptone, 0.05M HEPES sodium pH 7.0, 20% w/v Polyethylene glycol 3350	Resolution 1.60 Å R-free 0.199
6KU0 Crystal structure of MyoVa-GTD in complex with MICAL1-GTBM Deposited 2019-08-29	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1469–1853（385 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；1% w/v Tryptone, 0.05M HEPES sodium pH 7.0, 20% w/v Polyethylene glycol 3350	Resolution 1.60 Å R-free 0.199
8OF8 Cryo-EM structure of actomyosin-5a-S1 with the full-length lever (nucleotide free) Deposited 2023-03-14	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain M 1–907（907 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.50 Å
8R9V CryoEM structure of the primed actomyosin-5a complex Deposited 2023-11-30	Different construct Different mutation/modification 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 1–797（797 aa）	Mutation：S217A, Deletion DDEK 594-597	PO4 PHOSPHATE ION × 1 MG MAGNESIUM ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE；F-actin was mixed with myosin-5a (S1 1 IQ motif, residues 1-797, S217A, DDEK 594-597 deletion) that had been pre-incubated with ATP, and vitrified at 10 ms post-mixing	Resolution 4.40 Å
8RBF CryoEM structure of the post-powerstroke actomyosin-5a complex Deposited 2023-12-04	Different construct Different mutation/modification 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 5–767（763 aa）	Mutation：S217A, Deletion DDEK 594-597	MG MAGNESIUM ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE；F-actin was mixed with myosin-5a (S1 1 IQ motif, residues 1-797, S217A, DDEK 594-597 deletion) that had been pre-incubated with ATP, and vitrified at 120 ms post-mixing	Resolution 4.20 Å
8RBG CryoEM structure of primed myosin-5a (ADP-Pi state) Deposited 2023-12-04	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–797（797 aa）	Mutation：S217A, Deletion DDEK 594-597	PO4 PHOSPHATE ION × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.90 Å

8 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MYO5A_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 20–404； UniProt 1469–1853 Author chain B； PDBConstruct 20–404； UniProt 1469–1853 Author chain C； PDBConstruct 20–404； UniProt 1469–1853 Author chain D； PDBConstruct 20–404； UniProt 1469–1853 Author chain E； PDBConstruct 20–404； UniProt 1469–1853 Author chain F； PDBConstruct 20–404； UniProt 1469–1853 Author chain G； PDBConstruct 20–404； UniProt 1469–1853 Author chain H； PDBConstruct 20–404； UniProt 1469–1853

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3wb8
Deposition date deposition_date	2013-05-13
Structure title title	Crystal Structure of MyoVa-GTD
Keywords keywords	Helix bundle, MOTOR PROTEIN; MOTOR PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	58.90 Å
Radius of gyration Rg (electron density) rg_electron	59.62 Å
Forward intensity I(0) i0	1479340000.00
Molecular weight molecular_weight	327100.0 kDa
Excluded volume excluded_volume	412420 Å³
Envelope volume envelope_volume	607380 Å³
Hydration-shell volume shell_volume	91859 Å³
Envelope diameter envelope_diameter	220.5 Å
Shell Rg shell_rg	54.83 Å
Envelope Rg envelope_rg	58.64 Å
Shape Rg shape_rg	59.60 Å
Total Rg total_rg	59.52 Å
Total atoms total_atoms	22913
Residues n_residues	2861
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	201.9 Å
Rg (real space) rg_real	59.56 Å
Rg uncertainty (real space) rg_real_error	2.02 Å
I(0) (real space) i0_real	1.4790e+09
I(0) uncertainty (real space) i0_real_error	3.3770e+07
Rg (reciprocal space) rg_reciprocal	58.33 Å
I(0) (reciprocal space) i0_reciprocal	1476000000.0000
Solution quality estimate total_estimate	0.5854
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	52.4 Å
Skewness Skewness skewness	0.672
Kurtosis Kurtosis kurtosis	0.049
Angular range angular_range	— – 0.1350 Å⁻¹
Current regularization parameter α current_alpha	0.0002
Highest regularization parameter α highest_alpha	157800000.0000
Real-space data points n_real_points	28
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.698; Stabil: 1.000; Sysdev: 0.009; Positv: 1.000; Valcen: 0.937; Smooth: 0.547

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Unconventional myosin-Va
Molecular weight formula_weight	46122.3 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	23277

HHHHHHSSGLGVLFQGPGSKDFQGMLEYKREDEQKLVKNLILELKPRGVAVNLIPGLPAYILFMCVRHADYLNDDQKVRSLLTSTINSIKKVLKKRGDDFETVSFWLSNTCRFLHCLKQYSGEEGFMKHNTSRQNEHCLTNFDLAEYRQVLSDLAIQIYQQLVRVLENILQPMIVSGMLEHETIQGVSGVKPTGLRKRTSSIADEGTYTLDSILRQLNSFHSVMCQHGMDPELIKQVVKQMFYIVGAITLNNLLLRKDMCSWSKGMQIRYNVSQLEEWLRDKNLMNSGAKETLEPLIQAAQLLQVKKKTDDDAEAICSMCNALTTAQIVKVLNLYTPVNEFEERVSVSFIRTIQMRLRDRKDSPQLLMDAKHIFPVTFPFNPSSLALETIQIPASLGLGFIARV

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	22

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	356

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d3wb8a_
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.27 — DIL domain-like
Family Family family	a.118.27.1 — DIL domains from class V myosins

Domain ID domain_id	d3wb8b_
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.27 — DIL domain-like
Family Family family	a.118.27.1 — DIL domains from class V myosins

Domain ID domain_id	d3wb8c_
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.27 — DIL domain-like
Family Family family	a.118.27.1 — DIL domains from class V myosins

Domain ID domain_id	d3wb8d_
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.27 — DIL domain-like
Family Family family	a.118.27.1 — DIL domains from class V myosins

Domain ID domain_id	d3wb8e_
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.27 — DIL domain-like
Family Family family	a.118.27.1 — DIL domains from class V myosins

Domain ID domain_id	d3wb8f_
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.27 — DIL domain-like
Family Family family	a.118.27.1 — DIL domains from class V myosins

Domain ID domain_id	d3wb8g_
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.27 — DIL domain-like
Family Family family	a.118.27.1 — DIL domains from class V myosins

Domain ID domain_id	d3wb8h_
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.27 — DIL domain-like
Family Family family	a.118.27.1 — DIL domains from class V myosins

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8. Citations (1)

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Unit-cell length a length_a	68.984 Å
Unit-cell length b length_b	165.355 Å
Unit-cell length c length_c	173.020 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.06 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.499 Å
Low-resolution limit resolution_low	41.793 Å
R factor r_factor	0.1756
R_work r_work	0.1731
R_free r_free	0.2253

fit	/app/data/saxs_computation/wb/3wb8/3wb8.fit
pddf	/app/data/pr_computation/wb/3wb8/3wb8.pr.out
profile	/app/data/saxs_computation/wb/3wb8/3wb8.dat

Crystal Structure of MyoVa-GTD

1. Protein Identity and Related Structures Protein Identity & Related Structures

Unconventional myosin-Va

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction