SAXSdb — 9yop

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1. Structure Basics

entry_id	9yop
deposition_date	2025-10-13
title	Cryo-EM structure of human beta-cardiac myosin in the interacting-heads motif and S2-FH docked state
keywords	Cardiac Myosin, Interacting Heads Motif, Contractile Protein, Actin Binding; CONTRACTILE PROTEIN
method	ELECTRON MICROSCOPY

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	53.53 Å
rg_electron	53.65 Å
i0	1092210000.00
molecular_weight	277020.0 kDa
excluded_volume	347390 Å³
envelope_volume	519930 Å³
shell_volume	82288 Å³
envelope_diameter	181.3 Å
shell_rg	54.90 Å
envelope_rg	52.15 Å
shape_rg	53.64 Å
total_rg	53.74 Å
total_atoms	19465
n_residues	2411
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	184.5 Å
rg_real	53.54 Å
rg_real_error	1.53 Å
i0_real	1.0920e+09
i0_real_error	1.8450e+07
rg_reciprocal	53.50 Å
i0_reciprocal	1092000000.0000
total_estimate	0.8897
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	63.6 Å
skewness	0.253
kurtosis	-0.574
angular_range	— – 0.1450 Å⁻¹
current_alpha	0.0001
highest_alpha	76200000.0000
n_real_points	30
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.887; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.903

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Myosin-7,General control transcription factor GCN4,Enhanced Green fluorescent protein
formula_weight	150656.5 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	19465

MGDSEMAVFGAAAPYLRKSEKERLEAQTRPFDLKKDVFVPDDKQEFVKAKIVSREGGKVTAETEYGKTVTVKEDQVMQQNPPKFDKIEDMAMLTFLHEPAVLYNLKDRYGSWMIYTYSGLFCVTVNPYKWLPVYTPEVVAAYRGKKRSEAPPHIFSISDNAYQYMLTDRENQSILITGESGAGKTVNTKRVIQYFAVIAAIGDRSKKDQSPGKGTLEDQIIQANPALEAFGNAKTVRNDNSSRFGKFIRIHFGATGKLASADIETYLLEKSRVIFQLKAERDYHIFYQILSNKKPELLDMLLITNNPYDYAFISQGETTVASIDDAEELMATDNAFDVLGFTSEEKNSMYKLTGAIMHFGNMKFKLKQREEQAEPDGTEEADKSAYLMGLNSADLLKGLCHPRVKVGNEYVTKGQNVQQVIYATGALAKAVYERMFNWMVTRINATLETKQPRQYFIGVLDIAGFEIFDFNSFEQLCINFTNEKLQQFFNHHMFVLEQEEYKKEGIEWTFIDFGMDLQACIDLIEKPMGIMSILEEECMFPKATDMTFKAKLFDNHLGKSANFQKPRNIKGKPEAHFSLIHYAGIVDYNIIGWLQKNKDPLNETVVGLYQKSSLKLLSTLFANYAGADAPIEKGKGKAKKGSSFQTVSALHRENLNKLMTNLRSTHPHFVRCIIPNETKSPGVMDNPLVMHQLRCNGVLEGIRICRKGFPNRILYGDFRQRYRILNPAAIPEGQFIDSRKGAEKLLSSLDIDHNQYKFGHTKVFFKAGLLGLLEEMRDERLSRIITRIQAQSRGVLARMEYKKLLERRDSLLVIQWNIRAFMGVKNWPWMKLYFKIKPLLKSAEREKEMASMKEEFTRLKEALEKSEARRKELEEKMVSLLQEKNDLQLQVQAEQDNLADAEERCDQLIKNKIQLEAKVKEMNERLEDEEEMNAELTAKKRKLEDECSELKRDIDDLELTLAKVEKEKHATENKVKNLTEEMAGLDEIIAKLTKEKKALQEAHQQALDDLQAEEDKMKQLEDKVEELLSKNYHLENEVARLKKLVGERGSGKLGVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITLGMDELYKGLNDIFEAQKIEWHEDYKDDDDK

Source

organism	Aequorea victoria
ncbi_taxonomy_id	6100
host_organism	Mus musculus

Entity 2 polymer

description	Myosin light chain 1/3, skeletal muscle isoform
formula_weight	20620.5 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,D

MAPKKDVKKPAAAPAPAPAPAPAPAKPKEEKIDLSAIKIEFSKEQQEDFKEAFLLFDRTGECKITLSQVGDVLRALGTNPTNAEVKKVLGNPSNEEMNAKKIEFEQFLPMMQAISNNKDQGGYEDFVEGLRVFDKEGNGTVMGAELRHVLATLGEKMKEEEVEALLAGQEDSNGCINYEAFVKHIMSV

Entity 3 polymer

description	Myosin regulatory light chain 11
formula_weight	18978.4 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	E,F

MAPKKAKRRAGAEGSSNVFSMFDQTQIQEFKEAFTVIDQNRDGIIDKEDLRDTFAAMGRLNVKNEELDAMMKEASGPINFTVFLTMFGEKLKGADPEDVITGAFKVLDPEGKGTIKKQFLEELLTTQCDRFSQEEIKNMWAAFPPDVGGNVDYKNICYVITHGDAKDQE

Entity 4 non-polymer

description	ADENOSINE-5'-DIPHOSPHATE
formula_weight	427.2 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	PHOSPHATE ION
formula_weight	95.0 kDa
src_method	syn
entity_count	2

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	3.50 Å
resolution_method	—
num_particles	42643

fit	/app/data/saxs_computation/yo/9yop/9yop.fit
pddf	/app/data/pr_computation/yo/9yop/9yop.pr.out
profile	/app/data/saxs_computation/yo/9yop/9yop.dat

Cryo-EM structure of human beta-cardiac myosin in the interacting-heads motif and S2-FH docked state

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

EM 3D

5. Entities & Polymer Info (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 non-polymer

Entity 5 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)