← Back to search

9yp4

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

Method: ELECTRON MICROSCOPY D_max: 170.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9yp4
deposition_date	2025-10-13
title	Cryo-EM structure of human beta-cardiac myosin bound to omecamtiv mecarbil in the interacting-heads motif and S2-FH docked state
keywords	Cardiac Myosin, Interacting Heads Motif, Omecamtiv Mecarbil, Actin Binding, CONTRACTILE PROTEIN; CONTRACTILE PROTEIN
method	ELECTRON MICROSCOPY

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	51.51 Å
rg_electron	51.53 Å
i0	1114390000.00
molecular_weight	279350.0 kDa
excluded_volume	350140 Å³
envelope_volume	499450 Å³
shell_volume	81452 Å³
envelope_diameter	172.4 Å
shell_rg	54.19 Å
envelope_rg	50.13 Å
shape_rg	51.51 Å
total_rg	51.68 Å
total_atoms	19629
n_residues	2428
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

▼

3. P(r) Analysis (GNOM)

dmax	170.2 Å
rg_real	51.45 Å
rg_real_error	1.35 Å
i0_real	1.1140e+09
i0_real_error	2.2910e+07
rg_reciprocal	51.53 Å
i0_reciprocal	1114000000.0000
total_estimate	0.8305
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	60.4 Å
skewness	0.199
kurtosis	-0.617
angular_range	— – 0.1550 Å⁻¹
current_alpha	0.0001
highest_alpha	78810000.0000
n_real_points	32
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.934; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.000

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (6)

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	19629

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	methyl 4-(2-fluoro-3-{[(6-methylpyridin-3-yl)carbamoyl]amino}benzyl)piperazine-1-carboxylate
formula_weight	401.4 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

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

Entity 6 non-polymer

description	PHOSPHATE ION
formula_weight	95.0 kDa
src_method	syn
entity_count	2

▶

6. Citations (1)

▶

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	4.500 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	4.50 Å
resolution_method	—
num_particles	19218

fit	/app/data/saxs_computation/yp/9yp4/9yp4.fit
pddf	/app/data/pr_computation/yp/9yp4/9yp4.pr.out
profile	/app/data/saxs_computation/yp/9yp4/9yp4.dat

Cryo-EM structure of human beta-cardiac myosin bound to omecamtiv mecarbil 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

Refinement

EM 3D

5. Entities & Polymer Info (6)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)