SAXSdb — 9y9m

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1. Structure Basics

entry_id	9y9m
deposition_date	2025-09-14
title	Capping protein bound to the barbed end of cofilactin
keywords	Cytoskeleton, Actin, Filament, Helical, PROTEIN FIBRIL; PROTEIN FIBRIL
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	55.73 Å
rg_electron	56.05 Å
i0	1499030000.00
molecular_weight	322480.0 kDa
excluded_volume	403340 Å³
envelope_volume	586380 Å³
shell_volume	90984 Å³
envelope_diameter	210.3 Å
shell_rg	54.59 Å
envelope_rg	55.68 Å
shape_rg	56.09 Å
total_rg	55.88 Å
total_atoms	22641
n_residues	2849
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	198.0 Å
rg_real	56.19 Å
rg_real_error	2.47 Å
i0_real	1.4990e+09
i0_real_error	3.1200e+07
rg_reciprocal	55.34 Å
i0_reciprocal	1497000000.0000
total_estimate	0.8219
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	56.6 Å
skewness	0.605
kurtosis	-0.061
angular_range	— – 0.1400 Å⁻¹
current_alpha	0.0000
highest_alpha	146900000.0000
n_real_points	29
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.715; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.926; Smooth: 0.614

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Actin, alpha skeletal muscle
formula_weight	41978.8 kDa
ec_number	3.6.4.-
src_method	nat
entity_count	5

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E
atom_count	22655

CDEDETTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEKSYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVMSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWITKQEYDEAGPSIVHRKCF

Entity 2 polymer

description	F-actin-capping protein subunit alpha-1
formula_weight	32728.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	Y

MADFDDRVSDEEKVRIAAKFITHAPPGEFNEVFNDVRLLLNNDNLLREGAAHAFAQYNMDQFTPVKIEGYEDQVLITEHGDLGNSRFLDPRNKISFKFDHLRKEASDPQPEEADGGLKSWRESCDSALRAYVKDHYSNGFCTVYAKTIDGQQTIIACIESHQFQPKNFWNGRWRSEWKFTITPPTAQVVGVLKIQVHYYEDGNVQLVSHKDVQDSLTVSNEAQTAKEFIKIIENAENEYQTAISENYQTMSDTTFKALRRQLPVTRTKIDWNKILSYXXXXXXXXX

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 3 polymer

description	F-actin-capping protein subunit beta
formula_weight	30669.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	Z

MSDQQLDCALDLMRRLPPQQIEKNLSDLIDLVPSLCEDLLSSVDQPLKIARDKVVGKDYLLCDYNRDGDSYRSPWSNKYDPPLEDGAMPSARLRKLEVEANNAFDQYRDLYFEGGVSSVYLWDLDHGFAGVILIKKAGDGSKKIKGCWDSIHVVEVQEKSSGRTAHYKLTSTVMLWLQTNKSGSGTMNLGGSLTRQMEKDETVSDCSPHIANIGRLVEDMENKIRSTLNEIYFGKTKDIVNGLRSVQTFADKSKQEALKNDLVEALKRKQQC

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 4 polymer

description	Cofilin-2
formula_weight	18765.6 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	a,b,c

MASGVTVNDEVIKVFNDMKVRKSSTQEEIKKRKKAVLFCLSDDKRQIIVEEAKQILVGDIGDTVEDPYTSFVKLLPLNDCRYALYDATYETKESKKEDLVFIFWAPESAPLKSKMIYASSKDAIKKKFTGIKHEWQVNGLDDIKDRSTLGEKLGGNVVVSLEGKPL

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 5 non-polymer

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

Entity 6 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	5

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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	3.060 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.06 Å
resolution_method	—
num_particles	79486

fit	/app/data/saxs_computation/y9/9y9m/9y9m.fit
pddf	/app/data/pr_computation/y9/9y9m/9y9m.pr.out
profile	/app/data/saxs_computation/y9/9y9m/9y9m.dat

Capping protein bound to the barbed end of cofilactin

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

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 non-polymer

Entity 6 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)