SAXSdb — 9yim

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1. Structure Basics

entry_id	9yim
deposition_date	2025-10-01
title	Capping protein bound to the barbed end of F-actin
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	55.90 Å
rg_electron	56.67 Å
i0	1087320000.00
molecular_weight	271280.0 kDa
excluded_volume	338100 Å³
envelope_volume	477670 Å³
shell_volume	76287 Å³
envelope_diameter	217.6 Å
shell_rg	51.51 Å
envelope_rg	56.88 Å
shape_rg	56.71 Å
total_rg	56.39 Å
total_atoms	19030
n_residues	2398
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	199.7 Å
rg_real	56.66 Å
rg_real_error	2.64 Å
i0_real	1.0870e+09
i0_real_error	2.2600e+07
rg_reciprocal	55.26 Å
i0_reciprocal	1085000000.0000
total_estimate	0.7572
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	49.9 Å
skewness	0.676
kurtosis	-0.144
angular_range	— – 0.1400 Å⁻¹
current_alpha	0.0000
highest_alpha	88870000.0000
n_real_points	29
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.562; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.733; Smooth: 0.423

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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	41387.2 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	19039

TTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEKSYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVMSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWITKQEYDEAGPSIVHRKCF

Entity 2 polymer

description	F-actin-capping protein subunit alpha-1
formula_weight	32041.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	Y

VSDEEKVRIAAKFITHAPPGEFNEVFNDVRLLLNNDNLLREGAAHAFAQYNMDQFTPVKIEGYEDQVLITEHGDLGNSRFLDPRNKISFKFDHLRKEASDPQPEEADGGLKSWRESCDSALRAYVKDHYSNGFCTVYAKTIDGQQTIIACIESHQFQPKNFWNGRWRSEWKFTITPPTAQVVGVLKIQVHYYEDGNVQLVSHKDVQDSLTVSNEAQTAKEFIKIIENAENEYQTAISENYQTMSDTTFKALRRQLPVTRTKIDWNKILSYKIGKEMQN

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	30435.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	Z

SDQQLDCALDLMRRLPPQQIEKNLSDLIDLVPSLCEDLLSSVDQPLKIARDKVVGKDYLLCDYNRDGDSYRSPWSNKYDPPLEDGAMPSARLRKLEVEANNAFDQYRDLYFEGGVSSVYLWDLDHGFAGVILIKKAGDGSKKIKGCWDSIHVVEVQEKSSGRTAHYKLTSTVMLWLQTNKSGSGTMNLGGSLTRQMEKDETVSDCSPHIANIGRLVEDMENKIRSTLNEIYFGKTKDIVNGLRSVQTFADKSKQEALKNDLVEALKRKQQ

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 4 non-polymer

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

Entity 5 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	5

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	9

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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	2.620 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.62 Å
resolution_method	—
num_particles	275590

fit	/app/data/saxs_computation/yi/9yim/9yim.fit
pddf	/app/data/pr_computation/yi/9yim/9yim.pr.out
profile	/app/data/saxs_computation/yi/9yim/9yim.dat

Capping protein bound to the barbed end of F-actin

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 non-polymer

Entity 5 non-polymer

Entity 6 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)