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9xcg

Cryo-EM structure of csy3 with crRNA

Method: ELECTRON MICROSCOPY D_max: 272.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9xcg
deposition_date	2025-10-25
title	Cryo-EM structure of csy3 with crRNA
keywords	CRISPR-Cas system, IMMUNE SYSTEM-RNA complex; IMMUNE SYSTEM/RNA
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	94.81 Å
rg_electron	96.25 Å
i0	14627800000.00
molecular_weight	986960.0 kDa
excluded_volume	1217800 Å³
envelope_volume	2249700 Å³
shell_volume	211610 Å³
envelope_diameter	352.4 Å
shell_rg	82.29 Å
envelope_rg	91.44 Å
shape_rg	96.27 Å
total_rg	96.06 Å
total_atoms	134796
n_residues	8678
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	272.6 Å
rg_real	92.75 Å
rg_real_error	1.10 Å
i0_real	1.4210e+10
i0_real_error	2.9090e+08
rg_reciprocal	89.73 Å
i0_reciprocal	14390000000.0000
total_estimate	0.8493
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	85.2 Å
skewness	0.523
kurtosis	-0.413
angular_range	— – 0.0800 Å⁻¹
current_alpha	1.0110
highest_alpha	2617000000.0000
n_real_points	17
gnom_version	4.1.3
quality_criteria	AN1: 0.002; Oscil: 0.638; Stabil: 0.982; Sysdev: 1.000; Positv: 1.000; Valcen: 0.978; Smooth: 0.206

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

Entity 1 polymer

description	CRISPR-associated protein Csy3
formula_weight	36948.5 kDa
src_method	man
entity_count	26

Polymer

type	polypeptide(L)
strand_id	A,C,D,E,F,G,I,J,K,L,B,H,N,O,P,Q,S,T,U,V,W,Y,Z,a,b,f
atom_count	134796

MAKAATTLKTASVLAFERKLANSDALMYAGNWAQQDNWTAIAIQEKSVRGTISNRLKNALTSDPAKLDAEIQKANLQKVDVAALPFGADTLKIVFTLRVLGNLAQPSVCNDQDYQTALGDIITGYAQEQGFSTLAARYAENIANGRFLWRNRVGAEAIRVVVTKKGERSWEFNGEDYSLRQFSQPAGDLAALTQAIEKGLAGDASALFTVEAYVQLGNGQEVFPSQELVLDEKARNGKSKILYQVNDVAAIHSQKIGNALRTIDDWYPAADEAGPIAVEPYGSVTSRGKAYRQPREKMDFYTLLDNWVIKGDVPMPEQQHYVIATLIRGGVFGEKGE

Source

organism	Pectobacterium atrosepticum SCRI1043
ncbi_taxonomy_id	218491
host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

description	RNA (159-MER)
formula_weight	51550.7 kDa
src_method	man
entity_count	1

Polymer

type	polyribonucleotide
strand_id	M

ACGGCGAAAGCGGGCUUGAAAUUCACGGCGAAAUUCACGGCGGGCUUGAAAUUCACGGCGGGAUUCACGGCGGGCUUGAAAUUCACGGCGAAAUUCACGGCGGGCUUGAAAUUCACGGCGAAAUUCACGGCGGGCUUGAAAUUCACGGCGGGAUUCACG

Source

organism	Thiocystis violascens
ncbi_taxonomy_id	73141
host_organism	Escherichia coli BL21(DE3)

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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	4.85 Å
resolution_method	—
num_particles	140643

fit	/app/data/saxs_computation/xc/9xcg/9xcg.fit
pddf	/app/data/pr_computation/xc/9xcg/9xcg.pr.out
profile	/app/data/saxs_computation/xc/9xcg/9xcg.dat

Cryo-EM structure of csy3 with crRNA

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 (2)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)