;cryo-EM structure of RIBEYE B' filament ;

Method: ELECTRON MICROSCOPY D_max: 254.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9wbl
deposition_date	2025-08-14
title	;cryo-EM structure of RIBEYE B' filament ;
keywords	RIBEYE, CTBP2, ribbon synapse, filament, PROTEIN BINDING; PROTEIN BINDING
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	84.14 Å
rg_electron	85.69 Å
i0	8932790000.00
molecular_weight	779550.0 kDa
excluded_volume	968290 Å³
envelope_volume	1537800 Å³
shell_volume	163390 Å³
envelope_diameter	303.5 Å
shell_rg	67.77 Å
envelope_rg	85.05 Å
shape_rg	85.69 Å
total_rg	85.46 Å
total_atoms	54720
n_residues	6936
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	254.4 Å
rg_real	81.87 Å
rg_real_error	1.51 Å
i0_real	8.6810e+09
i0_real_error	1.6170e+08
rg_reciprocal	79.44 Å
i0_reciprocal	8814000000.0000
total_estimate	0.8521
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	67.0 Å
skewness	0.569
kurtosis	-0.463
angular_range	— – 0.0950 Å⁻¹
current_alpha	1.0920
highest_alpha	4568000000.0000
n_real_points	20
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.723; Stabil: 0.960; Sysdev: 1.000; Positv: 1.000; Valcen: 0.971; Smooth: 0.058

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4. Crystallography & Experiment

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5. Entities & Polymer Info (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	3.41 Å
resolution_method	—
num_particles	113042

description	Isoform 2 of C-terminal-binding protein 2
formula_weight	49028.7 kDa
src_method	man
entity_count	20

type	polypeptide(L)
strand_id	A,B,C,E,F,H,D,G,I,J,K,L,M,N,O,P,Q,R,S,T
atom_count	54720

;cryo-EM structure of RIBEYE B' filament ;

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 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)

organism	Mus musculus
common_name	house mouse
ncbi_taxonomy_id	10090
host_organism	Escherichia coli BL21(DE3)

description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
formula_weight	663.4 kDa
src_method	syn
entity_count	20

fit	/app/data/saxs_computation/wb/9wbl/9wbl.fit
pddf	/app/data/pr_computation/wb/9wbl/9wbl.pr.out
profile	/app/data/saxs_computation/wb/9wbl/9wbl.dat