SAXSdb — 9wbl

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Isoform 2 of C-terminal-binding protein 2

Mus musculus

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 20 PDB declaration: eicosameric（20） Consistent with protein copy count	Chain A； UniProt 545–988 Chain B； UniProt 545–988 Chain C； UniProt 545–988 Chain D； UniProt 545–988 Chain E； UniProt 545–988 Chain F； UniProt 545–988 Chain G； UniProt 545–988 Chain H； UniProt 545–988 Chain I； UniProt 545–988 Chain J； UniProt 545–988 Chain K； UniProt 545–988 Chain L； UniProt 545–988 Chain M； UniProt 545–988 Chain N； UniProt 545–988 Chain O； UniProt 545–988 Chain P； UniProt 545–988 Chain Q； UniProt 545–988 Chain R； UniProt 545–988 Chain S； UniProt 545–988 Chain T； UniProt 545–988	Not recorded	NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 20	ELECTRON MICROSCOPY mmCIF provides none of the parsed experimental conditions	Resolution 3.41 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9WBL	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9WBJ cryo-EM structure of RIBEYE SAM thick filament Deposited 2025-08-14	Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 34 PDB declaration: 34-meric	Chain A 280–375（96 aa） Chain B 280–375（96 aa） Chain C 280–375（96 aa） Chain D 280–375（96 aa） Chain E 280–375（96 aa） Chain F 280–375（96 aa） Chain G 280–375（96 aa） Chain H 280–375（96 aa） Chain I 280–375（96 aa） Chain J 280–375（96 aa） Chain K 280–375（96 aa） Chain L 280–375（96 aa） Chain M 280–375（96 aa） Chain N 280–375（96 aa） Chain O 280–375（96 aa） Chain P 280–375（96 aa） Chain Q 280–375（96 aa） Chain R 280–375（96 aa） Chain S 280–375（96 aa） Chain T 280–375（96 aa） Chain U 280–375（96 aa） Chain V 280–375（96 aa） Chain W 280–375（96 aa） Chain X 280–375（96 aa） Chain Y 280–375（96 aa） Chain Z 280–375（96 aa） Chain a 280–375（96 aa） Chain b 280–375（96 aa） Chain c 280–375（96 aa） Chain d 280–375（96 aa） Chain e 280–375（96 aa） Chain f 280–375（96 aa） Chain g 280–375（96 aa） Chain h 280–375（96 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 3.37 Å
9WBK cryo-EM structure of RIBEYE SAM thin filament Deposited 2025-08-14	Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 28 PDB declaration: 28-meric	Chain B 280–375（96 aa） Chain C 280–375（96 aa） Chain D 280–375（96 aa） Chain E 280–375（96 aa） Chain F 280–375（96 aa） Chain G 280–375（96 aa） Chain H 280–375（96 aa） Chain I 280–375（96 aa） Chain J 280–375（96 aa） Chain K 280–375（96 aa） Chain L 280–375（96 aa） Chain M 280–375（96 aa） Chain N 280–375（96 aa） Chain O 280–375（96 aa） Chain P 280–375（96 aa） Chain Q 280–375（96 aa） Chain R 280–375（96 aa） Chain S 280–375（96 aa） Chain T 280–375（96 aa） Chain U 280–375（96 aa） Chain V 280–375（96 aa） Chain W 280–375（96 aa） Chain X 280–375（96 aa） Chain Y 280–375（96 aa） Chain Z 280–375（96 aa） Chain a 280–375（96 aa） Chain b 280–375（96 aa） Chain c 280–375（96 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 3.39 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CTBP2_MOUSE
Isoform	P56546-2
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–448； UniProt 545–988 Author chain B； PDBConstruct 5–448； UniProt 545–988 Author chain C； PDBConstruct 5–448； UniProt 545–988 Author chain D； PDBConstruct 5–448； UniProt 545–988 Author chain E； PDBConstruct 5–448； UniProt 545–988 Author chain F； PDBConstruct 5–448； UniProt 545–988 Author chain G； PDBConstruct 5–448； UniProt 545–988 Author chain H； PDBConstruct 5–448； UniProt 545–988 Author chain I； PDBConstruct 5–448； UniProt 545–988 Author chain J； PDBConstruct 5–448； UniProt 545–988 Author chain K； PDBConstruct 5–448； UniProt 545–988 Author chain L； PDBConstruct 5–448； UniProt 545–988 Author chain M； PDBConstruct 5–448； UniProt 545–988 Author chain N； PDBConstruct 5–448； UniProt 545–988 Author chain O； PDBConstruct 5–448； UniProt 545–988 Author chain P； PDBConstruct 5–448； UniProt 545–988 Author chain Q； PDBConstruct 5–448； UniProt 545–988 Author chain R； PDBConstruct 5–448； UniProt 545–988 Author chain S； PDBConstruct 5–448； UniProt 545–988 Author chain T； PDBConstruct 5–448； UniProt 545–988

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9wbl
Deposition date deposition_date	2025-08-14
Structure title title	cryo-EM structure of RIBEYE B' filament
Keywords keywords	RIBEYE, CTBP2, ribbon synapse, filament, PROTEIN BINDING; PROTEIN BINDING
Experimental Method method	ELECTRON MICROSCOPY

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	84.14 Å
Radius of gyration Rg (electron density) rg_electron	85.69 Å
Forward intensity I(0) i0	8932790000.00
Molecular weight molecular_weight	779550.0 kDa
Excluded volume excluded_volume	968290 Å³
Envelope volume envelope_volume	1537800 Å³
Hydration-shell volume shell_volume	163390 Å³
Envelope diameter envelope_diameter	303.5 Å
Shell Rg shell_rg	67.77 Å
Envelope Rg envelope_rg	85.05 Å
Shape Rg shape_rg	85.69 Å
Total Rg total_rg	85.46 Å
Total atoms total_atoms	54720
Residues n_residues	6936
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	254.4 Å
Rg (real space) rg_real	81.87 Å
Rg uncertainty (real space) rg_real_error	1.51 Å
I(0) (real space) i0_real	8.6810e+09
I(0) uncertainty (real space) i0_real_error	1.6170e+08
Rg (reciprocal space) rg_reciprocal	79.44 Å
I(0) (reciprocal space) i0_reciprocal	8814000000.0000
Solution quality estimate total_estimate	0.8521
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	67.0 Å
Skewness Skewness skewness	0.569
Kurtosis Kurtosis kurtosis	-0.463
Angular range angular_range	— – 0.0950 Å⁻¹
Current regularization parameter α current_alpha	1.0920
Highest regularization parameter α highest_alpha	4568000000.0000
Real-space data points n_real_points	20
GNOM version gnom_version	4.1.3
Quality Criteria 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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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Isoform 2 of C-terminal-binding protein 2
Molecular weight formula_weight	49028.7 kDa
Source method src_method	man
Copy count entity_count	20

Polymer Polymer

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

HMGSARRTGAPIIVSTMLTPEPSIRPQIMNGPLHPRPLVALLDGRDCTVEMPILKDLATVAFCDAQSTQEIHEKVLNEAVGAMMYHTITLTREDLEKFKALRVIVRIGSGYDNVDIKAAGELGIAVCNIPSAAVEETADSTVCHILNLYRRNTWLYQALREGTRVQSVEQIREVASGAARIRGETLGLIGFGRTGQAVAVRAKAFGFSVIFYDPYLQDGIERSLGVQRVYTLQDLLYQSDCVSLHCNLNEHNHHLINDFTIKQMRQGAFLVNAARGGLVDEKALAQALKEGRIRGAALDVHESEPFSFAQGPLKDAPNLICTPHTAWYSEQASLEMREAAATEIRRAITGRIPESLRNCVNKEFFVTSAPWSVIDQQAIHPELNGATYRYPPGIVGVAPGGLPPAMEGIIPGGIPVTHNLPTVAHPSQAPSPNQPTKHGDNREHPNEQ

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Molecular weight formula_weight	663.4 kDa
Source method src_method	syn
Copy count entity_count	20

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.41 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	113042

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

cryo-EM structure of RIBEYE B' filament

1. Protein Identity and Related Structures Protein Identity & Related Structures

Isoform 2 of C-terminal-binding protein 2

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)