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9ya9

;Cryo-EM structure of ternary complex BCL6-CRBN-DDB1 with BMS-986458 (local refined), a potent and selective BCL6 ligand directed degrader (LDD) ;

Method: ELECTRON MICROSCOPY D_max: 101.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ya9
deposition_date	2025-09-15
title	;Cryo-EM structure of ternary complex BCL6-CRBN-DDB1 with BMS-986458 (local refined), a potent and selective BCL6 ligand directed degrader (LDD) ;
keywords	Cereblon, BCL6, LDD, degrader, E3, LIGASE; LIGASE
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	30.07 Å
rg_electron	29.62 Å
i0	70037000.00
molecular_weight	66500.0 kDa
excluded_volume	83627 Å³
envelope_volume	108430 Å³
shell_volume	31599 Å³
envelope_diameter	108.2 Å
shell_rg	35.47 Å
envelope_rg	29.47 Å
shape_rg	29.66 Å
total_rg	30.06 Å
total_atoms	9338
n_residues	570
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	101.8 Å
rg_real	30.16 Å
rg_real_error	1.08 Å
i0_real	7.0040e+07
i0_real_error	1.1980e+06
rg_reciprocal	30.12 Å
i0_reciprocal	70040000.0000
total_estimate	0.8709
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	36.5 Å
skewness	0.439
kurtosis	-0.142
angular_range	— – 0.2650 Å⁻¹
current_alpha	0.0000
highest_alpha	14050000.0000
n_real_points	54
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.837; Stabil: 0.996; Sysdev: 1.000; Positv: 1.000; Valcen: 0.959; Smooth: 0.859

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	B-cell lymphoma 6 protein
formula_weight	16431.9 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	9338

GSLDYKDDDDKENLYFQGADSCIQFTRHASDVLLNLNRLRSRDILTDVVIVVSREQFRAHKTVLMACSGLFYSIFTDQLKCNLSVINLDPEINPEGFCILLDFMYTSRLNLREGNIMAVMATAMYLQMEHVVDTCRKFIKASE

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 polymer

description	Protein cereblon
formula_weight	53582.0 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

MSYYHHHHHHDYDIPTTGLVPRGSMMAGEGDQQDAAHNMGNHLPLLPAESEEEDEMEVEDQDSKEAKKPNIINFDTSLPTSHTYLGADMEEFHGRTLHDDDSCQVIPVLPQVMMILIPGQTLPLQLFHPQEVSMVRNLIQKDRTFAVLAYSNVQEREAQFGTTAEIYAYREEQDFGIEIVKVKAIGRQRFKVLELRTQSDGIQQAKVQILPECVLPSTMSAVQLESLNKCQIFPSKPVSREDQCSYKWWQKYQKRKFHCANLTSWPRWLYSLYDAETLMDRIKKQLREWDENLKDDSLPSNPIDFSYRVAACLPIDDVLRIQLLKIGSAIQRLRCELDIMNKCTSLCCKQCQETEITTKNEIFSLSLCGPMAAYVNPHGYVHETLTVYKACNLNLIGRPSTEHSWFPGYAWTVAQCKICASHIGWKFTATKKDMSPQKFWGLTRSALLPTIPDTEDEISPDKVILCL

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 3 non-polymer

description	;(3R)-3-(6-{[(3R,4R)-1-{5-chloro-4-[(1-methyl-2-oxo-2,3-dihydro-1H-indol-5-yl)amino]pyrimidin-2-yl}-3-methylpiperidin-4-yl]amino}-1-methyl-1H-indazol-3-yl)piperidine-2,6-dione ;
formula_weight	628.1 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	1

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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	3.090 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.09 Å
resolution_method	—
num_particles	202942

fit	/app/data/saxs_computation/ya/9ya9/9ya9.fit
pddf	/app/data/pr_computation/ya/9ya9/9ya9.pr.out
profile	/app/data/saxs_computation/ya/9ya9/9ya9.dat

;Cryo-EM structure of ternary complex BCL6-CRBN-DDB1 with BMS-986458 (local refined), a potent and selective BCL6 ligand directed degrader (LDD) ;

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 (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)