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11mr

Cryo-EM structure of CRBN in complex with HBS1L and TNG-4857 (focused refinement)

Method: ELECTRON MICROSCOPY D_max: 134.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	11mr
deposition_date	2026-03-05
title	Cryo-EM structure of CRBN in complex with HBS1L and TNG-4857 (focused refinement)
keywords	FOCAD, PELO, ribosome, ubiquitin, CYTOSOLIC PROTEIN; CYTOSOLIC PROTEIN
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	35.74 Å
rg_electron	35.46 Å
i0	178372000.00
molecular_weight	111090.0 kDa
excluded_volume	140710 Å³
envelope_volume	182190 Å³
shell_volume	44036 Å³
envelope_diameter	141.8 Å
shell_rg	40.20 Å
envelope_rg	35.95 Å
shape_rg	35.43 Å
total_rg	35.91 Å
total_atoms	15718
n_residues	962
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	134.0 Å
rg_real	35.97 Å
rg_real_error	1.52 Å
i0_real	1.7840e+08
i0_real_error	3.0310e+06
rg_reciprocal	35.83 Å
i0_reciprocal	178300000.0000
total_estimate	0.8202
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	39.6 Å
skewness	0.561
kurtosis	0.037
angular_range	— – 0.2200 Å⁻¹
current_alpha	0.0000
highest_alpha	32840000.0000
n_real_points	45
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.635; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.782; Smooth: 0.972

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	HBS1-like protein
formula_weight	22947.0 kDa
ec_number	3.6.5.-
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,C
atom_count	15718

GKPPQRSIDKPFRLCVSDVFKDQGSGFCITGKIEAGYIQTGDRLLAMPPNETCTVKGITLHDEPVDWAAAGDHVSLTLVGMDIIKINVGCIFCGPKVPIKACTRFRARILIFNIEIPITKGFPVLLHYQTVSEPAVIKRLISVLNKSTGEVTKKKPKFLTKGQNALVELQTQRPIALELYKDFKELGRFMLRYGGSTIAAGVVTEIKE

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Trichoplusia ni

Entity 2 polymer

description	Protein cereblon
formula_weight	46378.3 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,D

GEAKKPNIINFDTSLPTSHTYLGADMEEFHGRTLHDDDSCQVIPVLPQVMMILIPGQTLPLQLFHPQEVSMVRNLIQKDRTFAVLAYSNVQEREAQFGTTAEIYAYREEQDFGIEIVKVKAIGRQRFKVLELRTQSDGIQQAKVQILPECVLPSTMSAVQLESLNKCQIFPSKPVSREDQCSYKWWQKYQKRKFHCANLTSWPRWLYSLYDAETLMDRIKKQLREWDENLKDDSLPSNPIDFSYRVAACLPIDDVLRIQLLKIGSAIQRLRCELDIMNKCTSLCCKQCQETEITTKNEIFSLSLCGPMAAYVNPHGYVHETLTVYKACNLNLIGRPSTEHSWFPGYAWTVAQCKICASHIGWKFTATKKDMSPQKFWGLTRSALLPTIPDTEDEISPDKVILCL

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 3 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	N-[(3S)-2,6-dioxopiperidin-3-yl]-2-fluoro-3-[(2-{4-[1-(trifluoromethyl)cyclopropyl]phenyl}propan-2-yl)carbamamido]benzamide
formula_weight	534.5 kDa
src_method	syn
entity_count	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	triclinic

resolution	2.60 Å
resolution_method	—
num_particles	661458

fit	/app/data/saxs_computation/1m/11mr/11mr.fit
pddf	/app/data/pr_computation/1m/11mr/11mr.pr.out
profile	/app/data/saxs_computation/1m/11mr/11mr.dat

Cryo-EM structure of CRBN in complex with HBS1L and TNG-4857 (focused refinement)

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 (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)