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9qkt

Cryo-EM structure of the CDK11B-cyclin L2-SAP30BP bound to OTS964 (conformation 1)

Method: ELECTRON MICROSCOPY D_max: 91.4 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qkt
deposition_date	2025-03-20
title	Cryo-EM structure of the CDK11B-cyclin L2-SAP30BP bound to OTS964 (conformation 1)
keywords	kinase, cyclin-dependent kinase, inhibitor, transcription, molecular complex, SPLICING; SPLICING
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	29.47 Å
rg_electron	28.55 Å
i0	96002700.00
molecular_weight	79198.0 kDa
excluded_volume	100160 Å³
envelope_volume	123310 Å³
shell_volume	35581 Å³
envelope_diameter	93.8 Å
shell_rg	36.18 Å
envelope_rg	28.64 Å
shape_rg	28.54 Å
total_rg	29.34 Å
total_atoms	5569
n_residues	679
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	91.4 Å
rg_real	29.39 Å
rg_real_error	0.50 Å
i0_real	9.6000e+07
i0_real_error	1.3960e+06
rg_reciprocal	29.43 Å
i0_reciprocal	96010000.0000
total_estimate	0.7306
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	32.2 Å
skewness	0.202
kurtosis	-0.622
angular_range	— – 0.2700 Å⁻¹
current_alpha	0.0000
highest_alpha	36480000.0000
n_real_points	55
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.958; Stabil: 1.000; Sysdev: 0.218; Positv: 1.000; Valcen: 1.000; Smooth: 0.965

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	SAP30-binding protein
formula_weight	34186.6 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	5649

SNAMAGKKNVLSSLAVYAEDSEPESDGEAGIEAVGSAAEEKGGLVSDAYGEDDFSRLGGDEDGYEEEEDENSRQSEDDDSETEKPEADDPKDNTEAEKRDPQELVASFSERVRNMSPDEIKIPPEPPGRCSNHLQDKIQKLYERKIKEGMDMNYIIQRKKEFRNPSIYEKLIQFCAIDELGTNYPKDMFDPHGWSEDSYYEALAKAQKIEMDKLEKAKKERTKIEFVTGTKKGTTTNATSTTTTTASTAVADAQKRKSKWDSAIPVTTIAQPTILTTTATLPAVVTVTTSASGSKTTVISAVGTIVKKAKQ

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Trichoplusia ni

Entity 2 polymer

description	Cyclin-L2
formula_weight	35690.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

SNAMAAAAAAAGAAGSAAPAAAAGAPGSGGAPSGSQGVLIGDRLYSGVLITLENCLLPDDKLRFTPSMSSGLDTDTETDLRVVGCELIQAAGILLRLPQVAMATGQVLFQRFFYTKSFVKHSMEHVSMACVHLASKIEEAPRRIRDVINVFHRLRQLRDKKKPVPLLLDQDYVNLKNQIIKAERRVLKELGFCVHVKHPHKIIVMYLQVLECERNQHLVQTSWNYMNDSLRTDVFVRFQPESIACACIYLAARTLEIPLPNRPHWFLLFGATEEEIQEICLKILQLYARKKVDLTHLEGEVEKRKHAIEEAKAQARGLLPGG

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Trichoplusia ni

Entity 3 polymer

description	Cyclin-dependent kinase 11B
formula_weight	50050.6 kDa
ec_number	2.7.11.22
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

SNAMSEDEERENENHLLVVPESRFDRDSGESEEAEEEVGEGTPQSSALTEGDYVPDSPALSPIELKQELPKYLPALQGCRSVEEFQCLNRIEEGTYGVVYRAKDKKTDEIVALKRLKMEKEKEGFPITSLREINTILKAQHPNIVTVREIVVGSNMDKIYIVMNYVEHDLKSLMETMKQPFLPGEVKTLMIQLLRGVKHLHDNWILHRDLKTSNLLLSHAGILKVGDFGLAREYGSPLKAYTPVVVTLWYRAPELLLGAKEYSTAVDMWSVGCIFGELLTQKPLFPGKSEIDQINKVFKDLGTPSEKIWPGYSELPAVKKMTFSEHPYNNLRKRFGALLSDQGFDLMNKFLTYFPGRRISAEDGLKHEYFRETPLPIDPSMFPTWPAKSEQQRVKRGTSPRPPEGGLGYSQLGDDDLKETGFHLTTTNQGASAAGPGFSLKF

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Trichoplusia ni

Entity 4 non-polymer

description	OTS964
formula_weight	392.5 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	80

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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	2.400 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.40 Å
resolution_method	—
num_particles	286108

fit	/app/data/saxs_computation/qk/9qkt/9qkt.fit
pddf	/app/data/pr_computation/qk/9qkt/9qkt.pr.out
profile	/app/data/saxs_computation/qk/9qkt/9qkt.dat

Cryo-EM structure of the CDK11B-cyclin L2-SAP30BP bound to OTS964 (conformation 1)

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 (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 non-polymer

Entity 5 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)