SAXSdb — 9r2i

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1. Structure Basics

entry_id	9r2i
deposition_date	2025-04-30
title	Cryo-EM structure of the complex CDK16:CCNY:14-3-3
keywords	Kinase, Phosphorylation, Cell signalling, Cryo-EM, 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	37.18 Å
rg_electron	36.77 Å
i0	258938000.00
molecular_weight	130090.0 kDa
excluded_volume	162920 Å³
envelope_volume	219390 Å³
shell_volume	49691 Å³
envelope_diameter	125.6 Å
shell_rg	43.05 Å
envelope_rg	36.13 Å
shape_rg	36.76 Å
total_rg	37.20 Å
total_atoms	18260
n_residues	1122
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	122.8 Å
rg_real	37.15 Å
rg_real_error	0.95 Å
i0_real	2.5890e+08
i0_real_error	4.3560e+06
rg_reciprocal	37.17 Å
i0_reciprocal	258900000.0000
total_estimate	0.8912
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	45.7 Å
skewness	0.283
kurtosis	-0.450
angular_range	— – 0.2150 Å⁻¹
current_alpha	0.0000
highest_alpha	58910000.0000
n_real_points	44
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.904; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.890

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	14-3-3 protein eta
formula_weight	28446.9 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	18260

GHMGDREQLLQRARLAEQAERYDDMASAMKAVTELNEPLSNEDRNLLSVAYKNVVGARRSSWRVISSIEQKTMADGNEKKLEKVKAYREKIEKELETVCNDVLSLLDKFLIKNCNDFQYESKVFYLKMKGDYYRYLAEVASGEKKNSVVEASEAAYKEAFEISKEQMQPTHPIRLGLALNFSVFYYEIQNAPEQACLLAKQAFDDAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDQQDEEAGEGN

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 polymer

description	Cyclin-dependent kinase 16
formula_weight	45088.8 kDa
ec_number	2.7.11.22
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

GPLGSRKISTEDINKRLSLPADIRLPEGYLEKLTLNSPIFDKPLSRRLRRVSLSEIGFGKLETYIKLDKLGEGTYATVYKGKSKLTDNLVALKEIRLEHEEGAPCTAIREVSLLKDLKHANIVTLHDIIHTEKSLTLVFEYLDKDLKQYLDDCGNIINMHNVKLFLFQLLRGLAYCHRQKVLHRDLKPQNLLINERGELKLADFGLARAKSIPTKTYSNEVVTLWYRPPDILLGSTDYSTQIDMWGVGCIFYEMATGRPLFPGSTVEEQLHFIFRILGTPTEETWPGILSNEEFKTYNYPKYRAEALLSHAPRLDSDGADLLTKLLQFEGRNRISAEDAMKHPFFLSLGERIHKLPDTTSIFALKEIQLQKEASLRSSSMPDSGRPAFRVVDTEF

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 3 polymer

description	Cyclin-Y
formula_weight	40004.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	D

GPLGSMGNTTSCCVSSSPKLRRNAHSRLESYRPDTDLSREDTGCNLQHISDRENIDDLNMEFNPSDHPRASTIFLSKSQTDVREKRKSLFINHHPPGQIARKRASCSTIFLDDSTVSQPNLKYTIKCVALAIYYHIKNRDPDGRMLLDIFDENLHPLSKSEVPPDYDKHNPEQKQIYRFVRTLFSAAQLTAECAIVTLVYLERLLTYAEIDICPANWKRIVLGAILLASKVWDDQAVWNVDYCQILKDITVEDMNELERQFLELLQFNINVPSSVYAKYYFDLRSLAEANNLSFPLEPLSRERAHKLEAISRLCEDKYKDLRRSARKRAASADNLTLPRWSPAIIS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 4 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
formula_weight	523.2 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	3.300 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.30 Å
resolution_method	—
num_particles	204710

fit	/app/data/saxs_computation/r2/9r2i/9r2i.fit
pddf	/app/data/pr_computation/r2/9r2i/9r2i.pr.out
profile	/app/data/saxs_computation/r2/9r2i/9r2i.dat

Cryo-EM structure of the complex CDK16:CCNY:14-3-3

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 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)