SAXSdb — 9skq

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1. Structure Basics

entry_id	9skq
deposition_date	2025-09-02
title	Cryo-EM structure of CAK-CDK1-cyclin B1
keywords	Complex, cell cycle, kinase, TRANSFERASE; TRANSFERASE
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	36.30 Å
rg_electron	35.93 Å
i0	279861000.00
molecular_weight	138680.0 kDa
excluded_volume	175190 Å³
envelope_volume	228340 Å³
shell_volume	53387 Å³
envelope_diameter	129.3 Å
shell_rg	41.84 Å
envelope_rg	35.62 Å
shape_rg	35.90 Å
total_rg	36.45 Å
total_atoms	9750
n_residues	1200
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	120.6 Å
rg_real	36.35 Å
rg_real_error	0.95 Å
i0_real	2.7990e+08
i0_real_error	4.4050e+06
rg_reciprocal	36.32 Å
i0_reciprocal	279900000.0000
total_estimate	0.8602
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	43.8 Å
skewness	0.451
kurtosis	-0.066
angular_range	— – 0.2200 Å⁻¹
current_alpha	0.0000
highest_alpha	103300000.0000
n_real_points	45
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.835; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.678

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	CDK-activating kinase assembly factor MAT1
formula_weight	38132.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H
atom_count	9750

MGSSHHHHHHENLYFQSNAMDDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKSNFRVQLFEDPTVDKEVEIRKKVLKIYNKREEDFPSLREYNDFLEEVEEIVFNLTNNVDLDNTKKKMEIYQKENKDVIQKNKLKLTREQEELEEALEVERQENEQRRLFIQKEEQLQQILKRKNKQAFLDELESSDLPVALLLAQHKDRSTQLEMQLEKPKPVKPVTFSTGIKMGQHISLAPIHKLEEALYEYQPLQIETYGPHVPELEMLGRLGYLNHVRAASPQDLAGGYTSSLACHRALQDAFSGLFWQPS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Trichoplusia ni

Entity 2 polymer

description	Cyclin-H
formula_weight	37721.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	I

XMYHNSSQKRHWTFSSEEQLARLRADANRKFRCKAVANGKVLPNDPVFLEPHEEMTLCKYYEKRLLEFCSVFKPAMPRSVVGTACMYFKRFYLNNSVMEYHPRIIMLTCAFLACKVDEFNVSSPQFVGNLRESPLGQEKALEQILEYELLLIQQLNFHLIVHNPYRPFEGFLIDLKTRYPILENPEILRKTADDFLNRIALTDAYLLYTPSQIALTAILSSASRAGITMESYLSESLMLKENRTCLSQLLDIMKSMRNLVKKYEPPRSEEVAVLKQKLERCHSAELALNVITKKRKGYEDDDYVSKKSKHEEEEWTDDDLVESL

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Trichoplusia ni

Entity 3 polymer

description	Cyclin-dependent kinase 7
formula_weight	43651.1 kDa
ec_number	2.7.11.22,2.7.11.23
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	J

MASWSHPQFEKGGGSGGGSGGGSWSHPQFEKSGGGSENLYFQSNAMALDVKSRAKRYEKLDFLGEGQFATVYKARDKNTNQIVAIKKIKLGHRSEAKDGINRTALREIKLLQELSHPNIIGLLDAFGHKSNISLVFDFMETDLEVIIKDNSLVLTPSHIKAYMLMTLQGLEYLHQHWILHRDLKPNNLLLDENGVLKLADFGLAKSFGSPNRAYTHQVVTRWYRAPELLFGARMYGVGVDMWAVGCILAELLLRVPFLPGDSDLDQLTRIFETLGTPTEEQWPDMCSLPDYVTFKSFPGIPLHHIFSAAGDDLLDLIQGLFLFNPCARITATQALKMKYFSNRPGPTPGCQLPRPNCPVETLKEQSNPALAIKRKRTEALEQGGLPKKLIF

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Trichoplusia ni

Entity 4 polymer

description	Cyclin-dependent kinase 1
formula_weight	34651.9 kDa
ec_number	2.7.11.22,2.7.11.23
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A

GPMGSMEDYTKIEKIGEGTYGVVYKGRHKTTGQVVAMKKIRLESEEEGVPSTAIREISLLKELRHPNIVSLQDVLMQDSRLYLIFEFLSMDLKKYLDSIPPGQYMDSSLVKSYLYQILQGIVFCHSRRVLHRDLKPQNLLIDDKGTIKLADFGLARAFGIPIRVYTHEVVTLWYRSPEVLLGSARYSTPVDIWSIGTIFAELATKKPLFHGDSEIDQLFRIFRALGTPNNEVWPEVESLQDYKNTFPKWKPGSLASHVKNLDENGLDLLSKMLIYDPAKRISGKMALNHPYFNDLDNQIKKM

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Trichoplusia ni

Entity 5 polymer

description	G2/mitotic-specific cyclin-B1
formula_weight	48800.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

GAMGSMALRVTRNSKINAENKAKINMAGAKRVPTAPAATSKPGLRPRTALGDIGNKVSEQLQAKMPMKKEAKPSATGKVIDKKLPKPLEKVPMLVPVPVSEPVPEPEPEPEPEPVKEEKLSPEPILVDTASPSPMETSGCAPAEEDLCQAFSDVILAVNDVDAEDGADPNLCSEYVKDIYAYLRQLEEEQAVRPKYLLGREVTGNMRAILIDWLVQVQMKFRLLQETMYMTVSIIDRFMQNNCVPKKMLQLVGVTAMFIASKYEEMYPPEIGDFAFVTDNTYTKHQIRQMEMKILRALNFGLGRPLPLHFLRRASKIGEVDVEQHTLAKYLMELTMLDYDMVHFPPSQIAAGAFCLALKILDNGEWTPTLQHYLSYTEESLLPVMQHLAKNVVMVNQGLTKHMTVKNKYATSKHAKISTLPQLNSALVQDLAKAVAKV

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Trichoplusia ni

Entity 6 non-polymer

description	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
formula_weight	506.2 kDa
src_method	syn
entity_count	2

Entity 7 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 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	3.400 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.40 Å
resolution_method	—
num_particles	68765

fit	/app/data/saxs_computation/sk/9skq/9skq.fit
pddf	/app/data/pr_computation/sk/9skq/9skq.pr.out
profile	/app/data/saxs_computation/sk/9skq/9skq.dat

Cryo-EM structure of CAK-CDK1-cyclin B1

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 (7)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 polymer

Polymer

Source

Entity 6 non-polymer

Entity 7 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)