← Back to search

9yxq

Cryo-EM structure of the Xenopus laevis mitotic centromere-associated kinesin (MCAK) bound to the paclitaxel-stabilized microtubule

Method: ELECTRON MICROSCOPY D_max: 216.0 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9yxq
deposition_date	2025-10-27
title	Cryo-EM structure of the Xenopus laevis mitotic centromere-associated kinesin (MCAK) bound to the paclitaxel-stabilized microtubule
keywords	microtubule, MCAK, kinesin, mitosis, cell cycle; CELL CYCLE
method	ELECTRON MICROSCOPY

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	77.87 Å
rg_electron	78.90 Å
i0	6722780000.00
molecular_weight	677680.0 kDa
excluded_volume	840500 Å³
envelope_volume	1205000 Å³
shell_volume	138450 Å³
envelope_diameter	289.4 Å
shell_rg	65.41 Å
envelope_rg	77.96 Å
shape_rg	78.91 Å
total_rg	78.69 Å
total_atoms	47551
n_residues	5950
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

▼

3. P(r) Analysis (GNOM)

dmax	216.0 Å
rg_real	73.71 Å
rg_real_error	1.12 Å
i0_real	6.4980e+09
i0_real_error	1.3480e+08
rg_reciprocal	74.92 Å
i0_reciprocal	6670000000.0000
total_estimate	0.9146
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	75.6 Å
skewness	0.494
kurtosis	-0.448
angular_range	— – 0.1000 Å⁻¹
current_alpha	0.1824
highest_alpha	200400000.0000
n_real_points	21
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.899; Stabil: 0.971; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.315

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (7)

Entity 1 polymer

description	Tubulin alpha-1B chain
formula_weight	50204.4 kDa
src_method	nat
entity_count	6

Polymer

type	polypeptide(L)
strand_id	1,3,6,8,A,a
atom_count	47551

MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Entity 2 polymer

description	Tubulin beta chain
formula_weight	49907.8 kDa
src_method	nat
entity_count	6

Polymer

type	polypeptide(L)
strand_id	2,4,5,7,B,b

MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEAAGNKYVPRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMMAACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRGLKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQYQDATADEQGEFEEEGEEDEA

Entity 3 polymer

description	Kinesin-like protein KIF2C
formula_weight	83721.8 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	M,m

MERLVATRLVTGLAVKIMRSNGVIHNANITSVNMDRSSVNVEWKEGEANKGKEISFADVISVNPELLDAVLAPTNVKENMPPQRNVSSQNHKRKTISKIPAPKEVAAKNSLLSESGAQSVLRERSTRMTAIHETLPYENEMEAESTPLPIQQNSVQARSRSTKVSIAEEPRLQTRISEIVEESLPSGRNNQGRRKSNIVKEMEKMKNKREEQRAQNYERRMKRAQDYDTSVPNWEFGKMIKEFRATMDCHRISMADPAEEHRICVCVRKRPLNKQELSKKEIDIISVPSKNIVLVHEPKLKVDLTKYLENQAFRFDFSFDETATNEVVYRFTARPLVQSIFEGGKATCFAYGQTGSGKTHTMGGDFSGKSQNVSKGVYAFASRDVFLLLDQPRYKHLDLDVFVTFFEIYNGKVFDLLNKKTKLRVLEDAKQEVQVVGLLEKQVISADDVFKMIEIGSACRTSGQTFANTSSSRSHACLQIILRRGSKLHGKFSLVDLAGNERGVDTASADRITRMEGAEINRSLLALKECIRALGQNKSHTPFRESKLTQILRDSFIGENSRTCMIAMLSPGFNSCEYTLNTLRYADRVKELSPQNAETNDDNLQMEDSGGSHASIEGLQLQDDFLLKDEELSTHNSFQDALNRVGELEDKAVDELRELVQKEPEWTNLLQMTEQPDYDLENFVMQAEYLIQERSKVLIALGDSINSLRLALQVEEQASKQISKKKRSNKSNSLEVLFQ

Source

organism	Xenopus laevis
common_name	African clawed frog
ncbi_taxonomy_id	8355
host_organism	Homo sapiens

Entity 4 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	11

Entity 5 non-polymer

description	GUANOSINE-5'-TRIPHOSPHATE
formula_weight	523.2 kDa
src_method	syn
entity_count	6

Entity 6 non-polymer

description	GUANOSINE-5'-DIPHOSPHATE
formula_weight	443.2 kDa
src_method	syn
entity_count	6

Entity 7 non-polymer

description	TAXOL
formula_weight	853.9 kDa
src_method	syn
entity_count	6

▶

6. Citations (1)

▶

resolution	3.39 Å
resolution_method	—
num_particles	109829

fit	/app/data/saxs_computation/yx/9yxq/9yxq.fit
pddf	/app/data/pr_computation/yx/9yxq/9yxq.pr.out
profile	/app/data/saxs_computation/yx/9yxq/9yxq.dat

Cryo-EM structure of the Xenopus laevis mitotic centromere-associated kinesin (MCAK) bound to the paclitaxel-stabilized microtubule

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

EM 3D

5. Entities & Polymer Info (7)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Source

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)