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9ymg

Human KIF18A-DARPin fusion protein bound to AMP-PNP and tubulin

Method: X-RAY DIFFRACTION D_max: 139.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ymg
deposition_date	2025-10-09
title	Human KIF18A-DARPin fusion protein bound to AMP-PNP and tubulin
keywords	kinesin, motor protein, microtubule, complex; MOTOR PROTEIN
method	X-RAY DIFFRACTION

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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	43.68 Å
rg_electron	43.04 Å
i0	1389250000.00
molecular_weight	301430.0 kDa
excluded_volume	374070 Å³
envelope_volume	487150 Å³
shell_volume	89530 Å³
envelope_diameter	151.6 Å
shell_rg	51.52 Å
envelope_rg	42.42 Å
shape_rg	43.03 Å
total_rg	43.39 Å
total_atoms	21148
n_residues	2694
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	139.6 Å
rg_real	43.43 Å
rg_real_error	0.93 Å
i0_real	1.3890e+09
i0_real_error	2.5870e+07
rg_reciprocal	43.68 Å
i0_reciprocal	1390000000.0000
total_estimate	0.8859
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	58.2 Å
skewness	0.125
kurtosis	-0.416
angular_range	— – 0.1800 Å⁻¹
current_alpha	0.0000
highest_alpha	327200000.0000
n_real_points	37
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.868; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.933

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4. Crystallography & Experiment

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5. Entities & Polymer Info (9)

Entity 1 polymer

description	Tubulin alpha-1B chain
formula_weight	50204.4 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,D
atom_count	21620

MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Entity 2 polymer

description	Tubulin beta chain
formula_weight	49793.7 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,E

MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEAAGNKYVPRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMMAACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRGLKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQYQDATADEEEDFGEEAEEEA

Entity 3 polymer

description	Kinesin-like protein KIF18A, DARPin fusion protein
formula_weight	59769.4 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,F

SNAMSVTEEDLCHHMKVVVRVRPENTKEKAAGFHKVVHVVDKHILVFDPKQEEVSFFHGKKTTNQNVIKKQNKDLKFVFDAVFDETSTQSEVFEHTTKPILRSFLNGYNCTVLAYGATGAGKTHTMLGSADEPGVMYLTMLHLYKCMDEIKEEKICSTAVSYLEVYNEQIRDLLVNSGPLAVREDTQKGVVVHGLTLHQPKSSEEILHLLDNGNKNRTQHPTDMNATSSRSHAVFQIYLRQQDKTASINQNVRIAKMSLIDLAGSERASTSGAKGTRFVEGTNINRSLLALGNVINALADSKRKNQHIPYRNSKLTRLLKDSLGGNCQTIMIAAVSPSSVFYDDTYNTLKYANRAKDIKSSLKSNVLNVNGGGGSGGGGSGGGGSGGGGSGGGGSGGSDLGKKLLEAARAGQDDEVRILMANGADVNATDASGLTPLHLAATYGHLEIVEVLLKHGADVNAIDIMGSTPLHLAALIGHLEIVEVLLKHGADVNAVDTWGDTPLHLAAIMGHLEIVEVLLKHGADVNAQDKFGKTAFDISIDNGNEDLAEILQKLN

Source

organism	synthetic construct
ncbi_taxonomy_id	32630
host_organism	Escherichia coli

Entity 4 non-polymer

description	GUANOSINE-5'-TRIPHOSPHATE
formula_weight	523.2 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	6

Entity 6 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	1

Entity 7 non-polymer

description	GUANOSINE-5'-DIPHOSPHATE
formula_weight	443.2 kDa
src_method	syn
entity_count	2

Entity 8 non-polymer

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

Entity 9 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	455

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6. Citations (1)

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length_a	105.380 Å
length_b	135.470 Å
length_c	117.670 Å
angle_alpha	90.00 °
angle_beta	107.67 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.406 Å
resolution_low	48.673 Å
r_factor	—
r_work	0.1907
r_free	0.2377

fit	/app/data/saxs_computation/ym/9ymg/9ymg.fit
pddf	/app/data/pr_computation/ym/9ymg/9ymg.pr.out
profile	/app/data/saxs_computation/ym/9ymg/9ymg.dat

Human KIF18A-DARPin fusion protein bound to AMP-PNP and tubulin

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

Diffraction

5. Entities & Polymer Info (9)

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

Entity 8 non-polymer

Entity 9 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)