SAXSdb — 9yab

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1. Structure Basics

entry_id	9yab
deposition_date	2025-09-15
title	KIF1A R350W bound to microtubules in the apo state
keywords	KIF1A, Kinesin-3 superfamily, KIF1A R350W mutant, motor domain, Apo, MOTOR PROTEIN; MOTOR 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	34.12 Å
rg_electron	33.34 Å
i0	310891000.00
molecular_weight	138100.0 kDa
excluded_volume	171030 Å³
envelope_volume	215410 Å³
shell_volume	52354 Å³
envelope_diameter	126.9 Å
shell_rg	41.26 Å
envelope_rg	33.67 Å
shape_rg	33.35 Å
total_rg	33.86 Å
total_atoms	9687
n_residues	1219
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	118.6 Å
rg_real	34.05 Å
rg_real_error	0.93 Å
i0_real	3.1090e+08
i0_real_error	5.0170e+06
rg_reciprocal	34.09 Å
i0_reciprocal	310900000.0000
total_estimate	0.8699
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	38.7 Å
skewness	0.300
kurtosis	-0.354
angular_range	— – 0.2300 Å⁻¹
current_alpha	0.0000
highest_alpha	96410000.0000
n_real_points	47
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.782; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.958

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

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

Polymer

type	polypeptide(L)
strand_id	A
atom_count	9687

MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Entity 2 polymer

description	Tubulin beta-2B chain
formula_weight	49999.9 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEATGNKYVPRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVMPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDSKNMMAACDPRHGRYLTVAAIFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRGLKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQYQDATADEQGEFEEEEGEDEA

Entity 3 polymer

description	Kinesin-like protein KIF1A
formula_weight	49317.5 kDa
ec_number	5.6.1.3
mutation	R350W
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	K

MAGASVKVAVRVRPFNSREMSRDSKCIIQMSGSTTTIVNPKQPKETPKSFSFDYSYWSHTSPEDINYASQKQVYRDIGEEMLQHAFEGYNVCIFAYGQTGAGKSYTMMGKQEKDQQGIIPQLCEDLFSRINDTTNDNMSYSVEVSYMEIYCERVRDLLNPKNKGNLRVREHPLLGPYVEDLSKLAVTSYNDIQDLMDSGNKARTVAATNMNETSSRSHAVFNIIFTQKRHDAETNITTEKVSKISLVDLAGSERADSTGAKGTRLKEGANINKSLTTLGKVISALAEMDSGPNKNKKKKKTDFIPYRDSVLTWLLRENLGGNSRTAMVAALSPADINYDETLSTLRYADWAKQIRCNAVINEDPNNKLIRELKDEVTRLRDLLYAQGLGDITDGAGVKQLEDKVEELASKNYHLENEVARLKKLVEFTSAWSHPQFEK

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21(DE3)

Entity 4 non-polymer

description	GUANOSINE-5'-TRIPHOSPHATE
formula_weight	523.2 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	1

Entity 6 non-polymer

description	GUANOSINE-5'-DIPHOSPHATE
formula_weight	443.2 kDa
src_method	syn
entity_count	1

Entity 7 non-polymer

description	TAXOL
formula_weight	853.9 kDa
src_method	syn
entity_count	1

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6. Citations (1)

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resolution	3.21 Å
resolution_method	—
num_particles	953398

fit	/app/data/saxs_computation/ya/9yab/9yab.fit
pddf	/app/data/pr_computation/ya/9yab/9yab.pr.out
profile	/app/data/saxs_computation/ya/9yab/9yab.dat

KIF1A R350W bound to microtubules in the apo state

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)