SAXSdb — 9yai

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1. Structure Basics

entry_id	9yai
deposition_date	2025-09-16
title	KIF1A R350W bound to microtubules in two-heads-bound state with AMP-PNP
keywords	KIF1A, Kinesin-3 superfamily, KIF1A R350W mutant, motor domain, AMP-PNP bound, cargo transport, 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	52.47 Å
rg_electron	52.78 Å
i0	1220180000.00
molecular_weight	281670.0 kDa
excluded_volume	348290 Å³
envelope_volume	465500 Å³
shell_volume	76374 Å³
envelope_diameter	194.0 Å
shell_rg	52.32 Å
envelope_rg	52.44 Å
shape_rg	52.78 Å
total_rg	52.74 Å
total_atoms	19749
n_residues	2478
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	188.3 Å
rg_real	52.82 Å
rg_real_error	2.70 Å
i0_real	1.2200e+09
i0_real_error	2.7060e+07
rg_reciprocal	52.17 Å
i0_reciprocal	1219000000.0000
total_estimate	0.8252
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	50.2 Å
skewness	0.505
kurtosis	-0.414
angular_range	— – 0.1500 Å⁻¹
current_alpha	0.0000
highest_alpha	154600000.0000
n_real_points	31
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.679; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.904; Smooth: 0.783

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	Kinesin-like protein KIF1A
formula_weight	49317.5 kDa
ec_number	5.6.1.3
mutation	R350W
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	K,N
atom_count	19749

MAGASVKVAVRVRPFNSREMSRDSKCIIQMSGSTTTIVNPKQPKETPKSFSFDYSYWSHTSPEDINYASQKQVYRDIGEEMLQHAFEGYNVCIFAYGQTGAGKSYTMMGKQEKDQQGIIPQLCEDLFSRINDTTNDNMSYSVEVSYMEIYCERVRDLLNPKNKGNLRVREHPLLGPYVEDLSKLAVTSYNDIQDLMDSGNKARTVAATNMNETSSRSHAVFNIIFTQKRHDAETNITTEKVSKISLVDLAGSERADSTGAKGTRLKEGANINKSLTTLGKVISALAEMDSGPNKNKKKKKTDFIPYRDSVLTWLLRENLGGNSRTAMVAALSPADINYDETLSTLRYADWAKQIRCNAVINEDPNNKLIRELKDEVTRLRDLLYAQGLGDITDGAGVKQLEDKVEELASKNYHLENEVARLKKLVEFTSAWSHPQFEK

Source

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

Entity 2 polymer

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

Polymer

type	polypeptide(L)
strand_id	A,E

MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Entity 3 polymer

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

Polymer

type	polypeptide(L)
strand_id	B,I

MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEATGNKYVPRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVMPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDSKNMMAACDPRHGRYLTVAAIFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRGLKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQYQDATADEQGEFEEEEGEDEA

Entity 4 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	3

Entity 5 non-polymer

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

Entity 6 non-polymer

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

Entity 7 non-polymer

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

Entity 8 non-polymer

description	TAXOL
formula_weight	853.9 kDa
src_method	syn
entity_count	2

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6. Citations (1)

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resolution	3.12 Å
resolution_method	—
num_particles	556086

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

KIF1A R350W bound to microtubules in two-heads-bound state with AMP-PNP

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 (8)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)