SAXSdb — 9t17

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1. Structure Basics

entry_id	9t17
deposition_date	2025-10-21
title	Cryo-EM reconstruction of the Kinesin KIF5A motor domain decorated GMPCPP microtubule
keywords	Microtubule-binding motor domain. Tubulin dimer., STRUCTURAL PROTEIN; STRUCTURAL 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	33.54 Å
rg_electron	32.88 Å
i0	286964000.00
molecular_weight	132810.0 kDa
excluded_volume	164590 Å³
envelope_volume	203940 Å³
shell_volume	50344 Å³
envelope_diameter	117.3 Å
shell_rg	40.72 Å
envelope_rg	33.20 Å
shape_rg	32.89 Å
total_rg	33.40 Å
total_atoms	9327
n_residues	1173
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	111.0 Å
rg_real	33.48 Å
rg_real_error	0.85 Å
i0_real	2.8700e+08
i0_real_error	4.4450e+06
rg_reciprocal	33.52 Å
i0_reciprocal	287000000.0000
total_estimate	0.8898
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	37.8 Å
skewness	0.280
kurtosis	-0.418
angular_range	— – 0.2350 Å⁻¹
current_alpha	0.0000
highest_alpha	83520000.0000
n_real_points	48
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.870; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.959

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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	48966.3 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	9327

MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDMAALEKDYEEVGVDSV

Entity 2 polymer

description	Tubulin beta-2B chain
formula_weight	48033.1 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEATGNKYVPRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVMPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDSKNMMAACDPRHGRYLTVAAIFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRGLKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQYQD

Entity 3 polymer

description	Kinesin heavy chain isoform 5A
formula_weight	36544.5 kDa
ec_number	5.6.1.3
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

MAETNNECSIKVLCRFRPLNQAEILRGDKFIPIFQGDDSVVIGGKPYVFDRVFPPNTTQEQVYHACAMQIVKDVLAGYNGTIFAYGQTSSGKTHTMEGKLHDPQLMGIIPRIARDIFNHIYSMDENLEFHIKVSYFEIYLDKIRDLLDVTKTNLSVHEDKNRVPFVKGCTERFVSSPEEILDVIDEGKSNRHVAVTNMNEHSSRSHSIFLINIKQENMETEQKLSGKLYLVDLAGSEKVSKTGAEGAVLDEAKNINKSLSALGNVISALAEGTKSYVPYRDSKMTRILQDSLGGNCRTTMFICCSPSSYNDAETKSTLMFGQRAKT

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

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	2

Entity 6 non-polymer

description	PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
formula_weight	521.2 kDa
src_method	syn
entity_count	1

Entity 7 non-polymer

description	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
formula_weight	505.2 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	2.770 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.77 Å
resolution_method	—
num_particles	117345

fit	/app/data/saxs_computation/t1/9t17/9t17.fit
pddf	/app/data/pr_computation/t1/9t17/9t17.pr.out
profile	/app/data/saxs_computation/t1/9t17/9t17.dat

Cryo-EM reconstruction of the Kinesin KIF5A motor domain decorated GMPCPP microtubule

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

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)