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9umu

Giraffe KIF5A motor domain in nucleotide free state bound to microtubule

Method: ELECTRON MICROSCOPY D_max: 110.2 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9umu
deposition_date	2025-04-23
title	Giraffe KIF5A motor domain in nucleotide free state bound to microtubule
keywords	Giraffe Kinesin motor KIF Microtubule, 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	33.99 Å
rg_electron	33.38 Å
i0	278314000.00
molecular_weight	131640.0 kDa
excluded_volume	163530 Å³
envelope_volume	205600 Å³
shell_volume	50474 Å³
envelope_diameter	121.2 Å
shell_rg	40.85 Å
envelope_rg	33.42 Å
shape_rg	33.39 Å
total_rg	33.89 Å
total_atoms	9240
n_residues	1170
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	110.2 Å
rg_real	33.92 Å
rg_real_error	0.76 Å
i0_real	2.7830e+08
i0_real_error	3.9480e+06
rg_reciprocal	33.96 Å
i0_reciprocal	278300000.0000
total_estimate	0.6793
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	37.5 Å
skewness	0.278
kurtosis	-0.431
angular_range	— – 0.2350 Å⁻¹
current_alpha	0.0000
highest_alpha	81650000.0000
n_real_points	48
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.897; Stabil: 1.000; Sysdev: 0.078; Positv: 1.000; Valcen: 0.998; Smooth: 0.902

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Tubulin alpha-1B chain
formula_weight	49574.8 kDa
ec_number	3.6.5.-
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	9240

MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDDSFNTFFSETGAGKHVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Entity 2 polymer

description	Tubulin beta chain
formula_weight	49717.6 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGTYHGDSDLQLDRISVYYNEATGGKYVPRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKEAESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQVFDAKNMMAACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRGLKMAVTFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQYQDATAEEEEDFGEEAEEEA

Entity 3 polymer

description	GcKIF5A
formula_weight	37340.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	J

MAETNNECSIKVLCRFRPLNQAEILRGDKFIPIFQGDDSVVIGGKPYVFDRVFPPNTTQEQVYHACAMQIVKDVLAGYNGTIFAYGQTSSGKTHTMEGKLHDPQLMGIIPRIVQDIFNHIYSMDENLEFHIKVSYFEIYLDKIRDLLDVTKTNLAVHEDKNRVPFVKGCTERFVSSPEEILDVIDEGKSNRHVAVTNMNEHSSRSHSIFLINIKQENMETEQKLSGKLYLVDLAGSEKVSKTGAEGAVLDEAKNINKSLSALGNVISALAEGTKSYVPYRDSKMTRILQDSLGGNCRTTMFICCSPSSFNDAETKSTLMFGQRAKTIKNTASVN

Source

organism	Giraffa camelopardalis
ncbi_taxonomy_id	9894
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	GUANOSINE-5'-DIPHOSPHATE
formula_weight	443.2 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	4.400 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	4.40 Å
resolution_method	—
num_particles	28333

fit	/app/data/saxs_computation/um/9umu/9umu.fit
pddf	/app/data/pr_computation/um/9umu/9umu.pr.out
profile	/app/data/saxs_computation/um/9umu/9umu.dat

Giraffe KIF5A motor domain in nucleotide free state bound to 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 (5)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Source

Entity 4 non-polymer

Entity 5 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)