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9wdb

Paclitaxel/GMPCPP-stabilized human alpha1A/beta3 S239C microtubule

Method: ELECTRON MICROSCOPY D_max: 100.1 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9wdb
deposition_date	2025-08-18
title	Paclitaxel/GMPCPP-stabilized human alpha1A/beta3 S239C microtubule
keywords	Cytoskeleton, microtubules, human tubulin isotypes, paclitaxel, 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	30.58 Å
rg_electron	29.93 Å
i0	158384000.00
molecular_weight	97857.0 kDa
excluded_volume	121290 Å³
envelope_volume	148110 Å³
shell_volume	41008 Å³
envelope_diameter	107.3 Å
shell_rg	37.49 Å
envelope_rg	30.12 Å
shape_rg	29.94 Å
total_rg	30.51 Å
total_atoms	13468
n_residues	859
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	100.1 Å
rg_real	30.62 Å
rg_real_error	0.62 Å
i0_real	1.5840e+08
i0_real_error	2.3550e+06
rg_reciprocal	30.60 Å
i0_reciprocal	158400000.0000
total_estimate	0.6898
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	34.7 Å
skewness	0.433
kurtosis	-0.276
angular_range	— – 0.2600 Å⁻¹
current_alpha	0.0000
highest_alpha	50210000.0000
n_real_points	53
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.843; Stabil: 1.000; Sysdev: 0.193; Positv: 1.000; Valcen: 0.989; Smooth: 0.866

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Tubulin alpha-1A chain
formula_weight	50188.4 kDa
ec_number	3.6.5.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	a
atom_count	13468

MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLIGQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRTIQFVDWCPTGFKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Trichoplusia ni

Entity 2 polymer

description	Tubulin beta-3 chain
formula_weight	50497.6 kDa
mutation	S239c
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	b

MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPSGNYVGDSDLQLERISVYYNEASSHKYVPRAILVDLEPGTMDSVRSGAFGHLFRPDNFIFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKECENCDCLQGFQLTHSLGGGTGSGMGTLLISKVREEYPDRIMNTFSVVPSPKVSDTVVEPYNATLSIHQLVENTDETYCIDNEALYDICFRTLKLATPTYGDLNHLVSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTARGSQQYRALTVPELTQQMFDAKNMMAACDPRHGRYLTVATVFRGRMSMKEVDEQMLAIQSKNSSYFVEWIPNNVKVAVCDIPPRGLKMSSTFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQYQDATAEEEGEMYEDDEEESEAQGPK

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Trichoplusia ni

Entity 3 non-polymer

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

Entity 4 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	TAXOL
formula_weight	853.9 kDa
src_method	syn
entity_count	1

Entity 6 non-polymer

description	PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
formula_weight	521.2 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	2.39 Å
resolution_method	—
num_particles	302424

fit	/app/data/saxs_computation/wd/9wdb/9wdb.fit
pddf	/app/data/pr_computation/wd/9wdb/9wdb.pr.out
profile	/app/data/saxs_computation/wd/9wdb/9wdb.dat

Paclitaxel/GMPCPP-stabilized human alpha1A/beta3 S239C 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

EM 3D

5. Entities & Polymer Info (6)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)