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9yed

T-ring-PomB complex in Vibrio cholerae

Method: ELECTRON MICROSCOPY D_max: 134.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9yed
deposition_date	2025-09-24
title	T-ring-PomB complex in Vibrio cholerae
keywords	In situ cryo-EM, sheathed flagellar motor, Vibrio cholerae, T-ring, PomB, assembled state, 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	39.01 Å
rg_electron	38.77 Å
i0	317484000.00
molecular_weight	140970.0 kDa
excluded_volume	175280 Å³
envelope_volume	246910 Å³
shell_volume	54830 Å³
envelope_diameter	145.0 Å
shell_rg	42.83 Å
envelope_rg	38.60 Å
shape_rg	38.74 Å
total_rg	39.14 Å
total_atoms	9930
n_residues	1230
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	134.4 Å
rg_real	39.21 Å
rg_real_error	1.14 Å
i0_real	3.1750e+08
i0_real_error	5.2300e+06
rg_reciprocal	39.09 Å
i0_reciprocal	317400000.0000
total_estimate	0.8527
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	42.6 Å
skewness	0.517
kurtosis	-0.076
angular_range	— – 0.2050 Å⁻¹
current_alpha	0.0000
highest_alpha	51180000.0000
n_real_points	42
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.778; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.764

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Sodium-type flagellar protein MotX
formula_weight	21729.6 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	AP1,EP1
atom_count	9930

ADLGEPVPIYSEAELIKLIEENKHLERVKADNCQIVEDIVARATRISLPSYEFLYGDMLAWGVCVDQDVELGLYYMENAAHQGLPAALEQLGRYYSRGTLVQQDKERAIPYLREAAAMGNLNARIQLAELLLRDYGSPLDYEDAYRWLYNSVTADQRTHNRIALLRQGLERRMPENIIARAKRRETFW

Entity 2 polymer

description	Sodium-type flagellar protein MotY
formula_weight	31307.1 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	BP1,FP1

LEVRYMATPQQSTWQMATNTPLECRLVHPIPNYGDAEFSSRAGKKINLDFELKMRRPMGDTRNVSLVSMPPVWRPGEGADRITNLQFFKQFDGYIGGQTAWSLLSELEKGRYPTFSYQDWQSRDQRIEVALSSVLFQQPYNEFSDCISKLLPYSFEDISFTILHYDQGTSVELNKASQKRLAQIAEYVRYNQDIDLVLVSTYTDSTDTNNNSQNLSEQRAEVLREYFKSIGLPEDRIQVQGYGKRRPIADNASPIGKDKNRRVVISLGRTQV

Entity 3 polymer

description	Chemotaxis protein PomB
formula_weight	17542.8 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	CP1,DP1

QQQAQAMSEQMETVAESIKKALSREIEQGAIEVENLGQQIDIRIREKGAFPEGSAFLQPKFRPLVRQIAELVKDIPGKVRVTGHTDNQKLDSELYRSNWDLSAQRAVSVAQEMEKVKDFDHLRLQVRGLADTQPLGPNDTEAQRATNRRVEISIL

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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	triclinic

resolution	4.98 Å
resolution_method	—
num_particles	697164

fit	/app/data/saxs_computation/ye/9yed/9yed.fit
pddf	/app/data/pr_computation/ye/9yed/9yed.pr.out
profile	/app/data/saxs_computation/ye/9yed/9yed.dat

T-ring-PomB complex in Vibrio cholerae

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 (3)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)