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9xd0

Structure of a membrane-bound inositol phosphorylceramide synthase and Aureobasidin A complex

Method: ELECTRON MICROSCOPY D_max: 84.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9xd0
deposition_date	2025-10-26
title	Structure of a membrane-bound inositol phosphorylceramide synthase and Aureobasidin A complex
keywords	membrane protein, inositol phosphorylceramide synthase, LIPID BINDING PROTEIN, TRANSFERASE; TRANSFERASE
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	24.28 Å
rg_electron	23.48 Å
i0	73616400.00
molecular_weight	49404.0 kDa
excluded_volume	50347 Å³
envelope_volume	83252 Å³
shell_volume	29039 Å³
envelope_diameter	88.0 Å
shell_rg	31.16 Å
envelope_rg	23.83 Å
shape_rg	23.50 Å
total_rg	24.19 Å
total_atoms	3781
n_residues	448
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	84.3 Å
rg_real	24.20 Å
rg_real_error	0.57 Å
i0_real	7.3620e+07
i0_real_error	1.1320e+06
rg_reciprocal	24.22 Å
i0_reciprocal	73620000.0000
total_estimate	0.8663
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	29.4 Å
skewness	0.279
kurtosis	-0.302
angular_range	— – 0.3250 Å⁻¹
current_alpha	0.0000
highest_alpha	17380000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.764; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.973; Smooth: 0.993

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Inositol phosphorylceramide synthase catalytic subunit AUR1
formula_weight	45223.0 kDa
ec_number	2.7.1.227
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3781

MANPFSRWFLSERPPNCHVADLETSLDPHQTLLKVQKYKPALSDWVHYIFLGSIMLFVFITNPAPWIFKILFYCFLGTLFIIPATSQFFFNALPILTWVALYFTSSYFPDDRRPPITVKVLPAVETILYGDNLSDILATSTNSFLDILAWLPYGLFHFGAPFVVAAILFVFGPPTVLQGYAFAFGYMNLFGVIMQNVFPAAPPWYKILYGLQSANYDMHGSPGGLARIDKLLGINMYTTAFSNSSVIFGAFPSLHSGCATMEALFFCYCFPKLKPLFIAYVCWLWWSTMYLTHHYFVDLMAGSVLSYVIFQYTKYTHLPIVDTSLFCRWSYTSIEKYDISKSDPLAADSNDIESVPLSNLELDFDLNMTDEPSVSPSLFDGSTSVSRSSATSITSLGVKRA

Source

organism	Saccharomyces cerevisiae S288C
ncbi_taxonomy_id	559292
host_organism	Homo sapiens

Entity 2 polymer

description	Inositol phosphorylceramide synthase regulatory subunit KEI1
formula_weight	25505.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MRSSLLTLPKSFLGFMPLYLAVEIVLGISILNKCSGAYGILALFTGHPLDFMQWIAYLWSVFTLIVFSQGLYLIHKPNLLVFSQICVLYTIDTISTCFFTLWFTTQWFTLEDTANIDGNNALQSNPISTGKLTERGIDISKQSATESYEYTMTILITLVSLIFRFYFNFILASFVQELLHHPKYLVDRDDVEQNLKNKPIWKRLWAKSQKGCYKLCKNLLE

Source

organism	Saccharomyces cerevisiae S288C
ncbi_taxonomy_id	559292
host_organism	Homo sapiens

Entity 3 polymer

description	Aureobasidin-A
formula_weight	1119.4 kDa
src_method	syn
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

VLXXVFFPI

Entity 4 non-polymer

description	TETRADECANE
formula_weight	198.4 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	(2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl tetradecanoate
formula_weight	635.9 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	3.530 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.53 Å
resolution_method	—
num_particles	228212

fit	/app/data/saxs_computation/xd/9xd0/9xd0.fit
pddf	/app/data/pr_computation/xd/9xd0/9xd0.pr.out
profile	/app/data/saxs_computation/xd/9xd0/9xd0.dat

Structure of a membrane-bound inositol phosphorylceramide synthase and Aureobasidin A complex

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

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Entity 4 non-polymer

Entity 5 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)