SAXSdb — 9xd0

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Inositol phosphorylceramide synthase catalytic subunit AUR1

Saccharomyces cerevisiae S288C

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 3 PDB declaration: dimeric（2） Count mismatch; review required	Chain A； UniProt 1–401	Not recorded	Inositol phosphorylceramide synthase regulatory subunit KEI1 × 1 （Q06346） Aureobasidin-A × 1 C14 TETRADECANE × 2 46E (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl tetradecanoate × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.53 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9XD0	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9IVC Cryo-EM structure of AbA-bound Aur1-Kei1 complex Deposited 2024-07-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–401（401 aa） Chain C 1–401（401 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.17 Å
9VJ4 Structure of a membrane-bound inositol phosphorylceramide synthase and ceramide complex Deposited 2025-06-19	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–401（401 aa）	Not recorded	UJO ~{N}-[(~{Z},2~{S},3~{R})-1,3-bis(oxidanyl)heptadec-4-en-2-yl]dodecanamide × 1 C14 TETRADECANE × 2 46E (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl tetradecanoate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	AUR1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–401； UniProt 1–401

Inositol phosphorylceramide synthase regulatory subunit KEI1

Saccharomyces cerevisiae S288C

UniProt Q06346

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 3 PDB declaration: dimeric（2） Count mismatch; review required	Chain B； UniProt 1–221	Not recorded	Inositol phosphorylceramide synthase catalytic subunit AUR1 × 1 （P36107） Aureobasidin-A × 1 C14 TETRADECANE × 2 46E (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl tetradecanoate × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.53 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9XD0	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9IVC Cryo-EM structure of AbA-bound Aur1-Kei1 complex Deposited 2024-07-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 1–221（221 aa） Chain D 1–221（221 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.17 Å
9VJ4 Structure of a membrane-bound inositol phosphorylceramide synthase and ceramide complex Deposited 2025-06-19	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–221（221 aa）	Not recorded	UJO ~{N}-[(~{Z},2~{S},3~{R})-1,3-bis(oxidanyl)heptadec-4-en-2-yl]dodecanamide × 1 C14 TETRADECANE × 2 46E (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl tetradecanoate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	KEI1_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–221； UniProt 1–221

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9xd0
Deposition date deposition_date	2025-10-26
Structure title title	Structure of a membrane-bound inositol phosphorylceramide synthase and Aureobasidin A complex
Keywords keywords	membrane protein, inositol phosphorylceramide synthase, LIPID BINDING PROTEIN, TRANSFERASE; TRANSFERASE
Experimental Method method	ELECTRON MICROSCOPY

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	24.28 Å
Radius of gyration Rg (electron density) rg_electron	23.48 Å
Forward intensity I(0) i0	73616400.00
Molecular weight molecular_weight	49404.0 kDa
Excluded volume excluded_volume	50347 Å³
Envelope volume envelope_volume	83252 Å³
Hydration-shell volume shell_volume	29039 Å³
Envelope diameter envelope_diameter	88.0 Å
Shell Rg shell_rg	31.16 Å
Envelope Rg envelope_rg	23.83 Å
Shape Rg shape_rg	23.50 Å
Total Rg total_rg	24.19 Å
Total atoms total_atoms	3781
Residues n_residues	448
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	84.3 Å
Rg (real space) rg_real	24.20 Å
Rg uncertainty (real space) rg_real_error	0.57 Å
I(0) (real space) i0_real	7.3620e+07
I(0) uncertainty (real space) i0_real_error	1.1320e+06
Rg (reciprocal space) rg_reciprocal	24.22 Å
I(0) (reciprocal space) i0_reciprocal	73620000.0000
Solution quality estimate total_estimate	0.8663
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	29.4 Å
Skewness Skewness skewness	0.279
Kurtosis Kurtosis kurtosis	-0.302
Angular range angular_range	— – 0.3250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	17380000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria 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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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Inositol phosphorylceramide synthase catalytic subunit AUR1
Molecular weight formula_weight	45223.0 kDa
EC 编号 ec_number	2.7.1.227
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3781

MANPFSRWFLSERPPNCHVADLETSLDPHQTLLKVQKYKPALSDWVHYIFLGSIMLFVFITNPAPWIFKILFYCFLGTLFIIPATSQFFFNALPILTWVALYFTSSYFPDDRRPPITVKVLPAVETILYGDNLSDILATSTNSFLDILAWLPYGLFHFGAPFVVAAILFVFGPPTVLQGYAFAFGYMNLFGVIMQNVFPAAPPWYKILYGLQSANYDMHGSPGGLARIDKLLGINMYTTAFSNSSVIFGAFPSLHSGCATMEALFFCYCFPKLKPLFIAYVCWLWWSTMYLTHHYFVDLMAGSVLSYVIFQYTKYTHLPIVDTSLFCRWSYTSIEKYDISKSDPLAADSNDIESVPLSNLELDFDLNMTDEPSVSPSLFDGSTSVSRSSATSITSLGVKRA

来源 Source

来源生物 organism	Saccharomyces cerevisiae S288C
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Inositol phosphorylceramide synthase regulatory subunit KEI1
Molecular weight formula_weight	25505.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MRSSLLTLPKSFLGFMPLYLAVEIVLGISILNKCSGAYGILALFTGHPLDFMQWIAYLWSVFTLIVFSQGLYLIHKPNLLVFSQICVLYTIDTISTCFFTLWFTTQWFTLEDTANIDGNNALQSNPISTGKLTERGIDISKQSATESYEYTMTILITLVSLIFRFYFNFILASFVQELLHHPKYLVDRDDVEQNLKNKPIWKRLWAKSQKGCYKLCKNLLE

来源 Source

来源生物 organism	Saccharomyces cerevisiae S288C
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	Aureobasidin-A
Molecular weight formula_weight	1119.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

VLXXVFFPI

Entity 4 Entity 4 non-polymer

Description description	TETRADECANE
Molecular weight formula_weight	198.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	(2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl tetradecanoate
Molecular weight formula_weight	635.9 kDa
Source method src_method	syn
Copy count entity_count	1

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.530 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	3.53 Å
Resolution测定方法 resolution_method	—
颗粒数 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

1. Protein Identity and Related Structures Protein Identity & Related Structures

Inositol phosphorylceramide synthase catalytic subunit AUR1

State in the Current Structure

Other States of the Same Protein in the Database

Inositol phosphorylceramide synthase regulatory subunit KEI1

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)