SAXSdb — 8iam

▼

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

Chimera of Long chain base biosynthesis protein 1 and Serine palmitoyltransferase 1

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 8	Serine palmitoyltransferase 2 × 2 （P40970） Protein ORM2 × 2 （Q06144） Serine palmitoyltransferase-regulating protein TSC3 × 2 （Q3E790） PYRIDOXAL-5'-PHOSPHATE × 2 N-[(2S,3R,4E)-1,3-dihydroxyoctadec-4-en-2-yl]tetracosanamide × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LCB1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 78–534； UniProt 102–558 Author chain E； PDBConstruct 78–534； UniProt 102–558

Chimera of Long chain base biosynthesis protein 1 and Serine palmitoyltransferase 1

Saccharomyces cerevisiae

UniProt Q94IB8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 8	Serine palmitoyltransferase 2 × 2 （P40970） Protein ORM2 × 2 （Q06144） Serine palmitoyltransferase-regulating protein TSC3 × 2 （Q3E790） PYRIDOXAL-5'-PHOSPHATE × 2 N-[(2S,3R,4E)-1,3-dihydroxyoctadec-4-en-2-yl]tetracosanamide × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LCB1_ARATH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–77； UniProt 1–77 Author chain E； PDBConstruct 1–77； UniProt 1–77

Serine palmitoyltransferase 2

Saccharomyces cerevisiae

UniProt P40970

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 8	Chimera of Long chain base biosynthesis protein 1 and Serine palmitoyltransferase 1 × 2 （P25045,Q94IB8） Protein ORM2 × 2 （Q06144） Serine palmitoyltransferase-regulating protein TSC3 × 2 （Q3E790） PYRIDOXAL-5'-PHOSPHATE × 2 N-[(2S,3R,4E)-1,3-dihydroxyoctadec-4-en-2-yl]tetracosanamide × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LCB2_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–561； UniProt 1–561 Author chain F； PDBConstruct 1–561； UniProt 1–561

Protein ORM2

Saccharomyces cerevisiae

UniProt Q06144

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 8	Chimera of Long chain base biosynthesis protein 1 and Serine palmitoyltransferase 1 × 2 （P25045,Q94IB8） Serine palmitoyltransferase 2 × 2 （P40970） Serine palmitoyltransferase-regulating protein TSC3 × 2 （Q3E790） PYRIDOXAL-5'-PHOSPHATE × 2 N-[(2S,3R,4E)-1,3-dihydroxyoctadec-4-en-2-yl]tetracosanamide × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ORM2_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain D； PDBConstruct 1–216； UniProt 1–216 Author chain H； PDBConstruct 1–216； UniProt 1–216

Serine palmitoyltransferase-regulating protein TSC3

Saccharomyces cerevisiae

UniProt Q3E790

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 8	Chimera of Long chain base biosynthesis protein 1 and Serine palmitoyltransferase 1 × 2 （P25045,Q94IB8） Serine palmitoyltransferase 2 × 2 （P40970） Protein ORM2 × 2 （Q06144） PYRIDOXAL-5'-PHOSPHATE × 2 N-[(2S,3R,4E)-1,3-dihydroxyoctadec-4-en-2-yl]tetracosanamide × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TSC3_YEAST
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain C； PDBConstruct 1–80； UniProt 1–80 Author chain G； PDBConstruct 1–80； UniProt 1–80

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	8iam
Deposition date deposition_date	2023-02-08
Structure title title	Cryo-EM structure of the yeast SPT-ORM2 (ORM2-S3D) complex
Keywords keywords	ceramide, phosphorylation, TRANSFERASE-INHIBITOR COMPLEX; TRANSFERASE/INHIBITOR
Experimental Method method	ELECTRON MICROSCOPY

▼

3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

8iam__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

8iam__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8iam__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	49.96 Å
Rg (electron density)	49.62 Å
Total Rg	49.79 Å
Atom count	20192
Residues	2536
Excluded volume	363070 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8iam__assembly_1__model_1`	octameric （8）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Chimera of Long chain base biosynthesis protein 1 and Serine palmitoyltransferase 1
Molecular weight formula_weight	59354.7 kDa
EC 编号 ec_number	2.3.1.50
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,E
Atom count atom_count	20192

MASNLVEMFNAALNWVTMILESPSARVVLFGVPIRGHFFVEGLLGVVIIILLTRKSYKPPKRPLTEQEIDELCDEWVPEPLVDPSATDEQSWRVAKTPVTMEMPIQNHITITRNNLQEKYTNVFNLASNNFLQLSATEPVKEVVKTTIKNYGVGACGPAGFYGNQDVHYTLEYDLAQFFGTQGSVLYGQDFCAAPSVLPAFTKRGDVIVADDQVSLPVQNALQLSRSTVYYFNHNDMNSLECLLNELTEQEKLEKLPAIPRKFIVTEGIFHNSGDLAPLPELTKLKNKYKFRLFVDETFSIGVLGATGRGLSEHFNMDRATAIDITVGSMATALGSTGGFVLGDSVMCLHQRIGSNAYCFSACLPAYTVTSVSKVLKLMDSNNDAVQTLQKLSKSLHDSFASDDSLRSYVIVTSSPVSAVLHLQLTPAYRSRKFGYTCEQLFETMSALQKKSQTNKFIEPYEEEEKFLQSIVDHALINYNVLITRNTIVLKQETLPIVPSLKICCNAAMSPEELKNACESVKQSILACCQESNK

Source Source

Source organism organism	Saccharomyces cerevisiae
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Serine palmitoyltransferase 2
Molecular weight formula_weight	63189.7 kDa
EC 编号 ec_number	2.3.1.50
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,F

MSTPANYTRVPLCEPEELPDDIQKENEYGTLDSPGHLYQVKSRHGKPLPEPVVDTPPYYISLLTYLNYLILIILGHVHDFLGMTFQKNKHLDLLEHDGLAPWFSNFESFYVRRIKMRIDDCFSRPTTGVPGRFIRCIDRISHNINEYFTYSGAVYPCMNLSSYNYLGFAQSKGQCTDAALESVDKYSIQSGGPRAQIGTTDLHIKAEKLVARFIGKEDALVFSMGYGTNANLFNAFLDKKCLVISDELNHTSIRTGVRLSGAAVRTFKHGDMVGLEKLIREQIVLGQPKTNRPWKKILICAEGLFSMEGTLCNLPKLVELKKKYKCYLFIDEAHSIGAMGPTGRGVCEIFGVDPKDVDILMGTFTKSFGAAGGYIAADQWIIDRLRLDLTTVSYSESMPAPVLAQTISSLQTISGEICPGQGTERLQRIAFNSRYLRLALQRLGFIVYGVADSPVIPLLLYCPSKMPAFSRMMLQRRIAVVVVAYPATPLIESRVRFCMSASLTKEDIDYLLRHVSEVGDKLNLKSNSGKSSYDGKRQRWDIEEVIRRTPEDCKDDKYFVN

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	Protein ORM2
Molecular weight formula_weight	24962.6 kDa
Mutation mutation	S46D,S47D,S48D
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,H

MIDRTKNESPAFEESPLTPNVSNLKPFPSQSNKISTPVTDHRRRRDDDVISHVEQETFEDENDQQMLPNMNATWVDQRGAWLIHIVVIVLLRLFYSLFGSTPKWTWTLTNMTYIIGFYIMFHLVKGTPFDFNGGAYDNLTMWEQINDETLYTPTRKFLLIVPIVLFLISNQYYRNDMTLFLSNLAVTVLIGVVPKLGITHRLRISIPGITGRAQIS

Source Source

Source organism organism	Saccharomyces cerevisiae
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Homo sapiens

Entity 4 Entity 4 polymer

Description description	Serine palmitoyltransferase-regulating protein TSC3
Molecular weight formula_weight	9590.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,G

MTQHKSSMVYIPTTKEAKRRNGKSEGILNTIEEVVEKLYWTYYIHLPFYLMASFDSFFLHVFFLTIFSLSFFGILKYCFL

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Homo sapiens

Entity 5 Entity 5 non-polymer

Description description	PYRIDOXAL-5'-PHOSPHATE
Molecular weight formula_weight	247.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	N-[(2S,3R,4E)-1,3-dihydroxyoctadec-4-en-2-yl]tetracosanamide
Molecular weight formula_weight	650.1 kDa
Source method src_method	syn
Copy count entity_count	2

▶

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	3.10 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	155763

Cryo-EM structure of the yeast SPT-ORM2 (ORM2-S3D) complex

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

Chimera of Long chain base biosynthesis protein 1 and Serine palmitoyltransferase 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Chimera of Long chain base biosynthesis protein 1 and Serine palmitoyltransferase 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Serine palmitoyltransferase 2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Protein ORM2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Serine palmitoyltransferase-regulating protein TSC3

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8iam__assembly_1__model_1

8iam__assembly_1__model_1 | I(q)

8iam__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

7. Citations (1)