8c81

Cryo-EM structure of the yeast SPT-Orm1-Sac1 complex

Method: ELECTRON MICROSCOPY

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

Protein ORM1

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Serine palmitoyltransferase 1 × 1 （P25045） Serine palmitoyltransferase 2 × 1 （P40970） Serine palmitoyltransferase-regulating protein TSC3 × 1 （Q3E790） Phosphatidylinositol-3-phosphatase SAC1 × 1 （P32368） ERGOSTEROL × 3 N-[(2S,3S,4R)-1,3,4-trihydroxyoctadecan-2-yl]hexacosanamide × 1 ;2-{[(4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranosyl)oxy]methyl}-4-{[(3beta,9beta,14beta,17beta,25R)-spirost-5-en-3-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranoside ; × 1 PYRIDOXAL-5'-PHOSPHATE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ORM1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–222； UniProt 1–222

Serine palmitoyltransferase 1

Saccharomyces cerevisiae

UniProt P25045

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Protein ORM1 × 1 （P53224） Serine palmitoyltransferase 2 × 1 （P40970） Serine palmitoyltransferase-regulating protein TSC3 × 1 （Q3E790） Phosphatidylinositol-3-phosphatase SAC1 × 1 （P32368） ERGOSTEROL × 3 N-[(2S,3S,4R)-1,3,4-trihydroxyoctadecan-2-yl]hexacosanamide × 1 ;2-{[(4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranosyl)oxy]methyl}-4-{[(3beta,9beta,14beta,17beta,25R)-spirost-5-en-3-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranoside ; × 1 PYRIDOXAL-5'-PHOSPHATE × 1	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	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–580； UniProt 1–558

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	Protein heterocomplex	Heteromer	Protein 5	Protein ORM1 × 1 （P53224） Serine palmitoyltransferase 1 × 1 （P25045） Serine palmitoyltransferase-regulating protein TSC3 × 1 （Q3E790） Phosphatidylinositol-3-phosphatase SAC1 × 1 （P32368） ERGOSTEROL × 3 N-[(2S,3S,4R)-1,3,4-trihydroxyoctadecan-2-yl]hexacosanamide × 1 ;2-{[(4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranosyl)oxy]methyl}-4-{[(3beta,9beta,14beta,17beta,25R)-spirost-5-en-3-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranoside ; × 1 PYRIDOXAL-5'-PHOSPHATE × 1	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	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–561； UniProt 1–561

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	Protein heterocomplex	Heteromer	Protein 5	Protein ORM1 × 1 （P53224） Serine palmitoyltransferase 1 × 1 （P25045） Serine palmitoyltransferase 2 × 1 （P40970） Phosphatidylinositol-3-phosphatase SAC1 × 1 （P32368） ERGOSTEROL × 3 N-[(2S,3S,4R)-1,3,4-trihydroxyoctadecan-2-yl]hexacosanamide × 1 ;2-{[(4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranosyl)oxy]methyl}-4-{[(3beta,9beta,14beta,17beta,25R)-spirost-5-en-3-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranoside ; × 1 PYRIDOXAL-5'-PHOSPHATE × 1	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 D； PDBConstruct 1–80； UniProt 1–80

Phosphatidylinositol-3-phosphatase SAC1

Saccharomyces cerevisiae

UniProt P32368

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Protein ORM1 × 1 （P53224） Serine palmitoyltransferase 1 × 1 （P25045） Serine palmitoyltransferase 2 × 1 （P40970） Serine palmitoyltransferase-regulating protein TSC3 × 1 （Q3E790） ERGOSTEROL × 3 N-[(2S,3S,4R)-1,3,4-trihydroxyoctadecan-2-yl]hexacosanamide × 1 ;2-{[(4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranosyl)oxy]methyl}-4-{[(3beta,9beta,14beta,17beta,25R)-spirost-5-en-3-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranoside ; × 1 PYRIDOXAL-5'-PHOSPHATE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SAC1_YEAST
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain E； PDBConstruct 1–623； UniProt 1–623

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	8c81
Deposition date deposition_date	2023-01-18
Last revision last_revision	2023-10-11
Structure title title	Cryo-EM structure of the yeast SPT-Orm1-Sac1 complex
Keywords keywords	Serine-Palmitoyl-Transferase, SPT, Orm-Protein, TRANSFERASE; TRANSFERASE
Experimental Method method	ELECTRON MICROSCOPY

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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.

8c81__assembly_1__model_1

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

Download this curve (.dat)

8c81__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8c81__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	43.18 Å
Rg (electron density)	43.03 Å
Total Rg	43.20 Å
Atom count	15709
Residues	1938
Excluded volume	281780 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8c81__assembly_1__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Description description	Protein ORM1
Molecular weight formula_weight	25221.7 kDa
Mutation mutation	S51A, S52A, S53A
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	15709

MTELDYQGTAEAASTSYSRNQTDLKPFPSAGSASSSIKTTEPVKDHRRRRAAAIISHVEPETFEDENDQQLLPNMNATWVDQRGAWIIHVVIIILLKLFYNLFPGVTTEWSWTLTNMTYVIGSYVMFHLIKGTPFDFNGGAYDNLTMWEQIDDETLYTPSRKFLISVPIALFLVSTHYAHYDLKLFSWNCFLTTFGAVVPKLPVTHRLRISIPGITGRAQIS

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	Saccharomyces cerevisiae

Entity 2 Entity 2 polymer

Description description	Serine palmitoyltransferase 1
Molecular weight formula_weight	64985.5 kDa
EC 编号 ec_number	2.3.1.50
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MAHIPEVLPDYKDHDGDYKDHDIDYKDDDDKKSIPIPAFIVTTSSYLWYYFNLVLTQIPGGQFIVSYIKKSHHDDPYRTTVEIGLILYGIIYYLSKPQQKKSLQAQKPNLSPQEIDALIEDWEPEPLVDPSATDEQSWRVAKTPVTMEMPIQNHITITRNNLQEKYTNVFNLASNNFLQLSATEPVKEVVKTTIKNYGVGACGPAGFYGNQDVHYTLEYDLAQFFGTQGSVLYGQDFCAAPSVLPAFTKRGDVIVADDQVSLPVQNALQLSRSTVYYFNHNDMNSLECLLNELTEQEKLEKLPAIPRKFIVTEGIFHNSGDLAPLPELTKLKNKYKFRLFVDETFSIGVLGATGRGLSEHFNMDRATAIDITVGSMATALGSTGGFVLGDSVMCLHQRIGSNAYCFSACLPAYTVTSVSKVLKLMDSNNDAVQTLQKLSKSLHDSFASDDSLRSYVIVTSSPVSAVLHLQLTPAYRSRKFGYTCEQLFETMSALQKKSQTNKFIEPYEEEEKFLQSIVDHALINYNVLITRNTIVLKQETLPIVPSLKICCNAAMSPEELKNACESVKQSILACCQESNK

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	Saccharomyces cerevisiae

Entity 3 Entity 3 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	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

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	Saccharomyces cerevisiae

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	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

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	Saccharomyces cerevisiae

Entity 5 Entity 5 polymer

Description description	Phosphatidylinositol-3-phosphatase SAC1
Molecular weight formula_weight	71214.4 kDa
EC 编号 ec_number	3.1.3.64
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MTGPIVYVQNADGIFFKLAEGKGTNDAVIHLANQDQGVRVLGAEEFPVQGEVVKIASLMGFIKLKLNRYAIIANTVEETGRFNGHVFYRVLQHSIVSTKFNSRIDSEEAEYIKLLELHLKNSTFYFSYTYDLTNSLQRNEKVGPAASWKTADERFFWNHYLTEDLRNFAHQDPRIDSFIQPVIYGYAKTVDAVLNATPIVLGLITRRSIFRAGTRYFRRGVDKDGNVGNFNETEQILLAENPESEKIHVFSFLQTRGSVPIYWAEINNLKYKPNLVLGENSLDATKKHFDQQKELYGDNYLVNLVNQKGHELPVKEGYESVVHALNDPKIHYVYFDFHHECRKMQWHRVKLLIDHLEKLGLSNEDFFHKVIDSNGNTVEIVNEQHSVVRTNCMDCLDRTNVVQSVLAQWVLQKEFESADVVATGSTWEDNAPLLTSYQNLWADNADAVSVAYSGTGALKTDFTRTGKRTRLGAFNDFLNSASRYYQNNWTDGPRQDSYDLFLGGFRPHTASIKSPFPDRRPVYIQLIPMIICAALTVLGATIFFPKDRFTSSKNLLYFAGASIVLALSTKFMFKNGIQFVNWPKLVDVGFLVVHQTHDKEQQFKGLKYAQSPKFSKPDPLKRD

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	Saccharomyces cerevisiae

Entity 6 Entity 6 non-polymer

Description description	ERGOSTEROL
Molecular weight formula_weight	396.6 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 7 Entity 7 non-polymer

Description description	N-[(2S,3S,4R)-1,3,4-trihydroxyoctadecan-2-yl]hexacosanamide
Molecular weight formula_weight	696.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

Description description	;2-{[(4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranosyl)oxy]methyl}-4-{[(3beta,9beta,14beta,17beta,25R)-spirost-5-en-3-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranoside ;
Molecular weight formula_weight	1165.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 non-polymer

Description description	PYRIDOXAL-5'-PHOSPHATE
Molecular weight formula_weight	247.1 kDa
Source method src_method	syn
Copy count entity_count	1

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Resolution resolution	3.300 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	3.30 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	53236

Cryo-EM structure of the yeast SPT-Orm1-Sac1 complex

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

Protein ORM1

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 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

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

Phosphatidylinositol-3-phosphatase SAC1

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

8c81__assembly_1__model_1

8c81__assembly_1__model_1 | I(q)

8c81__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (9)

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 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

7. Citations (1)