1olm

Supernatant Protein Factor in Complex with RRR-alpha-Tocopherylquinone: A Link between Oxidized Vitamin E and Cholesterol Biosynthesis

Method: X-RAY DIFFRACTION

▼

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

SEC14-LIKE PROTEIN 2

HOMO SAPIENS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	RRR-ALPHA-TOCOPHERYLQUINONE × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	RRR-ALPHA-TOCOPHERYLQUINONE × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	RRR-ALPHA-TOCOPHERYLQUINONE × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	S142_HUMAN
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–403； UniProt 1–403 Author chain C； PDBConstruct 1–403； UniProt 1–403 Author chain E； PDBConstruct 1–403； UniProt 1–403

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	1olm
Deposition date deposition_date	2003-08-08
Structure title title	Supernatant Protein Factor in Complex with RRR-alpha-Tocopherylquinone: A Link between Oxidized Vitamin E and Cholesterol Biosynthesis
Keywords keywords	;LIPID-BINDING PROTEIN, CHOLESTEROL BIOSYNTHESIS, OXIDIZED VITAMIN E, LIPID-BINDING, TRANSPORT, TRANSCRIPTION REGULATION, ACTIVATOR, LIPID BINDING PROTEIN ;; LIPID BINDING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

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.

1olm__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1olm__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1olm__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	25.88 Å
Rg (electron density)	24.65 Å
Total Rg	25.39 Å
Atom count	3236
Residues	397
Excluded volume	58127 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1olm__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1olm__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1olm__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	SEC14-LIKE PROTEIN 2
Molecular weight formula_weight	46208.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	10464

MSGRVGDLSPRQKEALAKFRENVQDVLPALPNPDDYFLLRWLRARSFDLQKSEAMLRKHVEFRKQKDIDNIISWQPPEVIQQYLSGGMCGYDLDGCPVWYDIIGPLDAKGLLFSASKQDLLRTKMRECELLLQECAHQTTKLGRKVETITIIYDCEGLGLKHLWKPAVEAYGEFLCMFEENYPETLKRLFVVKAPKLFPVAYNLIKPFLSEDTRKKIMVLGANWKEVLLKHISPDQVPVEYGGTMTDPDGNPKCKSKINYGGDIPRKYYVRDQVKQQYEHSVQISRGSSHQVEYEILFPGCVLRWQFMSDGADVGFGIFLKTKMGERQRAGEMTEVLPNQRYNSHLVPEDGTLTCSDPGIYVLRFDNTYSFIHAKKVNFTVEVLLPDKASEEKMKQLGAGTPK

Source Source

Source organism organism	HOMO SAPIENS
Common name common_name	HUMAN
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	SEC14-LIKE PROTEIN 2
Molecular weight formula_weight	46236.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MSGRVGDLSPRQKEALAKFRENVQDVLPALPNPDDYFLLRWLRARSFDLQKSEAMLRKHVEFRKQKDIDNIISWQPPEVIQQYLSGGMCGYDLDGCPVWYDIIGPLDAKGLLFSASKQDLLRTKMRECELLLQECAHQTTKLGRKVETITIIYDCEGLGLKHLWKPAVEAYGEFLCMFEENYPETLKRLFVVKAPKLFPVAYNLIKPFLSEDTRKKIMVLGANWKEVLLKHISPDQVPVEYGGTMTDPDGNPKCKSKINYGGDIPRKYYVRDQVKQQYEHSVQISRGSSHQVEYEILFPGCVLRWQFMSDGADVGFGIFLKKKMGERQRAGEMTEVLPNQRYNSHLVPEDGTLTCSDPGIYVLRFDNTYSFIHAKKVNFTVEVLLPDKASEEKMKQLGAGTPK

Source Source

Source organism organism	HOMO SAPIENS
Common name common_name	HUMAN
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	ESCHERICHIA COLI

Entity 3 Entity 3 non-polymer

Description description	RRR-ALPHA-TOCOPHERYLQUINONE
Molecular weight formula_weight	446.7 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	875

▼

6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (9 domains)

Domain ID domain_id	d1olma1
Class class	a — All alpha proteins
Fold Fold fold	a.5 — RuvA C-terminal domain-like
Superfamily Superfamily superfamily	a.5.3 — CRAL/TRIO N-terminal domain
Family Family family	a.5.3.1 — CRAL/TRIO N-terminal domain

Domain ID domain_id	d1olma2
Class class	b — All beta proteins
Fold Fold fold	b.132 — Supernatant protein factor (SPF), C-terminal domain
Superfamily Superfamily superfamily	b.132.1 — Supernatant protein factor (SPF), C-terminal domain
Family Family family	b.132.1.1 — Supernatant protein factor (SPF), C-terminal domain

Domain ID domain_id	d1olma3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.13 — SpoIIaa-like
Superfamily Superfamily superfamily	c.13.1 — CRAL/TRIO domain
Family Family family	c.13.1.1 — CRAL/TRIO domain

Domain ID domain_id	d1olmc1
Class class	a — All alpha proteins
Fold Fold fold	a.5 — RuvA C-terminal domain-like
Superfamily Superfamily superfamily	a.5.3 — CRAL/TRIO N-terminal domain
Family Family family	a.5.3.1 — CRAL/TRIO N-terminal domain

Domain ID domain_id	d1olmc2
Class class	b — All beta proteins
Fold Fold fold	b.132 — Supernatant protein factor (SPF), C-terminal domain
Superfamily Superfamily superfamily	b.132.1 — Supernatant protein factor (SPF), C-terminal domain
Family Family family	b.132.1.1 — Supernatant protein factor (SPF), C-terminal domain

Domain ID domain_id	d1olmc3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.13 — SpoIIaa-like
Superfamily Superfamily superfamily	c.13.1 — CRAL/TRIO domain
Family Family family	c.13.1.1 — CRAL/TRIO domain

Domain ID domain_id	d1olme1
Class class	a — All alpha proteins
Fold Fold fold	a.5 — RuvA C-terminal domain-like
Superfamily Superfamily superfamily	a.5.3 — CRAL/TRIO N-terminal domain
Family Family family	a.5.3.1 — CRAL/TRIO N-terminal domain

Domain ID domain_id	d1olme2
Class class	b — All beta proteins
Fold Fold fold	b.132 — Supernatant protein factor (SPF), C-terminal domain
Superfamily Superfamily superfamily	b.132.1 — Supernatant protein factor (SPF), C-terminal domain
Family Family family	b.132.1.1 — Supernatant protein factor (SPF), C-terminal domain

Domain ID domain_id	d1olme3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.13 — SpoIIaa-like
Superfamily Superfamily superfamily	c.13.1 — CRAL/TRIO domain
Family Family family	c.13.1.1 — CRAL/TRIO domain

CATH v4.4 (6 domains)

Domain ID domain_id	1olmA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	525 — Phosphatidylinositol Transfer Protein Sec14p
Homologous superfamily homologous superfamily	10 — CRAL-TRIO lipid binding domain

Domain ID domain_id	1olmA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	680 — GOLD domain

Domain ID domain_id	1olmC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	525 — Phosphatidylinositol Transfer Protein Sec14p
Homologous superfamily homologous superfamily	10 — CRAL-TRIO lipid binding domain

Domain ID domain_id	1olmC02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	680 — GOLD domain

Domain ID domain_id	1olmE01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	525 — Phosphatidylinositol Transfer Protein Sec14p
Homologous superfamily homologous superfamily	10 — CRAL-TRIO lipid binding domain

Domain ID domain_id	1olmE02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	680 — GOLD domain

▶

Unit-cell length a length_a	60.856 Å
Unit-cell length b length_b	84.621 Å
Unit-cell length c length_c	87.452 Å
Unit-cell angle α angle_alpha	116.20 °
Unit-cell angle β angle_beta	102.64 °
Unit-cell angle γ angle_gamma	100.24 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	1.950 Å
Low-resolution limit resolution_low	19.650 Å
R factor r_factor	0.1810
R_work r_work	0.1800
R_free r_free	0.2110

Supernatant Protein Factor in Complex with RRR-alpha-Tocopherylquinone: A Link between Oxidized Vitamin E and Cholesterol Biosynthesis

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

SEC14-LIKE PROTEIN 2

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1olm__assembly_3__model_1

1olm__assembly_3__model_1 | I(q)

1olm__assembly_3__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (9 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Supernatant Protein Factor in Complex with RRR-alpha-Tocopherylquinone: A Link between Oxidized Vitamin E and Cholesterol Biosynthesis

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

SEC14-LIKE PROTEIN 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1olm__assembly_3__model_1

1olm__assembly_3__model_1 | I(q)

1olm__assembly_3__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (9 domains)

CATH v4.4 (6 domains)

7. Citations (1)