SAXSdb — 3q8g

▼

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

CRAL-TRIO domain-containing protein YKL091C

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	1,2-dioleoyl-sn-glycero-3-phosphoethanolamine × 1 GLYCEROL × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YKJ1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 11–320； UniProt 1–310

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	3q8g
Deposition date deposition_date	2011-01-06
Structure title title	Resurrection of a functional phosphatidylinositol transfer protein from a pseudo-Sec14 scaffold by directed evolution
Keywords keywords	;CRAL-TRIO, string motif, signaling protein, directed evolution, PIPT, SEC14, phospholipid transporter, lipid, phosphatidylinositol, phosphatidylcholine ;; SIGNALING 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.

3q8g__assembly_1__model_1

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

Download this curve (.dat)

3q8g__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3q8g__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.32 Å
Rg (electron density)	19.32 Å
Total Rg	20.37 Å
Atom count	2562
Residues	306
Excluded volume	46190 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3q8g__assembly_1__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	CRAL-TRIO domain-containing protein YKL091C
Molecular weight formula_weight	37355.7 kDa
Mutation mutation	E126A
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	2809

MGHHHHHHHHMTTSILDTYPQICSPNALPGTPGNLTKEQEEALLQFRSILLEKNYKERLDDSTLLRFLRARKFDINASVEMFVETERWREEYGANTIIEDYENNKEAEDKERIKLAKMYPQYYHHVDKDGRPLYFAELGGINLKKMYKITTEKQMLRNLVKEYELFATYRVPACSRRAGYLIETSCTVLDLKGISLSNAYHVLSYIKDVADISQNYYPERMGKFYIIHSPFGFSTMFKMVKPFLDPVTVSKIFILGSSYKKELLKQIPIENLPVKYGGTSVLHNPNDKFYYSDIGPWRDPRYIGPEGEIPNIFGKFTVTS

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	yeast
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
Molecular weight formula_weight	744.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	222

▼

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3q8ga1
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.5.3.0 — automated matches

Domain ID domain_id	d3q8ga2
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.13.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	3q8gA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	20 — N-terminal domain of phosphatidylinositol transfer protein sec14p

Domain ID domain_id	3q8gA02
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

▶

Unit-cell length a length_a	49.503 Å
Unit-cell length b length_b	71.388 Å
Unit-cell length c length_c	99.650 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	49.830 Å
R factor r_factor	0.1935
R_work r_work	0.1916
R_free r_free	0.2289

Resurrection of a functional phosphatidylinositol transfer protein from a pseudo-Sec14 scaffold by directed evolution

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

CRAL-TRIO domain-containing protein YKL091C

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

3q8g__assembly_1__model_1

3q8g__assembly_1__model_1 | I(q)

3q8g__assembly_1__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Resurrection of a functional phosphatidylinositol transfer protein from a pseudo-Sec14 scaffold by directed evolution

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

CRAL-TRIO domain-containing protein YKL091C

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

3q8g__assembly_1__model_1

3q8g__assembly_1__model_1 | I(q)

3q8g__assembly_1__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)