SAXSdb — 4a4k

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

ANTIVIRAL HELICASE SKI2

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	ZINC ION × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	ZINC ION × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	ZINC ION × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	ZINC ION × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	ZINC ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SKI2_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–256； UniProt 835–1085 Author chain C； PDBConstruct 6–256； UniProt 835–1085 Author chain E； PDBConstruct 6–256； UniProt 835–1085 Author chain G； PDBConstruct 6–256； UniProt 835–1085 Author chain I； PDBConstruct 6–256； UniProt 835–1085

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	4a4k
Deposition date deposition_date	2011-10-17
Structure title title	Crystal structure of the S. cerevisiae Ski2 insertion domain
Keywords keywords	DEXH HELICASE, HYDROLASE, RNA DEGRADATION, EXOSOME; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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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.

4a4k__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4a4k__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4a4k__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	20.73 Å
Rg (electron density)	19.66 Å
Total Rg	20.42 Å
Atom count	1844
Residues	245
Excluded volume	32850 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4a4k__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4a4k__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4a4k__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`4a4k__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`4a4k__assembly_5__model_1`	monomeric （1）	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 (2)

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6. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

Domain ID domain_id	4a4kA01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1500 — YheA-like fold
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	4a4kA02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	1160 —

Domain ID domain_id	4a4kC01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1500 — YheA-like fold
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	4a4kC02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	1160 —

Domain ID domain_id	4a4kE01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1500 — YheA-like fold
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	4a4kE02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	1160 —

Domain ID domain_id	4a4kG01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1500 — YheA-like fold
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	4a4kG02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	1160 —

Domain ID domain_id	4a4kI01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1500 — YheA-like fold
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	4a4kI02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	1160 —

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Unit-cell length a length_a	230.463 Å
Unit-cell length b length_b	123.139 Å
Unit-cell length c length_c	153.201 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	131.05 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	20

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	3.250 Å
Low-resolution limit resolution_low	57.159 Å
R factor r_factor	0.2370
R_work r_work	0.2359
R_free r_free	0.2565

Description description	ANTIVIRAL HELICASE SKI2
Molecular weight formula_weight	29709.8 kDa
EC 编号 ec_number	3.6.4.13
Source method src_method	man
Copy count entity_count	5

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G,I
Atom count atom_count	9089

Crystal structure of the S. cerevisiae Ski2 insertion domain

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

ANTIVIRAL HELICASE SKI2

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

4a4k__assembly_2__model_1

4a4k__assembly_2__model_1 | I(q)

4a4k__assembly_2__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

6. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

7. Citations (1)

Source organism organism	SACCHAROMYCES CEREVISIAE
Common name common_name	;BAKER'S YEAST ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	ESCHERICHIA COLI

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	5

Crystal structure of the S. cerevisiae Ski2 insertion domain

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

ANTIVIRAL HELICASE SKI2

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

4a4k__assembly_2__model_1

4a4k__assembly_2__model_1 | I(q)

4a4k__assembly_2__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

6. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

7. Citations (1)