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4buj

Crystal structure of the S. cerevisiae Ski2-3-8 complex

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

ANTIVIRAL HELICASE SKI2

SACCHAROMYCES CEREVISIAE

UniProt P35207

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 4 SUPERKILLER PROTEIN 3 × 1 （P17883） ANTIVIRAL PROTEIN SKI8 × 2 （Q02793） SULFATE ION × 11 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 4 SUPERKILLER PROTEIN 3 × 1 （P17883） ANTIVIRAL PROTEIN SKI8 × 2 （Q02793） SULFATE ION × 9 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
4a4k 4a4k 4a4k 4a4k 4a4k 4a4z

6 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
4buj 4buj 5mc6 8q9t 8qca 8qcb 8qcf

7 assemblies

View Construct and Data Evidence
UniProt name SKI2_YEAST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 5–212； UniProt 1–208 Author chain A； PDBConstruct 305–838； UniProt 301–834 Author chain A； PDBConstruct 843–1044； UniProt 1086–1287 Author chain E； PDBConstruct 5–212； UniProt 1–208 Author chain E； PDBConstruct 305–838； UniProt 301–834 Author chain E； PDBConstruct 843–1044； UniProt 1086–1287

SUPERKILLER PROTEIN 3

SACCHAROMYCES CEREVISIAE

UniProt P17883

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 4 ANTIVIRAL HELICASE SKI2 × 1 （P35207） ANTIVIRAL PROTEIN SKI8 × 2 （Q02793） SULFATE ION × 11 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 4 ANTIVIRAL HELICASE SKI2 × 1 （P35207） ANTIVIRAL PROTEIN SKI8 × 2 （Q02793） SULFATE ION × 9 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
4buj 4buj 5mc6 8q9t 8qca 8qcb

6 assemblies

View Construct and Data Evidence
UniProt name SKI3_YEAST
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 5–1436； UniProt 1–1432 Author chain F； PDBConstruct 5–1436； UniProt 1–1432

ANTIVIRAL PROTEIN SKI8

SACCHAROMYCES CEREVISIAE

UniProt Q02793

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 4 ANTIVIRAL HELICASE SKI2 × 1 （P35207） SUPERKILLER PROTEIN 3 × 1 （P17883） SULFATE ION × 11 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 4 ANTIVIRAL HELICASE SKI2 × 1 （P35207） SUPERKILLER PROTEIN 3 × 1 （P17883） SULFATE ION × 9 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1s4u 1sq9

2 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
4buj 4buj 5mc6 8q9t 8qca 8qcb 8urq 8uru

8 assemblies

View Construct and Data Evidence
UniProt name SKI8_YEAST
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 1–397； UniProt 1–397 Author chain D； PDBConstruct 1–397； UniProt 1–397 Author chain G； PDBConstruct 1–397； UniProt 1–397 Author chain H； PDBConstruct 1–397； UniProt 1–397

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_id4buj
Deposition date deposition_date2013-06-20
Structure title titleCrystal structure of the S. cerevisiae Ski2-3-8 complex
Keywords keywordsHYDROLASE, DEXH BOX HELICASE, RNA DEGRADATION, TPR, PROTEIN COMPLEX; HYDROLASE
Experimental Method methodX-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.

4buj__assembly_2__model_1

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

Download this curve (.dat)

4buj__assembly_2__model_1 | I(q)

10-2 10-1 106 107 108 109 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

4buj__assembly_2__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）54.50 Å
Rg (electron density)54.65 Å
Total Rg54.17 Å
Atom count20822
Residues2970
Excluded volume364360 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 4buj__assembly_1__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 4buj__assembly_2__model_1 tetrameric （4） 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 (4)

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6. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

Domain ID domain_id4bujA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id4bujA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id4bujA03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology3380 — Sec63 N-terminal domain-like fold
Homologous superfamily homologous superfamily30 —
Domain ID domain_id4bujC00
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily10 — YVTN repeat-like/Quinoprotein amine dehydrogenase
Domain ID domain_id4bujD00
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily10 — YVTN repeat-like/Quinoprotein amine dehydrogenase
Domain ID domain_id4bujE01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id4bujE02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id4bujE03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology3380 — Sec63 N-terminal domain-like fold
Homologous superfamily homologous superfamily30 —
Domain ID domain_id4bujG00
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily10 — YVTN repeat-like/Quinoprotein amine dehydrogenase
Domain ID domain_id4bujH00
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily10 — YVTN repeat-like/Quinoprotein amine dehydrogenase
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7. Citations (1)