SAXSdb — 5c0y

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

Exosome complex exonuclease RRP6

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Monomer	Protein 1 RNA 1	poly U RNA × 1 water × 2	Consistent with all polymers
2	Protein–RNA	Monomer	Protein 1 RNA 1	poly U RNA × 1 MAGNESIUM ION × 1 water × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RRP6_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–402； UniProt 122–518 Author chain B； PDBConstruct 6–402； UniProt 122–518

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	5c0y
Deposition date deposition_date	2015-06-12
Structure title title	Crystal structure of the Rrp6 catalytic domain bound to poly(U) RNA
Keywords keywords	Exoribonuclease, Hydrolase, RNA processing and degradation, nuclear RNA 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.

5c0y__assembly_2__model_1

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

Download this curve (.dat)

5c0y__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5c0y__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	23.98 Å
Rg (electron density)	23.35 Å
Total Rg	24.21 Å
Atom count	3307
Residues	397
Excluded volume	58568 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5c0y__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5c0y__assembly_2__model_1`	dimeric （2）	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)

Entity 1 Entity 1 polymer

Description description	Exosome complex exonuclease RRP6
Molecular weight formula_weight	47072.4 kDa
EC 编号 ec_number	3.1.13.-
Mutation mutation	D296N
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	7106

GPDSMNFSPTKRVEKPQLKFKSPIDNSESHPFIPLLKEKPNALKPLSESLRLVDDDENNPSHYPHPYEYEIDHQEYSPEILQIREEIPSKSWDDSVPIWVDTSTELESMLEDLKNTKEIAVDLEHHDYRSYYGIVCLMQISTRERDYLVDTLKLRENLHILNEVFTNPSIVKVFHGAFMNIIWLQRDLGLYVVGLFDTYHASKAIGLPRHSLAYLLENFANFKTSKKYQLADWRIRPLSKPMTAYARADTHFLLNIYDQLRNKLIESNKLAGVLYESRNVAKRRFEYSKYRPLTPSSEVYSPIEKESPWKILMYQYNIPPEREVLVRELYQWRDLIARRDDESPRFVMPNQLLAALVAYTPTDVIGVVSLTNGVTEHVRQNAKLLANLIRDALRNIKNTNEE

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	poly U RNA
Molecular weight formula_weight	4547.5 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	D,C

UUUUUUUUUUUUUUU

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 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	588

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	5c0yA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	10 — Ribonuclease H-like superfamily/Ribonuclease H

Domain ID domain_id	5c0yA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	80 — HRDC domain

Domain ID domain_id	5c0yB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	10 — Ribonuclease H-like superfamily/Ribonuclease H

Domain ID domain_id	5c0yB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	80 — HRDC domain

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Unit-cell length a length_a	110.186 Å
Unit-cell length b length_b	110.186 Å
Unit-cell length c length_c	78.883 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 31
Space-group number int_tables_number	144
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	47.710 Å
R factor r_factor	0.1507
R_work r_work	0.1481
R_free r_free	0.1801

Crystal structure of the Rrp6 catalytic domain bound to poly(U) RNA

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

Exosome complex exonuclease RRP6

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

5c0y__assembly_2__model_1

5c0y__assembly_2__model_1 | I(q)

5c0y__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of the Rrp6 catalytic domain bound to poly(U) RNA

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

Exosome complex exonuclease RRP6

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

5c0y__assembly_2__model_1

5c0y__assembly_2__model_1 | I(q)

5c0y__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)