SAXSdb — 4wfd

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

Exosome complex exonuclease RRP6

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Exosome complex protein LRP1 × 1 （P38801） ATP-dependent RNA helicase DOB1 × 1 （P47047） YTTRIUM (III) ION × 8 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Exosome complex protein LRP1 × 1 （P38801） ATP-dependent RNA helicase DOB1 × 1 （P47047） YTTRIUM (III) ION × 7 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 3	Exosome complex protein LRP1 × 1 （P38801） ATP-dependent RNA helicase DOB1 × 1 （P47047） YTTRIUM (III) ION × 7 water × 3	Consistent with protein count

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 5–115； UniProt 1–111 Author chain D； PDBConstruct 5–115； UniProt 1–111 Author chain G； PDBConstruct 5–115； UniProt 1–111

Exosome complex protein LRP1

Saccharomyces cerevisiae

UniProt P38801

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Exosome complex exonuclease RRP6 × 1 （Q12149） ATP-dependent RNA helicase DOB1 × 1 （P47047） YTTRIUM (III) ION × 8 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Exosome complex exonuclease RRP6 × 1 （Q12149） ATP-dependent RNA helicase DOB1 × 1 （P47047） YTTRIUM (III) ION × 7 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 3	Exosome complex exonuclease RRP6 × 1 （Q12149） ATP-dependent RNA helicase DOB1 × 1 （P47047） YTTRIUM (III) ION × 7 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LRP1_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–103； UniProt 1–103 Author chain E； PDBConstruct 1–103； UniProt 1–103 Author chain H； PDBConstruct 1–103； UniProt 1–103

ATP-dependent RNA helicase DOB1

OrganismNot specified

UniProt P47047

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Exosome complex exonuclease RRP6 × 1 （Q12149） Exosome complex protein LRP1 × 1 （P38801） YTTRIUM (III) ION × 8 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Exosome complex exonuclease RRP6 × 1 （Q12149） Exosome complex protein LRP1 × 1 （P38801） YTTRIUM (III) ION × 7 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 3	Exosome complex exonuclease RRP6 × 1 （Q12149） Exosome complex protein LRP1 × 1 （P38801） YTTRIUM (III) ION × 7 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MTR4_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–19； UniProt 1–19 Author chain F； PDBConstruct 1–19； UniProt 1–19 Author chain I； PDBConstruct 1–19； UniProt 1–19

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	4wfd
Deposition date deposition_date	2014-09-14
Structure title title	Structure of the Rrp6-Rrp47-Mtr4 interaction
Keywords keywords	Rrp6-Rrp47 complex, nuclear exosome, RNA degradation, RNA processing, hydrolase; 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.

4wfd__assembly_3__model_1

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

Download this curve (.dat)

4wfd__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4wfd__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	19.20 Å
Rg (electron density)	18.12 Å
Total Rg	19.08 Å
Atom count	1424
Residues	183
Excluded volume	25767 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4wfd__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4wfd__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4wfd__assembly_3__model_1`	trimeric （3）	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 (5)

Entity 1 Entity 1 polymer

Description description	Exosome complex exonuclease RRP6
Molecular weight formula_weight	12862.2 kDa
EC 编号 ec_number	3.1.13.-
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D,G
Atom count atom_count	4711

GPDSMTSENPDVLLSRVINVVRAASSLASQDVDFYKNLDRGFSKDLKSKADKLADMANEIILSIDEHHESFELKEEDISDLWNNFGNIMDNLLEMSDHSLDKLNCAINSKSRGSD

Source Source

Source organism organism	Saccharomyces cerevisiae
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	Exosome complex protein LRP1
Molecular weight formula_weight	12023.1 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,E,H

MEDIEKIKPYVRSFSKALDELKPEIEKLTSKSLDEQLLLLSDERAKLELINRYAYVLSSLMFANMKVLGVKDMSPILGELKRVKSYMDKAKQYDNRITKSNEK

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	ATP-dependent RNA helicase DOB1
Molecular weight formula_weight	2314.5 kDa
EC 编号 ec_number	3.6.4.13
Source method src_method	syn
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,F,I

MDSTDLFDVFEETPVELPTK

Entity 4 Entity 4 non-polymer

Description description	YTTRIUM (III) ION
Molecular weight formula_weight	88.9 kDa
Source method src_method	syn
Copy count entity_count	22

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	129

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Unit-cell length a length_a	142.745 Å
Unit-cell length b length_b	142.745 Å
Unit-cell length c length_c	63.450 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	18

Space group space_group	P 3 1 2
Space-group number int_tables_number	149
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	47.420 Å
R factor r_factor	0.2028
R_work r_work	0.2007
R_free r_free	0.2426

Structure of the Rrp6-Rrp47-Mtr4 interaction

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

Exosome complex protein LRP1

State in the Current Structure

Other States of the Same Protein in the Database

ATP-dependent RNA helicase DOB1

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

4wfd__assembly_3__model_1

4wfd__assembly_3__model_1 | I(q)

4wfd__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Citations (1)

Structure of the Rrp6-Rrp47-Mtr4 interaction

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

Exosome complex protein LRP1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

ATP-dependent RNA helicase DOB1

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

4wfd__assembly_3__model_1

4wfd__assembly_3__model_1 | I(q)

4wfd__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Citations (1)