4ba2

Archaeal exosome (Rrp4-Rrp41(D182A)-Rrp42) bound to inorganic phosphate

Method: X-RAY DIFFRACTION

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

PROBABLE EXOSOME COMPLEX EXONUCLEASE 2

SULFOLOBUS SOLFATARICUS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 9 RNA 3	PROBABLE EXOSOME COMPLEX EXONUCLEASE 1 × 3 （Q9UXC2） PROBABLE EXOSOME COMPLEX RNA-BINDING PROTEIN 1 × 3 （Q9UXC4） 5'-R(APAPAPAP)-3' × 3 PENTAETHYLENE GLYCOL × 3 PHOSPHATE ION × 6 SODIUM ION × 3 water × 12	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ECX2_SULSO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–277； UniProt 1–275

PROBABLE EXOSOME COMPLEX EXONUCLEASE 1

SULFOLOBUS SOLFATARICUS

UniProt Q9UXC2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 9 RNA 3	PROBABLE EXOSOME COMPLEX EXONUCLEASE 2 × 3 （Q9UXC0） PROBABLE EXOSOME COMPLEX RNA-BINDING PROTEIN 1 × 3 （Q9UXC4） 5'-R(APAPAPAP)-3' × 3 PENTAETHYLENE GLYCOL × 3 PHOSPHATE ION × 6 SODIUM ION × 3 water × 12	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ECX1_SULSO
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 3–250； UniProt 1–248

PROBABLE EXOSOME COMPLEX RNA-BINDING PROTEIN 1

SULFOLOBUS SOLFATARICUS

UniProt Q9UXC4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 9 RNA 3	PROBABLE EXOSOME COMPLEX EXONUCLEASE 2 × 3 （Q9UXC0） PROBABLE EXOSOME COMPLEX EXONUCLEASE 1 × 3 （Q9UXC2） 5'-R(APAPAPAP)-3' × 3 PENTAETHYLENE GLYCOL × 3 PHOSPHATE ION × 6 SODIUM ION × 3 water × 12	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ECR1_SULSO
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain I； PDBConstruct 3–251； UniProt 1–249

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	4ba2
Deposition date deposition_date	2012-09-10
Structure title title	Archaeal exosome (Rrp4-Rrp41(D182A)-Rrp42) bound to inorganic phosphate
Keywords keywords	HYDROLASE-RNA COMPLEX, ARCHAEA, RNA DEGRADATION, PHOSPHOROLYTIC REACTION MECHANISM; HYDROLASE/RNA
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.

4ba2__assembly_1__model_1

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

Download this curve (.dat)

4ba2__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4ba2__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	38.51 Å
Rg (electron density)	37.59 Å
Total Rg	38.13 Å
Atom count	16665
Residues	2175
Excluded volume	296960 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4ba2__assembly_1__model_1`	dodecameric （12）	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 (8)

Entity 1 Entity 1 polymer

Description description	PROBABLE EXOSOME COMPLEX EXONUCLEASE 2
Molecular weight formula_weight	30422.8 kDa
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	5717

GHMSSTPSNQNIIPIIKKESIVSLFEKGIRQDGRKLTDYRPLSITLDYAKKADGSALVKLGTTMVLAGTKLEIDKPYEDTPNQGNLIVNVELLPLAYETFEPGPPDENAIELARVVDRSLRDSKALDLTKLVIEPGKSVWTVWLDVYVLDYGGNVLDACTLASVAALYNTKVYKVEQHSNGISVNKNEVVGKLPLNYPVVTISVAKVDKYLVVDPDLDEESIMDAKISFSYTPDLKIVGIQKSGKGSMSLQDIDQAENTARSTAVKLLEELKKHLGI

Source Source

Source organism organism	SULFOLOBUS SOLFATARICUS
NCBI taxonomy ID ncbi_taxonomy_id	2287
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	PROBABLE EXOSOME COMPLEX EXONUCLEASE 1
Molecular weight formula_weight	27764.1 kDa
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GHMREMLQVERPKLILDDGKRTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKAIAAVYGPKEMHPRHLSLPDRAVLRVRYHMTPFSTDERKNPAPSRREIELSKVIREALESAVLVELFPRTAIDVFTEILQADAGSRLVSLMAASLALADAGIPMRDLIAGVAVGKADGVIILDLNETEAMWGEADMPIAMMPSLNQVTLFQLNGSMTPDEFRQAFDLAVKGINIIYNLEREALKSKYVEFKEEGV

Source Source

Source organism organism	SULFOLOBUS SOLFATARICUS
NCBI taxonomy ID ncbi_taxonomy_id	2287
Host organism host_organism	ESCHERICHIA COLI

Entity 3 Entity 3 polymer

Description description	PROBABLE EXOSOME COMPLEX RNA-BINDING PROTEIN 1
Molecular weight formula_weight	28225.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I

GHMNMSQSQEIVLQPRSIVVPGELLAEGEFQIPWSPYILKINSKYYSTVVGLFDVKDTQFEVIPLEGSFYYPKINDIVIGLVEDVEIYGWVVDIKAPYKAYLPASNLLGRSINVGEDLRRYLDVGDYVIARIENFDRSIDPVLSVKGKDLGRVSNGIVIDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVANNGRIWATCPSRFSEEILIEAIRKIENESHIKGLTDRIKQFIEEKLGERNASSGETKTNS

Source Source

Source organism organism	SULFOLOBUS SOLFATARICUS
NCBI taxonomy ID ncbi_taxonomy_id	2287
Host organism host_organism	ESCHERICHIA COLI

Entity 4 Entity 4 polymer

Description description	5'-R(APAPAPAP)-3'
Molecular weight formula_weight	1271.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	R

AAAA

Entity 5 Entity 5 non-polymer

Description description	PENTAETHYLENE GLYCOL
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	105

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6. Fold Classification (SCOP + CATH) 13 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d4ba2a1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.14 — Ribosomal protein S5 domain 2-like
Superfamily Superfamily superfamily	d.14.1 — Ribosomal protein S5 domain 2-like
Family Family family	d.14.1.4 — Ribonuclease PH domain 1-like

Domain ID domain_id	d4ba2a2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.101 — Ribonuclease PH domain 2-like
Superfamily Superfamily superfamily	d.101.1 — Ribonuclease PH domain 2-like
Family Family family	d.101.1.1 — Ribonuclease PH domain 2-like

Domain ID domain_id	d4ba2a3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4ba2b1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.14 — Ribosomal protein S5 domain 2-like
Superfamily Superfamily superfamily	d.14.1 — Ribosomal protein S5 domain 2-like
Family Family family	d.14.1.4 — Ribonuclease PH domain 1-like

Domain ID domain_id	d4ba2b2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.101 — Ribonuclease PH domain 2-like
Superfamily Superfamily superfamily	d.101.1 — Ribonuclease PH domain 2-like
Family Family family	d.101.1.1 — Ribonuclease PH domain 2-like

Domain ID domain_id	d4ba2i1
Class class	b — All beta proteins
Fold Fold fold	b.84 — Barrel-sandwich hybrid
Superfamily Superfamily superfamily	b.84.4 — Ribosomal L27 protein-like
Family Family family	b.84.4.2 — ECR1 N-terminal domain-like

Domain ID domain_id	d4ba2i2
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
Family Family family	b.40.4.5 — Cold shock DNA-binding domain-like

Domain ID domain_id	d4ba2i3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.51 — Eukaryotic type KH-domain (KH-domain type I)
Superfamily Superfamily superfamily	d.51.1 — Eukaryotic type KH-domain (KH-domain type I)
Family Family family	d.51.1.1 — Eukaryotic type KH-domain (KH-domain type I)

CATH v4.4 (5 domains)

Domain ID domain_id	4ba2A01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily	70 — GHMP Kinase, N-terminal domain

Domain ID domain_id	4ba2B01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily	70 — GHMP Kinase, N-terminal domain

Domain ID domain_id	4ba2I01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain

Domain ID domain_id	4ba2I02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

Domain ID domain_id	4ba2I03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1370 — Ribosomal Protein S8; Chain: A, domain 1
Homologous superfamily homologous superfamily	10 — K Homology domain, type 1

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Unit-cell length a length_a	134.830 Å
Unit-cell length b length_b	134.830 Å
Unit-cell length c length_c	134.830 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	12

Space group space_group	P 21 3
Space-group number int_tables_number	198
Crystal system crystal_system	—

Resolution resolution	2.501 Å
Low-resolution limit resolution_low	38.922 Å
R factor r_factor	0.1890
R_work r_work	0.1854
R_free r_free	0.2589

Archaeal exosome (Rrp4-Rrp41(D182A)-Rrp42) bound to inorganic phosphate

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

PROBABLE EXOSOME COMPLEX EXONUCLEASE 2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

PROBABLE EXOSOME COMPLEX EXONUCLEASE 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

PROBABLE EXOSOME COMPLEX RNA-BINDING PROTEIN 1

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

4ba2__assembly_1__model_1

4ba2__assembly_1__model_1 | I(q)

4ba2__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 (8)

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

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 13 domains

SCOP 2.08 (8 domains)

CATH v4.4 (5 domains)

7. Citations (1)