2ba0

Archaeal exosome core

Method: X-RAY DIFFRACTION

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

Archaeal exosome RNA binding protein RRP4

Archaeoglobus fulgidus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 9	Archaeal exosome RNA binding protein RRP41 × 3 （O29757） Archaeal exosome RNA binding protein RRP42 × 3 （O29756） water × 9	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ECR1_ARCFU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–223； UniProt 1–223 Author chain B； PDBConstruct 1–223； UniProt 1–223 Author chain C； PDBConstruct 1–223； UniProt 1–223

Archaeal exosome RNA binding protein RRP41

Archaeoglobus fulgidus

UniProt O29757

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 9	Archaeal exosome RNA binding protein RRP4 × 3 （O29758） Archaeal exosome RNA binding protein RRP42 × 3 （O29756） water × 9	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ECX1_ARCFU
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–258； UniProt 1–258 Author chain E； PDBConstruct 1–258； UniProt 1–258 Author chain F； PDBConstruct 1–258； UniProt 1–258

Archaeal exosome RNA binding protein RRP42

Archaeoglobus fulgidus

UniProt O29756

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 9	Archaeal exosome RNA binding protein RRP4 × 3 （O29758） Archaeal exosome RNA binding protein RRP41 × 3 （O29757） water × 9	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ECX2_ARCFU
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain G； PDBConstruct 1–259； UniProt 1–259 Author chain H； PDBConstruct 1–259； UniProt 1–259 Author chain I； PDBConstruct 1–259； UniProt 1–259

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	2ba0
Deposition date deposition_date	2005-10-13
Structure title title	Archaeal exosome core
Keywords keywords	EXOSOME, RNASE PH, RNA DEGRADATION, EXORIBONUCLEASE, RNA BINDING, S1DOMAIN, KH DOMAIN, ARCHAEAL, RNA BINDING PROTEIN; RNA BINDING PROTEIN
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.

2ba0__assembly_1__model_1

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

Download this curve (.dat)

2ba0__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2ba0__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	39.92 Å
Rg (electron density)	39.06 Å
Total Rg	39.67 Å
Atom count	16809
Residues	2154
Excluded volume	302110 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2ba0__assembly_1__model_1`	nonameric （9）	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	Archaeal exosome RNA binding protein RRP4
Molecular weight formula_weight	25589.9 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	16910

MRKIVLPGDLLSTNPRAAGYGTYVEGGKVYAKIIGLFDQTETHVRVIPLKGRYTPSVGDVVIGIIREVAANGWAVDIYSPYQAFLPVSENPEMKPNKKPNEVLDIGDAIIAKVLNIDPKMKVTLTMKDRICRPIRFGRIVAINPARVPRVIGKKGSMIKLLKSELDVQIVVGQNGLIWVNGDRRKVSIAEEAIYLIEQEAHTEGLTDRVAEFIKRRKADVGIQHHHHHH

Source Source

Source organism organism	Archaeoglobus fulgidus
NCBI taxonomy ID ncbi_taxonomy_id	2234
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Archaeal exosome RNA binding protein RRP41
Molecular weight formula_weight	28888.3 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	F,E,D

MSEFNEKPEKLIVDGLRLDGRKFDELRPIKIEASVLKRADGSCYLEMGKNKVIAAVFGPREVHPRHLQDPSKAIIRYRYNMAPFSVEERKRPGPDRRSIEISKVSKEAFEAVIMKELFPRSAIDIFVEVLQADAGSRTACLNAASVALVDAGVPMKGMITSVAVGKADGQLVLDPMKEEDNFGEADMPFAFLIRNGKIESIALLQMDGRMTRDEVKQAIELAKKGALQIYEMQREAILRRYIEVGEEMDEITEGGEDA

Source Source

Source organism organism	Archaeoglobus fulgidus
NCBI taxonomy ID ncbi_taxonomy_id	2234
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Archaeal exosome RNA binding protein RRP42
Molecular weight formula_weight	28677.6 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	I,H,G

MPEDILVDIKRDYVLSKLRDNERIDGRGFDEFRKVEIIPNVIEKAEGSALVKLGDTQVVVGVKMQPGEPYPDTPDRGVIIVNAELVPLASPTFEPGPPDENSIELARVVDRGIRESEAVDLSKLVIEEGEKVWIVFVDIHALDDDGNLLDASALAAIAALMNTKVPAERFDLGEDYLLPVRDLPVSVTSLIVGNKYLVDPSREEMSVGDTTLTITTDKDDNVVAMQKSGGYLLDEKLFDELLDVSINCARKLREKFKEI

Source Source

Source organism organism	Archaeoglobus fulgidus
NCBI taxonomy ID ncbi_taxonomy_id	2234
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	101

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6. Fold Classification (SCOP + CATH) 36 domains

SCOP 2.08 (21 domains)

Domain ID domain_id	d2ba0a1
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	d2ba0a2
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	d2ba0a3
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)

Domain ID domain_id	d2ba0b1
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	d2ba0b2
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	d2ba0b3
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)

Domain ID domain_id	d2ba0c1
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	d2ba0c2
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	d2ba0c3
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)

Domain ID domain_id	d2ba0d1
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	d2ba0d2
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	d2ba0e1
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	d2ba0e2
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	d2ba0f1
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	d2ba0f2
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	d2ba0g1
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	d2ba0g2
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	d2ba0h1
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	d2ba0h2
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	d2ba0i1
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	d2ba0i2
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

CATH v4.4 (15 domains)

Domain ID domain_id	2ba0A01
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	2ba0A02
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	2ba0A03
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

Domain ID domain_id	2ba0B01
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	2ba0B02
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	2ba0B03
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

Domain ID domain_id	2ba0C01
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	2ba0C02
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	2ba0C03
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

Domain ID domain_id	2ba0D01
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	2ba0E01
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	2ba0F01
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	2ba0G01
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	2ba0H01
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	2ba0I01
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

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Unit-cell length a length_a	101.570 Å
Unit-cell length b length_b	129.590 Å
Unit-cell length c length_c	102.330 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	101.56 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.2160
R_free r_free	0.2640

Archaeal exosome core

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

Archaeal exosome RNA binding protein RRP4

State in the Current Structure

Other States of the Same Protein in the Database

Archaeal exosome RNA binding protein RRP41

State in the Current Structure

Other States of the Same Protein in the Database

Archaeal exosome RNA binding protein RRP42

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

2ba0__assembly_1__model_1

2ba0__assembly_1__model_1 | I(q)

2ba0__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (4)

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 water

6. Fold Classification (SCOP + CATH) 36 domains

SCOP 2.08 (21 domains)

CATH v4.4 (15 domains)

7. Citations (1)

Archaeal exosome core

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

Archaeal exosome RNA binding protein RRP4

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Archaeal exosome RNA binding protein RRP41

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Archaeal exosome RNA binding protein RRP42

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

2ba0__assembly_1__model_1

2ba0__assembly_1__model_1 | I(q)

2ba0__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (4)

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 water

6. Fold Classification (SCOP + CATH) 36 domains

SCOP 2.08 (21 domains)

CATH v4.4 (15 domains)

7. Citations (1)