2jeb

Structure of a 9-subunit archaeal exosome bound to Mn ions

Method: X-RAY DIFFRACTION

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

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 heterocomplex	Heteromer	Protein 9	EXOSOME COMPLEX EXONUCLEASE 1 × 3 （Q9UXC2） EXOSOME COMPLEX RNA-BINDING PROTEIN 1 × 3 （Q9UXC4） MANGANESE (II) ION × 6 PENTAETHYLENE GLYCOL × 3 CHLORIDE ION × 3 water × 9	Consistent with protein count

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

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 heterocomplex	Heteromer	Protein 9	EXOSOME COMPLEX EXONUCLEASE 2 × 3 （Q9UXC0） EXOSOME COMPLEX RNA-BINDING PROTEIN 1 × 3 （Q9UXC4） MANGANESE (II) ION × 6 PENTAETHYLENE GLYCOL × 3 CHLORIDE ION × 3 water × 9	Consistent with protein count

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

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 heterocomplex	Heteromer	Protein 9	EXOSOME COMPLEX EXONUCLEASE 2 × 3 （Q9UXC0） EXOSOME COMPLEX EXONUCLEASE 1 × 3 （Q9UXC2） MANGANESE (II) ION × 6 PENTAETHYLENE GLYCOL × 3 CHLORIDE ION × 3 water × 9	Consistent with protein count

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	2jeb
Deposition date deposition_date	2007-01-16
Structure title title	Structure of a 9-subunit archaeal exosome bound to Mn ions
Keywords keywords	;NUCLEASE, HYDROLASE, RNA-BINDING, EXONUCLEASE, PHOSPHOROLYTIC, EXORIBONUCLEASE, RNA DEGRADATION, RNA, RRP4, RRP42, RRP41, EXOSOME, ARCHAEAL, RNASE PH ;; 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.

2jeb__assembly_1__model_1

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

Download this curve (.dat)

2jeb__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2jeb__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	37.95 Å
Rg (electron density)	37.14 Å
Total Rg	37.69 Å
Atom count	15774
Residues	2109
Excluded volume	284190 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2jeb__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 (7)

Entity 1 Entity 1 polymer

Description description	EXOSOME COMPLEX EXONUCLEASE 2
Molecular weight formula_weight	30422.8 kDa
EC 编号 ec_number	3.1.13.-
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	5434

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	EXOSOME COMPLEX EXONUCLEASE 1
Molecular weight formula_weight	27764.1 kDa
EC 编号 ec_number	3.1.13.-
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	EXOSOME COMPLEX RNA-BINDING PROTEIN 1
Molecular weight formula_weight	28225.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I

GHMNMSQSQKIVLQPRSIVVPGELLAEGEFQIPWSPYILKINSKYYSTVVGLFDVKDTQFEVIPLEGSFYYPKINDIVIGLVEDVEIYGWVVDIKAPYKAYLPASNLLGRSINVGEDLRRYLDVGDYVIARIENFDRSIDPVLSVKGKDLGRVSNGIVIDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVANNGRIWATCPSRFSEEILIEAIRKIENESHIKGLTDRIKQFIEEKLGERNASSGETKTNS

Source Source

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

Entity 4 Entity 4 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	2

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	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	168

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (7 domains)

Domain ID domain_id	d2jeba1
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	d2jeba2
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	d2jeba3
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	d2jebb1
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	d2jebb2
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	d2jebi1
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.84.4.0 — automated matches

Domain ID domain_id	d2jebi2
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.40.4.11 — DNA replication initiator (cdc21/cdc54) N-terminal domain

CATH v4.4 (5 domains)

Domain ID domain_id	2jebA01
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	2jebB01
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	2jebI01
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	2jebI02
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	2jebI03
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	133.640 Å
Unit-cell length b length_b	133.640 Å
Unit-cell length c length_c	133.640 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	2.400 Å
Low-resolution limit resolution_low	44.540 Å
R factor r_factor	0.2010
R_work r_work	0.1980
R_free r_free	0.2580

Structure of a 9-subunit archaeal exosome bound to Mn ions

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

EXOSOME COMPLEX EXONUCLEASE 2

State in the Current Structure

Other States of the Same Protein in the Database

EXOSOME COMPLEX EXONUCLEASE 1

State in the Current Structure

Other States of the Same Protein in the Database

EXOSOME COMPLEX RNA-BINDING PROTEIN 1

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

2jeb__assembly_1__model_1

2jeb__assembly_1__model_1 | I(q)

2jeb__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 (7)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (7 domains)

CATH v4.4 (5 domains)

7. Citations (1)

Structure of a 9-subunit archaeal exosome bound to Mn ions

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

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

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

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

2jeb__assembly_1__model_1

2jeb__assembly_1__model_1 | I(q)

2jeb__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 (7)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (7 domains)

CATH v4.4 (5 domains)

7. Citations (1)