3m85

Archaeoglobus fulgidus exosome y70a with RNA bound to the active site

Method: X-RAY DIFFRACTION

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

Putative uncharacterized protein AF_0206

Archaeoglobus fulgidus

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 （O29757） Probable exosome complex exonuclease 2 × 3 （O29756） 5'-R(CPUPCPCPCPC)-3' × 3 ZINC ION × 3 water × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O30033_ARCFU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–179； UniProt 1–179 Author chain B； PDBConstruct 1–179； UniProt 1–179 Author chain C； PDBConstruct 1–179； UniProt 1–179

Probable exosome complex exonuclease 1

archaeoglobus fulgidus

UniProt O29757

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	Putative uncharacterized protein AF_0206 × 3 （O30033） Probable exosome complex exonuclease 2 × 3 （O29756） 5'-R(CPUPCPCPCPC)-3' × 3 ZINC ION × 3 water × 2	Consistent with all polymers

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

Probable exosome complex exonuclease 2

archaeoglobus fulgidus

UniProt O29756

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	Putative uncharacterized protein AF_0206 × 3 （O30033） Probable exosome complex exonuclease 1 × 3 （O29757） 5'-R(CPUPCPCPCPC)-3' × 3 ZINC ION × 3 water × 2	Consistent with all polymers

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	3m85
Deposition date deposition_date	2010-03-17
Structure title title	Archaeoglobus fulgidus exosome y70a with RNA bound to the active site
Keywords keywords	exosome, RNA, Exonuclease, Hydrolase, Nuclease, HYDROLASE-RNA complex; 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.

3m85__assembly_1__model_1

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

Download this curve (.dat)

3m85__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3m85__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	38.61 Å
Rg (electron density)	37.67 Å
Total Rg	38.26 Å
Atom count	16104
Residues	2058
Excluded volume	287620 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3m85__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 (6)

Entity 1 Entity 1 polymer

Description description	Putative uncharacterized protein AF_0206
Molecular weight formula_weight	19625.6 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	16110

MRFVMPGDRIGSAEEYVKGEGVYEEGGELFAAVAGKLIIKDRVAKVESISPIPEIVKGDVVLGRVVDLRNSIALIEVSSKKGENRGPSNRGIGILHVSNVDEGYVKEISEAVGYLDILKARVIGDNLRLSTKEEEMGVLRALCSNCKTEMVREGDILKCPECGRVEKRKISTDYGKGEW

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	Probable exosome complex exonuclease 1
Molecular weight formula_weight	28860.3 kDa
EC 编号 ec_number	3.1.13.-
Mutation mutation	R65E
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E,F

MSEFNEKPEKLIVDGLRLDGRKFDELRPIKIEASVLKRADGSCYLEMGKNKVIAAVFGPREVHPEHLQDPSKAIIRYRYNMAPFSVEERKRPGPDRRSIEISKVSKEAFEAVIMKELFPRSAIDIFVEVLQADAGSRTACLNAASVALVDAGVPMKGMITSVAVGKADGQLVLDPMKEEDNFGEADMPFAFLIRNGKIESIALLQMDGRMTRDEVKQAIELAKKGALQIYEMQREAILRRYIEVGEEMDEITEGGEDA

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	Probable exosome complex exonuclease 2
Molecular weight formula_weight	28585.5 kDa
EC 编号 ec_number	3.1.13.-
Mutation mutation	Y70A
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,H,I

MPEDILVDIKRDYVLSKLRDNERIDGRGFDEFRKVEIIPNVIEKAEGSALVKLGDTQVVVGVKMQPGEPAPDTPDRGVIIVNAELVPLASPTFEPGPPDENSIELARVVDRGIRESEAVDLSKLVIEEGEKVWIVFVDIHALDDDGNLLDASALAAIAALMNTKVPAERFDLGEDYLLPVRDLPVSVTSLIVGNKYLVDPSREEMSVGDTTLTITTDKDDNVVAMQKSGGYLLDEKLFDELLDVSINCARKLREKFKEI

Source Source

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

Entity 4 Entity 4 polymer

Description description	5'-R(CPUPCPCPCPC)-3'
Molecular weight formula_weight	1787.1 kDa
Source method src_method	syn
Copy count entity_count	3

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	X,Y,Z

CUCCCC

Entity 5 Entity 5 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	6

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6. Fold Classification (SCOP + CATH) 27 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d3m85d1
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	d3m85d2
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	d3m85e1
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	d3m85e2
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	d3m85f1
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	d3m85f2
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	d3m85g1
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	d3m85g2
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	d3m85h1
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	d3m85h2
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	d3m85i1
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	d3m85i2
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	3m85A01
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	3m85A02
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	3m85A03
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	70 — Ubiquitin Ligase Nedd4; Chain: W;
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	3m85B01
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	3m85B02
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	3m85B03
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	70 — Ubiquitin Ligase Nedd4; Chain: W;
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	3m85C01
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	3m85C02
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	3m85C03
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	70 — Ubiquitin Ligase Nedd4; Chain: W;
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	3m85D01
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	3m85E01
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	3m85F01
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	3m85G01
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	3m85H01
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	3m85I01
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	138.020 Å
Unit-cell length b length_b	138.020 Å
Unit-cell length c length_c	262.250 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	24

Space group space_group	P 43 2 2
Space-group number int_tables_number	95
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	19.984 Å
R factor r_factor	0.1995
R_work r_work	0.1906
R_free r_free	0.2778

Archaeoglobus fulgidus exosome y70a with RNA bound to the active site

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

Putative uncharacterized protein AF_0206

State in the Current Structure

Other States of the Same Protein in the Database

Probable exosome complex exonuclease 1

State in the Current Structure

Other States of the Same Protein in the Database

Probable exosome complex exonuclease 2

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

3m85__assembly_1__model_1

3m85__assembly_1__model_1 | I(q)

3m85__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 (6)

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 water

6. Fold Classification (SCOP + CATH) 27 domains

SCOP 2.08 (12 domains)

CATH v4.4 (15 domains)

7. Citations (1)

Archaeoglobus fulgidus exosome y70a with RNA bound to the active site

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

Putative uncharacterized protein AF_0206

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 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3m85__assembly_1__model_1

3m85__assembly_1__model_1 | I(q)

3m85__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 (6)

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 water

6. Fold Classification (SCOP + CATH) 27 domains

SCOP 2.08 (12 domains)

CATH v4.4 (15 domains)

7. Citations (1)