3h43

N-terminal domain of the proteasome-activating nucleotidase of Methanocaldococcus jannaschii

Method: X-RAY DIFFRACTION

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

Proteasome-activating nucleotidase

Methanocaldococcus jannaschii

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	water × 6	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 6	water × 6	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 12	water × 12	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PSMR_METJA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–77； UniProt 74–150 Author chain B； PDBConstruct 1–77； UniProt 74–150 Author chain C； PDBConstruct 1–77； UniProt 74–150 Author chain D； PDBConstruct 1–77； UniProt 74–150 Author chain E； PDBConstruct 1–77； UniProt 74–150 Author chain F； PDBConstruct 1–77； UniProt 74–150 Author chain G； PDBConstruct 1–77； UniProt 74–150 Author chain H； PDBConstruct 1–77； UniProt 74–150 Author chain I； PDBConstruct 1–77； UniProt 74–150 Author chain J； PDBConstruct 1–77； UniProt 74–150 Author chain K； PDBConstruct 1–77； UniProt 74–150 Author chain L； PDBConstruct 1–77； UniProt 74–150

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	3h43
Deposition date deposition_date	2009-04-17
Structure title title	N-terminal domain of the proteasome-activating nucleotidase of Methanocaldococcus jannaschii
Keywords keywords	Proteasome, regulatory particle, nucleosidase, ATP-binding, Cytoplasm, Nucleotide-binding, 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.

3h43__assembly_3__model_1

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

Download this curve (.dat)

3h43__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3h43__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	31.07 Å
Rg (electron density)	29.72 Å
Total Rg	30.67 Å
Atom count	7179
Residues	899
Excluded volume	130000 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3h43__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3h43__assembly_2__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3h43__assembly_3__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 (2)

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6. Fold Classification (SCOP + CATH) 28 domains

SCOP 2.08 (28 domains)

Domain ID domain_id	d3h43a1
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.39 — Proteasome regulatory subunits coiled coil regions
Family Family family	h.1.39.1 — Proteasome regulatory subunits coiled coil regions

Domain ID domain_id	d3h43a2
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.17 — Proteasome regulatory subunits PAN/Rpt, OB-fold domain
Family Family family	b.40.17.1 — Proteasome regulatory subunits PAN/Rpt, OB-fold domain

Domain ID domain_id	d3h43b1
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.39 — Proteasome regulatory subunits coiled coil regions
Family Family family	h.1.39.1 — Proteasome regulatory subunits coiled coil regions

Domain ID domain_id	d3h43b2
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.17 — Proteasome regulatory subunits PAN/Rpt, OB-fold domain
Family Family family	b.40.17.1 — Proteasome regulatory subunits PAN/Rpt, OB-fold domain

Domain ID domain_id	d3h43c1
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.39 — Proteasome regulatory subunits coiled coil regions
Family Family family	h.1.39.1 — Proteasome regulatory subunits coiled coil regions

Domain ID domain_id	d3h43c2
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.17 — Proteasome regulatory subunits PAN/Rpt, OB-fold domain
Family Family family	b.40.17.1 — Proteasome regulatory subunits PAN/Rpt, OB-fold domain

Domain ID domain_id	d3h43d1
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.39 — Proteasome regulatory subunits coiled coil regions
Family Family family	h.1.39.1 — Proteasome regulatory subunits coiled coil regions

Domain ID domain_id	d3h43d2
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.17 — Proteasome regulatory subunits PAN/Rpt, OB-fold domain
Family Family family	b.40.17.1 — Proteasome regulatory subunits PAN/Rpt, OB-fold domain

Domain ID domain_id	d3h43e1
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.39 — Proteasome regulatory subunits coiled coil regions
Family Family family	h.1.39.1 — Proteasome regulatory subunits coiled coil regions

Domain ID domain_id	d3h43e2
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.17 — Proteasome regulatory subunits PAN/Rpt, OB-fold domain
Family Family family	b.40.17.1 — Proteasome regulatory subunits PAN/Rpt, OB-fold domain

Domain ID domain_id	d3h43f1
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.39 — Proteasome regulatory subunits coiled coil regions
Family Family family	h.1.39.1 — Proteasome regulatory subunits coiled coil regions

Domain ID domain_id	d3h43f2
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.17 — Proteasome regulatory subunits PAN/Rpt, OB-fold domain
Family Family family	b.40.17.1 — Proteasome regulatory subunits PAN/Rpt, OB-fold domain

Domain ID domain_id	d3h43g1
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.39 — Proteasome regulatory subunits coiled coil regions
Family Family family	h.1.39.1 — Proteasome regulatory subunits coiled coil regions

Domain ID domain_id	d3h43g2
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.17 — Proteasome regulatory subunits PAN/Rpt, OB-fold domain
Family Family family	b.40.17.1 — Proteasome regulatory subunits PAN/Rpt, OB-fold domain

Domain ID domain_id	d3h43h1
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.39 — Proteasome regulatory subunits coiled coil regions
Family Family family	h.1.39.1 — Proteasome regulatory subunits coiled coil regions

Domain ID domain_id	d3h43h2
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.17 — Proteasome regulatory subunits PAN/Rpt, OB-fold domain
Family Family family	b.40.17.1 — Proteasome regulatory subunits PAN/Rpt, OB-fold domain

Domain ID domain_id	d3h43h3
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	d3h43i1
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.39 — Proteasome regulatory subunits coiled coil regions
Family Family family	h.1.39.1 — Proteasome regulatory subunits coiled coil regions

Domain ID domain_id	d3h43i2
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.17 — Proteasome regulatory subunits PAN/Rpt, OB-fold domain
Family Family family	b.40.17.1 — Proteasome regulatory subunits PAN/Rpt, OB-fold domain

Domain ID domain_id	d3h43i3
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	d3h43j1
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.39 — Proteasome regulatory subunits coiled coil regions
Family Family family	h.1.39.1 — Proteasome regulatory subunits coiled coil regions

Domain ID domain_id	d3h43j2
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.17 — Proteasome regulatory subunits PAN/Rpt, OB-fold domain
Family Family family	b.40.17.1 — Proteasome regulatory subunits PAN/Rpt, OB-fold domain

Domain ID domain_id	d3h43k1
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.39 — Proteasome regulatory subunits coiled coil regions
Family Family family	h.1.39.1 — Proteasome regulatory subunits coiled coil regions

Domain ID domain_id	d3h43k2
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.17 — Proteasome regulatory subunits PAN/Rpt, OB-fold domain
Family Family family	b.40.17.1 — Proteasome regulatory subunits PAN/Rpt, OB-fold domain

Domain ID domain_id	d3h43k3
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	d3h43l1
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.39 — Proteasome regulatory subunits coiled coil regions
Family Family family	h.1.39.1 — Proteasome regulatory subunits coiled coil regions

Domain ID domain_id	d3h43l2
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.17 — Proteasome regulatory subunits PAN/Rpt, OB-fold domain
Family Family family	b.40.17.1 — Proteasome regulatory subunits PAN/Rpt, OB-fold domain

Domain ID domain_id	d3h43l3
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

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Unit-cell length a length_a	126.640 Å
Unit-cell length b length_b	129.620 Å
Unit-cell length c length_c	60.610 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	48

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	40.890 Å
R factor r_factor	0.2170
R_work r_work	0.2170
R_free r_free	0.2620

Description description	Proteasome-activating nucleotidase
Molecular weight formula_weight	9757.0 kDa
Source method src_method	man
Copy count entity_count	12

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L
Atom count atom_count	7312

N-terminal domain of the proteasome-activating nucleotidase of Methanocaldococcus jannaschii

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

Proteasome-activating nucleotidase

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

3h43__assembly_3__model_1

3h43__assembly_3__model_1 | I(q)

3h43__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 28 domains

SCOP 2.08 (28 domains)

7. Citations (1)

Source organism organism	Methanocaldococcus jannaschii
Common name common_name	Methanococcus jannaschii
NCBI taxonomy ID ncbi_taxonomy_id	2190
Host organism host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	133

N-terminal domain of the proteasome-activating nucleotidase of Methanocaldococcus jannaschii

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

Proteasome-activating nucleotidase

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

3h43__assembly_3__model_1

3h43__assembly_3__model_1 | I(q)

3h43__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 28 domains

SCOP 2.08 (28 domains)

7. Citations (1)