3h4p

Proteasome 20S core particle from Methanocaldococcus jannaschii

Method: X-RAY DIFFRACTION

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

Proteasome subunit alpha

Methanocaldococcus jannaschii

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 28	Proteasome subunit beta × 14 （Q58634）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PSMA_METJA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–264； UniProt 1–261 Author chain B； PDBConstruct 4–264； UniProt 1–261 Author chain C； PDBConstruct 4–264； UniProt 1–261 Author chain D； PDBConstruct 4–264； UniProt 1–261 Author chain E； PDBConstruct 4–264； UniProt 1–261 Author chain F； PDBConstruct 4–264； UniProt 1–261 Author chain G； PDBConstruct 4–264； UniProt 1–261 Author chain H； PDBConstruct 4–264； UniProt 1–261 Author chain I； PDBConstruct 4–264； UniProt 1–261 Author chain J； PDBConstruct 4–264； UniProt 1–261 Author chain K； PDBConstruct 4–264； UniProt 1–261 Author chain L； PDBConstruct 4–264； UniProt 1–261 Author chain M； PDBConstruct 4–264； UniProt 1–261 Author chain N； PDBConstruct 4–264； UniProt 1–261

Proteasome subunit beta

Methanocaldococcus jannaschii

UniProt Q58634

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 28	Proteasome subunit alpha × 14 （Q60177）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PSMB_METJA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain a； PDBConstruct 2–219； UniProt 7–224 Author chain b； PDBConstruct 2–219； UniProt 7–224 Author chain c； PDBConstruct 2–219； UniProt 7–224 Author chain d； PDBConstruct 2–219； UniProt 7–224 Author chain e； PDBConstruct 2–219； UniProt 7–224 Author chain f； PDBConstruct 2–219； UniProt 7–224 Author chain g； PDBConstruct 2–219； UniProt 7–224 Author chain h； PDBConstruct 2–219； UniProt 7–224 Author chain i； PDBConstruct 2–219； UniProt 7–224 Author chain j； PDBConstruct 2–219； UniProt 7–224 Author chain k； PDBConstruct 2–219； UniProt 7–224 Author chain l； PDBConstruct 2–219； UniProt 7–224 Author chain m； PDBConstruct 2–219； UniProt 7–224 Author chain n； PDBConstruct 2–219； UniProt 7–224

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	3h4p
Deposition date deposition_date	2009-04-20
Structure title title	Proteasome 20S core particle from Methanocaldococcus jannaschii
Keywords keywords	20S, Proteasome, core particle, Hydrolase, Protease, Threonine protease; 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.

3h4p__assembly_1__model_1

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

Download this curve (.dat)

3h4p__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3h4p__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	60.12 Å
Rg (electron density)	59.80 Å
Total Rg	59.99 Å
Atom count	46648
Residues	6076
Excluded volume	843080 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3h4p__assembly_1__model_1`	28-meric （28）	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)

Entity 1 Entity 1 polymer

Description description	Proteasome subunit alpha
Molecular weight formula_weight	29647.1 kDa
EC 编号 ec_number	3.4.25.1
Source method src_method	man
Copy count entity_count	14

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L,M,N
Atom count atom_count	46648

GSHMQMVPPSAYDRAITVFSPEGRLYQVEYAREAVRRGTTAIGIACKDGVVLAVDRRITSKLVKIRSIEKIFQIDDHVAAATSGLVADARVLIDRARLEAQIYRLTYGEEISIEMLAKKICDIKQAYTQHGGVRPFGVSLLIAGIDKNEARLFETDPSGALIEYKATAIGSGRPVVMELLEKEYRDDITLDEGLELAITALTKANEDIKPENVDVCIITVKDAQFKKIPVEEIKKLIEKVKKKLNEENKKEEENREETKEKQEE

Source Source

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

Entity 2 Entity 2 polymer

Description description	Proteasome subunit beta
Molecular weight formula_weight	23787.7 kDa
EC 编号 ec_number	3.4.25.1
Source method src_method	man
Copy count entity_count	14

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	a,b,c,d,e,f,g,h,i,j,k,l,m,n

MTTTVGLICDDAVILATDKRASLGNLVADKEAKKLYKIDDYIAMTIAGSVGDAQAIVRLLIAEAKLYKMRTGRNIPPLACATLLSNILHSSRMFPFLTQIIIGGYDLLEGAKLFSLDPLGGMNEEKTFTATGSGSPIAYGVLEAGYDRDMSVEEGIKLALNALKSAMERDTFSGNGISLAVITKDGVKIFEDEEIEKILDSMKAKPKKKTTKRSRRKSK

Source Source

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

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6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (14 domains)

Domain ID domain_id	d3h4pa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.153 — Ntn hydrolase-like
Superfamily Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family Family family	d.153.1.4 — Proteasome subunits

Domain ID domain_id	d3h4pb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.153 — Ntn hydrolase-like
Superfamily Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family Family family	d.153.1.4 — Proteasome subunits

Domain ID domain_id	d3h4pc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.153 — Ntn hydrolase-like
Superfamily Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family Family family	d.153.1.4 — Proteasome subunits

Domain ID domain_id	d3h4pd_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.153 — Ntn hydrolase-like
Superfamily Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family Family family	d.153.1.4 — Proteasome subunits

Domain ID domain_id	d3h4pe_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.153 — Ntn hydrolase-like
Superfamily Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family Family family	d.153.1.4 — Proteasome subunits

Domain ID domain_id	d3h4pf_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.153 — Ntn hydrolase-like
Superfamily Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family Family family	d.153.1.4 — Proteasome subunits

Domain ID domain_id	d3h4pg_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.153 — Ntn hydrolase-like
Superfamily Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family Family family	d.153.1.4 — Proteasome subunits

Domain ID domain_id	d3h4ph_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.153 — Ntn hydrolase-like
Superfamily Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family Family family	d.153.1.4 — Proteasome subunits

Domain ID domain_id	d3h4pi_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.153 — Ntn hydrolase-like
Superfamily Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family Family family	d.153.1.4 — Proteasome subunits

Domain ID domain_id	d3h4pj_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.153 — Ntn hydrolase-like
Superfamily Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family Family family	d.153.1.4 — Proteasome subunits

Domain ID domain_id	d3h4pk_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.153 — Ntn hydrolase-like
Superfamily Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family Family family	d.153.1.4 — Proteasome subunits

Domain ID domain_id	d3h4pl_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.153 — Ntn hydrolase-like
Superfamily Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family Family family	d.153.1.4 — Proteasome subunits

Domain ID domain_id	d3h4pm_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.153 — Ntn hydrolase-like
Superfamily Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family Family family	d.153.1.4 — Proteasome subunits

Domain ID domain_id	d3h4pn_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.153 — Ntn hydrolase-like
Superfamily Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family Family family	d.153.1.4 — Proteasome subunits

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Unit-cell length a length_a	206.720 Å
Unit-cell length b length_b	219.540 Å
Unit-cell length c length_c	149.020 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	56

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

Resolution resolution	4.100 Å
Low-resolution limit resolution_low	49.975 Å
R factor r_factor	0.2573
R_work r_work	0.2536
R_free r_free	0.3245

Proteasome 20S core particle from Methanocaldococcus jannaschii

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

Proteasome subunit alpha

State in the Current Structure

Other States of the Same Protein in the Database

Proteasome subunit beta

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

3h4p__assembly_1__model_1

3h4p__assembly_1__model_1 | I(q)

3h4p__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (14 domains)

7. Citations (1)

Proteasome 20S core particle from Methanocaldococcus jannaschii

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

Proteasome subunit alpha

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Proteasome subunit beta

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

3h4p__assembly_1__model_1

3h4p__assembly_1__model_1 | I(q)

3h4p__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (14 domains)

7. Citations (1)