3j47

Formation of an intricate helical bundle dictates the assembly of the 26S proteasome lid

Method: ELECTRON MICROSCOPY

▼

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

26S proteasome regulatory subunit RPN11

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	26S proteasome regulatory subunit RPN8 × 1 （Q08723） 26S proteasome regulatory subunit RPN9 × 1 （Q04062） 26S proteasome regulatory subunit RPN5 × 1 （Q12250） 26S proteasome regulatory subunit RPN6 × 1 （Q12377） 26S proteasome regulatory subunit RPN7 × 1 （Q06103） 26S proteasome regulatory subunit RPN3 × 1 （P40016） 26S proteasome regulatory subunit RPN12 × 1 （P32496）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPN11_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain V； PDBConstruct 1–69； UniProt 230–298

26S proteasome regulatory subunit RPN8

OrganismNot specified

UniProt Q08723

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	26S proteasome regulatory subunit RPN11 × 1 （P43588） 26S proteasome regulatory subunit RPN9 × 1 （Q04062） 26S proteasome regulatory subunit RPN5 × 1 （Q12250） 26S proteasome regulatory subunit RPN6 × 1 （Q12377） 26S proteasome regulatory subunit RPN7 × 1 （Q06103） 26S proteasome regulatory subunit RPN3 × 1 （P40016） 26S proteasome regulatory subunit RPN12 × 1 （P32496）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPN8_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain U； PDBConstruct 1–121； UniProt 188–308

26S proteasome regulatory subunit RPN9

OrganismNot specified

UniProt Q04062

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	26S proteasome regulatory subunit RPN11 × 1 （P43588） 26S proteasome regulatory subunit RPN8 × 1 （Q08723） 26S proteasome regulatory subunit RPN5 × 1 （Q12250） 26S proteasome regulatory subunit RPN6 × 1 （Q12377） 26S proteasome regulatory subunit RPN7 × 1 （Q06103） 26S proteasome regulatory subunit RPN3 × 1 （P40016） 26S proteasome regulatory subunit RPN12 × 1 （P32496）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPN9_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain O； PDBConstruct 1–28； UniProt 360–387

26S proteasome regulatory subunit RPN5

OrganismNot specified

UniProt Q12250

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	26S proteasome regulatory subunit RPN11 × 1 （P43588） 26S proteasome regulatory subunit RPN8 × 1 （Q08723） 26S proteasome regulatory subunit RPN9 × 1 （Q04062） 26S proteasome regulatory subunit RPN6 × 1 （Q12377） 26S proteasome regulatory subunit RPN7 × 1 （Q06103） 26S proteasome regulatory subunit RPN3 × 1 （P40016） 26S proteasome regulatory subunit RPN12 × 1 （P32496）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPN5_YEAST
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain P； PDBConstruct 1–34； UniProt 409–442

26S proteasome regulatory subunit RPN6

OrganismNot specified

UniProt Q12377

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	26S proteasome regulatory subunit RPN11 × 1 （P43588） 26S proteasome regulatory subunit RPN8 × 1 （Q08723） 26S proteasome regulatory subunit RPN9 × 1 （Q04062） 26S proteasome regulatory subunit RPN5 × 1 （Q12250） 26S proteasome regulatory subunit RPN7 × 1 （Q06103） 26S proteasome regulatory subunit RPN3 × 1 （P40016） 26S proteasome regulatory subunit RPN12 × 1 （P32496）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPN6_YEAST
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain Q； PDBConstruct 1–25； UniProt 407–431

26S proteasome regulatory subunit RPN7

OrganismNot specified

UniProt Q06103

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	26S proteasome regulatory subunit RPN11 × 1 （P43588） 26S proteasome regulatory subunit RPN8 × 1 （Q08723） 26S proteasome regulatory subunit RPN9 × 1 （Q04062） 26S proteasome regulatory subunit RPN5 × 1 （Q12250） 26S proteasome regulatory subunit RPN6 × 1 （Q12377） 26S proteasome regulatory subunit RPN3 × 1 （P40016） 26S proteasome regulatory subunit RPN12 × 1 （P32496）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPN7_YEAST
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain R； PDBConstruct 1–26； UniProt 397–422

26S proteasome regulatory subunit RPN3

OrganismNot specified

UniProt P40016

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	26S proteasome regulatory subunit RPN11 × 1 （P43588） 26S proteasome regulatory subunit RPN8 × 1 （Q08723） 26S proteasome regulatory subunit RPN9 × 1 （Q04062） 26S proteasome regulatory subunit RPN5 × 1 （Q12250） 26S proteasome regulatory subunit RPN6 × 1 （Q12377） 26S proteasome regulatory subunit RPN7 × 1 （Q06103） 26S proteasome regulatory subunit RPN12 × 1 （P32496）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPN3_YEAST
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain S； PDBConstruct 1–24； UniProt 455–478

26S proteasome regulatory subunit RPN12

OrganismNot specified

UniProt P32496

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	26S proteasome regulatory subunit RPN11 × 1 （P43588） 26S proteasome regulatory subunit RPN8 × 1 （Q08723） 26S proteasome regulatory subunit RPN9 × 1 （Q04062） 26S proteasome regulatory subunit RPN5 × 1 （Q12250） 26S proteasome regulatory subunit RPN6 × 1 （Q12377） 26S proteasome regulatory subunit RPN7 × 1 （Q06103） 26S proteasome regulatory subunit RPN3 × 1 （P40016）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPN12_YEAST
Isoform	—
PDB entities	8
Chains and sequence ranges	Author chain T； PDBConstruct 1–17； UniProt 256–272

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3j47
Deposition date deposition_date	2013-06-27
Structure title title	Formation of an intricate helical bundle dictates the assembly of the 26S proteasome lid
Keywords keywords	alpha helix bundle, hybrid method, flexible fitting, PROTEIN BINDING; PROTEIN BINDING
Experimental Method method	ELECTRON MICROSCOPY

▼

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.

3j47__assembly_1__model_1

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

Download this curve (.dat)

3j47__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3j47__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.66 Å
Rg (electron density)	24.61 Å
Total Rg	25.20 Å
Atom count	2498
Residues	308
Excluded volume	44769 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3j47__assembly_1__model_1`	octameric （8）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	26S proteasome regulatory subunit RPN11
Molecular weight formula_weight	8013.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	V
Atom count atom_count	2498

YEEKEESNLAATKSMVKIAEQYSKRIEEEKELTEEELKTRYVGRQDPKKHLSETADETLENNIVSVLTA

Entity 2 Entity 2 polymer

Description description	26S proteasome regulatory subunit RPN8
Molecular weight formula_weight	13965.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	U

IRLTNQLKSLKGLQSKLKDVVEYLDKVINKELPINHTILGKLQDVFNLLPNLGTPDDDEIDVENHDRINISNNLQKALTVKTNDELMVIYISNLVRSIIAFDDLIENKIQNKKIQEQRVKD

Entity 3 Entity 3 polymer

Description description	26S proteasome regulatory subunit RPN9
Molecular weight formula_weight	3353.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	O

GDQITKMKDRLVEWNDQVEKLGKKMEAR

Entity 4 Entity 4 polymer

Description description	26S proteasome regulatory subunit RPN5
Molecular weight formula_weight	3984.5 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P

SQLLNEWSHNVDELLEHIETIGHLITKEEIMHGL

Entity 5 Entity 5 polymer

Description description	26S proteasome regulatory subunit RPN6
Molecular weight formula_weight	2741.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Q

ATYDSALELVGQLNKVVDQLFEKAS

Entity 6 Entity 6 polymer

Description description	26S proteasome regulatory subunit RPN7
Molecular weight formula_weight	2890.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	R

NAQYHLLVKQGDGLLTKLQKYGAAVR

Entity 7 Entity 7 polymer

Description description	26S proteasome regulatory subunit RPN3
Molecular weight formula_weight	2924.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	S

EDPQQVFDERIKFANQLHDEYLVS

Entity 8 Entity 8 polymer

Description description	26S proteasome regulatory subunit RPN12
Molecular weight formula_weight	1955.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	T

KTNIIEKAMDYAISIEN

▶

Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	1

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

Resolution resolution	7.40 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	2464694

Formation of an intricate helical bundle dictates the assembly of the 26S proteasome lid

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

26S proteasome regulatory subunit RPN11

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

26S proteasome regulatory subunit RPN8

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

26S proteasome regulatory subunit RPN9

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

26S proteasome regulatory subunit RPN5

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

26S proteasome regulatory subunit RPN6

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

26S proteasome regulatory subunit RPN7

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

26S proteasome regulatory subunit RPN3

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

26S proteasome regulatory subunit RPN12

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

3j47__assembly_1__model_1

3j47__assembly_1__model_1 | I(q)

3j47__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer