SAXSdb — 2n3w

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

26S proteasome regulatory subunit RPN1

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Ubiquitin-60S ribosomal protein L40 × 2 （P62987）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPN1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–131； UniProt 482–612

Ubiquitin-60S ribosomal protein L40

Homo sapiens

UniProt P62987

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	26S proteasome regulatory subunit RPN1 × 1 （P38764）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RL40_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–76； UniProt 1–76 Author chain C； PDBConstruct 1–76； UniProt 1–76

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	2n3w
Deposition date deposition_date	2015-06-10
Structure title title	Solution structure of the Rpn1 T1 site with K48-linked diubiquitin in the contracted binding mode
Keywords keywords	PROTEIN BINDING; PROTEIN BINDING
Experimental Method method	SOLUTION NMR

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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.

2n3w__assembly_1__model_6

Assembly 1 · Model 6 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2n3w__assembly_1__model_6 | I(q)

100 plotted points; both axes use logarithmic scales.

2n3w__assembly_1__model_6 | P(r) · Pending

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

Rg（Guinier）	21.52 Å
Rg (electron density)	20.40 Å
Total Rg	21.36 Å
Atom count	4380
Residues	283
Excluded volume	38831 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2n3w__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	2	`2n3w__assembly_1__model_2`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	3	`2n3w__assembly_1__model_3`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	4	`2n3w__assembly_1__model_4`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	5	`2n3w__assembly_1__model_5`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	6	`2n3w__assembly_1__model_6`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	7	`2n3w__assembly_1__model_7`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	8	`2n3w__assembly_1__model_8`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	9	`2n3w__assembly_1__model_9`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	10	`2n3w__assembly_1__model_10`	trimeric （3）	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	26S proteasome regulatory subunit RPN1
Molecular weight formula_weight	13636.6 kDa
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	43800

DTKISSAAILGLGIAFAGSKNDEVLGLLLPIAASTDLPIETAAMASLALAHVFVGTCNGDITTSIMDNFLERTAIELKTDWVRFLALALGILYMGQGEQVDDVLETISAIEHPMTSAIEVLVGSCAYTGTG

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Ubiquitin-60S ribosomal protein L40
Molecular weight formula_weight	8576.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,C

MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2n3wb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

Domain ID domain_id	d2n3wc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

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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	—

Solution structure of the Rpn1 T1 site with K48-linked diubiquitin in the contracted binding mode

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

26S proteasome regulatory subunit RPN1

State in the Current Structure

Other States of the Same Protein in the Database

Ubiquitin-60S ribosomal protein L40

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

2n3w__assembly_1__model_6

2n3w__assembly_1__model_6 | I(q)

2n3w__assembly_1__model_6 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

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) 2 domains

SCOP 2.08 (2 domains)

7. Citations (1)

Solution structure of the Rpn1 T1 site with K48-linked diubiquitin in the contracted binding mode

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

26S proteasome regulatory subunit RPN1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ubiquitin-60S ribosomal protein L40

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

2n3w__assembly_1__model_6

2n3w__assembly_1__model_6 | I(q)

2n3w__assembly_1__model_6 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

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) 2 domains

SCOP 2.08 (2 domains)

7. Citations (1)