SAXSdb — 2dzo

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

Probable 26S proteasome regulatory subunit p28

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	26S protease regulatory subunit 6B homolog × 1 （P33298） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	26S protease regulatory subunit 6B homolog × 1 （P33298） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PSDA_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–228； UniProt 1–228 Author chain C； PDBConstruct 1–228； UniProt 1–228

26S protease regulatory subunit 6B homolog

Saccharomyces cerevisiae

UniProt P33298

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Probable 26S proteasome regulatory subunit p28 × 1 （P50086） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Probable 26S proteasome regulatory subunit p28 × 1 （P50086） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PRS6B_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 2–82； UniProt 348–428 Author chain D； PDBConstruct 2–82； UniProt 348–428

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	2dzo
Deposition date deposition_date	2006-09-29
Structure title title	Crystal structure analysis of yeast Nas6p complexed with the proteasome subunit, rpt3
Keywords keywords	;ankyrin repeats, a-helical domain, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, PROTEIN BINDING ;; PROTEIN BINDING
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.

2dzo__assembly_1__model_1

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

Download this curve (.dat)

2dzo__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2dzo__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.05 Å
Rg (electron density)	20.46 Å
Total Rg	21.30 Å
Atom count	2242
Residues	285
Excluded volume	40043 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2dzo__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2dzo__assembly_2__model_1`	dimeric （2）	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 (3)

Entity 1 Entity 1 polymer

Description description	Probable 26S proteasome regulatory subunit p28
Molecular weight formula_weight	25648.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	4763

MSNYPLHQACMENEFFKVQELLHSKPSLLLQKDQDGRIPLHWSVSFQAHEITSFLLSKMENVNLDDYPDDSGWTPFHIACSVGNLEVVKSLYDRPLKPDLNKITNQGVTCLHLAVGKKWFEVSQFLIENGASVRIKDKFNQIPLHRAASVGSLKLIELLCGLGKSAVNWQDKQGWTPLFHALAEGHGDAAVLLVEKYGAEYDLVDNKGAKAEDVALNEQVKKFFLNNV

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	26S protease regulatory subunit 6B homolog
Molecular weight formula_weight	9208.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MERRLIFGTIASKMSLAPEADLDSLIIRNDSLSGAVIAAIMQEAGLRAVRKNRYVILQSDLEEAYATQVKTDNTVDKFDFYK

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	206

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2dzoa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.211 — beta-hairpin-alpha-hairpin repeat
Superfamily Superfamily superfamily	d.211.1 — Ankyrin repeat
Family Family family	d.211.1.1 — Ankyrin repeat

Domain ID domain_id	d2dzoc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.211 — beta-hairpin-alpha-hairpin repeat
Superfamily Superfamily superfamily	d.211.1 — Ankyrin repeat
Family Family family	d.211.1.1 — Ankyrin repeat

CATH v4.4 (4 domains)

Domain ID domain_id	2dzoA00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	20 — Ankyrin repeat-containing domain

Domain ID domain_id	2dzoB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	60 —

Domain ID domain_id	2dzoC00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	20 — Ankyrin repeat-containing domain

Domain ID domain_id	2dzoD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	60 —

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Unit-cell length a length_a	99.599 Å
Unit-cell length b length_b	99.599 Å
Unit-cell length c length_c	73.082 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 31
Space-group number int_tables_number	144
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2120
R_work r_work	0.2120
R_free r_free	0.2820

Crystal structure analysis of yeast Nas6p complexed with the proteasome subunit, rpt3

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

Probable 26S proteasome regulatory subunit p28

State in the Current Structure

Other States of the Same Protein in the Database

26S protease regulatory subunit 6B homolog

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

2dzo__assembly_1__model_1

2dzo__assembly_1__model_1 | I(q)

2dzo__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure analysis of yeast Nas6p complexed with the proteasome subunit, rpt3

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

Probable 26S proteasome regulatory subunit p28

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 protease regulatory subunit 6B homolog

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

2dzo__assembly_1__model_1

2dzo__assembly_1__model_1 | I(q)

2dzo__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)