2bwb

Crystal structure of the UBA domain of Dsk2 from S. cerevisiae

Method: X-RAY DIFFRACTION D_max: 98.7 Å Quality: GOOD

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

UBIQUITIN-LIKE PROTEIN DSK2

SACCHAROMYCES CEREVISIAE

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 326–371	Fragment：UBA DOMAIN, RESIDUES 326-371	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；1.6 M TRISODIUM CITRATE PH 7.0	Resolution 2.30 Å R-free 0.307
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 326–371	Fragment：UBA DOMAIN, RESIDUES 326-371	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；1.6 M TRISODIUM CITRATE PH 7.0	Resolution 2.30 Å R-free 0.307
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 326–371	Fragment：UBA DOMAIN, RESIDUES 326-371	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；1.6 M TRISODIUM CITRATE PH 7.0	Resolution 2.30 Å R-free 0.307
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 326–371	Fragment：UBA DOMAIN, RESIDUES 326-371	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；1.6 M TRISODIUM CITRATE PH 7.0	Resolution 2.30 Å R-free 0.307
5	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain E； UniProt 326–371	Fragment：UBA DOMAIN, RESIDUES 326-371	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；1.6 M TRISODIUM CITRATE PH 7.0	Resolution 2.30 Å R-free 0.307
6	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain F； UniProt 326–371	Fragment：UBA DOMAIN, RESIDUES 326-371	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；1.6 M TRISODIUM CITRATE PH 7.0	Resolution 2.30 Å R-free 0.307
7	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain G； UniProt 326–371	Fragment：UBA DOMAIN, RESIDUES 326-371	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；1.6 M TRISODIUM CITRATE PH 7.0	Resolution 2.30 Å R-free 0.307
8	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain H； UniProt 326–371	Fragment：UBA DOMAIN, RESIDUES 326-371	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；1.6 M TRISODIUM CITRATE PH 7.0	Resolution 2.30 Å R-free 0.307
9	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain I； UniProt 326–371	Fragment：UBA DOMAIN, RESIDUES 326-371	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；1.6 M TRISODIUM CITRATE PH 7.0	Resolution 2.30 Å R-free 0.307

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 2BWB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1WR1 The complex structure of Dsk2p UBA with ubiquitin Deposited 2004-10-08	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 328–373（46 aa） Fragment：C-TERMINAL UBA DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) 20mM potassium phosphate, 5mM potassium chloride NMR sample composition U-15N, 13C ubiquitin + DSK2-UBA complex (0.9mM) \| 20mM Phosphate buffer (pH 6.8); 5mM potassium chloride; 1mM EDTA; 5% D2O NMR sample composition U-15N, 13C DSK2-UBA + ubiquitin complex (1.0mM) \| 20mM Phosphate buffer (pH 6.8); 5mM potassium chloride; 1mM EDTA; 5% D2O	Resolution not provided
2BWE The crystal structure of the complex between the UBA and UBL domains of Dsk2 Deposited 2005-07-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 10 PDB declaration: decameric	Chain A 328–373（46 aa） Fragment：UBA DOMAIN, RESIDUES 324-327 Chain B 328–373（46 aa） Fragment：UBA DOMAIN, RESIDUES 324-327 Chain C 328–373（46 aa） Fragment：UBA DOMAIN, RESIDUES 324-327 Chain D 328–373（46 aa） Fragment：UBA DOMAIN, RESIDUES 324-327 Chain E 328–373（46 aa） Fragment：UBA DOMAIN, RESIDUES 324-327 Chain F 328–373（46 aa） Fragment：UBA DOMAIN, RESIDUES 324-327 Chain G 328–373（46 aa） Fragment：UBA DOMAIN, RESIDUES 324-327 Chain H 328–373（46 aa） Fragment：UBA DOMAIN, RESIDUES 324-327 Chain I 328–373（46 aa） Fragment：UBA DOMAIN, RESIDUES 324-327 Chain T 1–75（75 aa） Fragment：UBL DOMAIN, RESIDUES 1-75	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；277 K；10-15% METHOXY PEG 5K BUFFERED WITH 0.1M MES PH 6.5 AT 4C	Resolution 3.10 Å R-free 0.267
2BWE The crystal structure of the complex between the UBA and UBL domains of Dsk2 Deposited 2005-07-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain N 328–373（46 aa） Fragment：UBA DOMAIN, RESIDUES 324-327 Chain O 328–373（46 aa） Fragment：UBA DOMAIN, RESIDUES 324-327 Chain P 328–373（46 aa） Fragment：UBA DOMAIN, RESIDUES 324-327 Chain Q 328–373（46 aa） Fragment：UBA DOMAIN, RESIDUES 324-327 Chain R 328–373（46 aa） Fragment：UBA DOMAIN, RESIDUES 324-327 Chain U 1–75（75 aa） Fragment：UBL DOMAIN, RESIDUES 1-75	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；277 K；10-15% METHOXY PEG 5K BUFFERED WITH 0.1M MES PH 6.5 AT 4C	Resolution 3.10 Å R-free 0.267
2BWE The crystal structure of the complex between the UBA and UBL domains of Dsk2 Deposited 2005-07-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain J 328–373（46 aa） Fragment：UBA DOMAIN, RESIDUES 324-327 Chain K 328–373（46 aa） Fragment：UBA DOMAIN, RESIDUES 324-327 Chain L 328–373（46 aa） Fragment：UBA DOMAIN, RESIDUES 324-327 Chain M 328–373（46 aa） Fragment：UBA DOMAIN, RESIDUES 324-327 Chain S 1–75（75 aa） Fragment：UBL DOMAIN, RESIDUES 1-75	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；277 K；10-15% METHOXY PEG 5K BUFFERED WITH 0.1M MES PH 6.5 AT 4C	Resolution 3.10 Å R-free 0.267
2BWF Crystal structure of the UBL domain of Dsk2 from S. cerevisiae Deposited 2005-07-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–75（75 aa） Fragment：UBL DOMAIN, RESIDUES 1-75	Not recorded	FMT FORMIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.00	Resolution 1.15 Å R-free 0.195
2BWF Crystal structure of the UBL domain of Dsk2 from S. cerevisiae Deposited 2005-07-13	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–75（75 aa） Fragment：UBL DOMAIN, RESIDUES 1-75	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.00	Resolution 1.15 Å R-free 0.195
3M63 Crystal structure of Ufd2 in complex with the ubiquitin-like (UBL) domain of Dsk2 Deposited 2010-03-15	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–75（75 aa） Fragment：UNP residues 1-75, Ubiquitin-like domain	Not recorded	1PE PENTAETHYLENE GLYCOL × 1 K POTASSIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；298 K；16-18% PEG 3500 200 mM Tripotassium citrate, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.40 Å R-free 0.270
4UN2 Crystal structure of the UBA domain of Dsk2 in complex with Ubiquitin Deposited 2014-05-23	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 328–373（46 aa） Fragment：UBA DOMAIN, RESIDUES 328-373	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；0.2M MAGNESIUM CHLORIDE, 0.1M TRIS PH 8.5, 20% PEG 8000	Resolution 1.51 Å R-free 0.196

5 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DSK2_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–46； UniProt 326–371 Author chain B； PDBConstruct 1–46； UniProt 326–371 Author chain C； PDBConstruct 1–46； UniProt 326–371 Author chain D； PDBConstruct 1–46； UniProt 326–371 Author chain E； PDBConstruct 1–46； UniProt 326–371 Author chain F； PDBConstruct 1–46； UniProt 326–371 Author chain G； PDBConstruct 1–46； UniProt 326–371 Author chain H； PDBConstruct 1–46； UniProt 326–371 Author chain I； PDBConstruct 1–46； UniProt 326–371

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2bwb
Deposition date deposition_date	2005-07-13
Structure title title	Crystal structure of the UBA domain of Dsk2 from S. cerevisiae
Keywords keywords	UBIQUITIN, UBA, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	30.72 Å
Radius of gyration Rg (electron density) rg_electron	30.64 Å
Forward intensity I(0) i0	39726000.00
Molecular weight molecular_weight	45171.0 kDa
Excluded volume excluded_volume	54807 Å³
Envelope volume envelope_volume	76060 Å³
Hydration-shell volume shell_volume	23132 Å³
Envelope diameter envelope_diameter	100.6 Å
Shell Rg shell_rg	33.62 Å
Envelope Rg envelope_rg	30.64 Å
Shape Rg shape_rg	30.65 Å
Total Rg total_rg	30.89 Å
Total atoms total_atoms	3187
Residues n_residues	398
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	98.7 Å
Rg (real space) rg_real	30.82 Å
Rg uncertainty (real space) rg_real_error	1.22 Å
I(0) (real space) i0_real	3.9730e+07
I(0) uncertainty (real space) i0_real_error	6.4740e+05
Rg (reciprocal space) rg_reciprocal	30.78 Å
I(0) (reciprocal space) i0_reciprocal	39720000.0000
Solution quality estimate total_estimate	0.8724
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	38.0 Å
Skewness Skewness skewness	0.240
Kurtosis Kurtosis kurtosis	-0.718
Angular range angular_range	— – 0.2600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2434000.0000
Real-space data points n_real_points	53
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.914; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.799; Smooth: 0.803

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (9 domains)

Domain ID domain_id	d2bwba_
Class class	a — All alpha proteins
Fold Fold fold	a.5 — RuvA C-terminal domain-like
Superfamily Superfamily superfamily	a.5.2 — UBA-like
Family Family family	a.5.2.1 — UBA domain

Domain ID domain_id	d2bwbb_
Class class	a — All alpha proteins
Fold Fold fold	a.5 — RuvA C-terminal domain-like
Superfamily Superfamily superfamily	a.5.2 — UBA-like
Family Family family	a.5.2.1 — UBA domain

Domain ID domain_id	d2bwbc_
Class class	a — All alpha proteins
Fold Fold fold	a.5 — RuvA C-terminal domain-like
Superfamily Superfamily superfamily	a.5.2 — UBA-like
Family Family family	a.5.2.1 — UBA domain

Domain ID domain_id	d2bwbd_
Class class	a — All alpha proteins
Fold Fold fold	a.5 — RuvA C-terminal domain-like
Superfamily Superfamily superfamily	a.5.2 — UBA-like
Family Family family	a.5.2.1 — UBA domain

Domain ID domain_id	d2bwbe_
Class class	a — All alpha proteins
Fold Fold fold	a.5 — RuvA C-terminal domain-like
Superfamily Superfamily superfamily	a.5.2 — UBA-like
Family Family family	a.5.2.1 — UBA domain

Domain ID domain_id	d2bwbf_
Class class	a — All alpha proteins
Fold Fold fold	a.5 — RuvA C-terminal domain-like
Superfamily Superfamily superfamily	a.5.2 — UBA-like
Family Family family	a.5.2.1 — UBA domain

Domain ID domain_id	d2bwbg_
Class class	a — All alpha proteins
Fold Fold fold	a.5 — RuvA C-terminal domain-like
Superfamily Superfamily superfamily	a.5.2 — UBA-like
Family Family family	a.5.2.1 — UBA domain

Domain ID domain_id	d2bwbh_
Class class	a — All alpha proteins
Fold Fold fold	a.5 — RuvA C-terminal domain-like
Superfamily Superfamily superfamily	a.5.2 — UBA-like
Family Family family	a.5.2.1 — UBA domain

Domain ID domain_id	d2bwbi_
Class class	a — All alpha proteins
Fold Fold fold	a.5 — RuvA C-terminal domain-like
Superfamily Superfamily superfamily	a.5.2 — UBA-like
Family Family family	a.5.2.1 — UBA domain

CATH v4.4 (9 domains)

Domain ID domain_id	2bwbA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	10 — Ubiquitin-associated (UBA) domain

Domain ID domain_id	2bwbB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	10 — Ubiquitin-associated (UBA) domain

Domain ID domain_id	2bwbC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	10 — Ubiquitin-associated (UBA) domain

Domain ID domain_id	2bwbD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	10 — Ubiquitin-associated (UBA) domain

Domain ID domain_id	2bwbE00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	10 — Ubiquitin-associated (UBA) domain

Domain ID domain_id	2bwbF00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	10 — Ubiquitin-associated (UBA) domain

Domain ID domain_id	2bwbG00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	10 — Ubiquitin-associated (UBA) domain

Domain ID domain_id	2bwbH00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	10 — Ubiquitin-associated (UBA) domain

Domain ID domain_id	2bwbI00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	10 — Ubiquitin-associated (UBA) domain

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8. Citations (1)

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Unit-cell length a length_a	116.311 Å
Unit-cell length b length_b	44.069 Å
Unit-cell length c length_c	111.525 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	114.87 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	36

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	101.020 Å
R factor r_factor	0.2460
R_work r_work	0.2430
R_free r_free	0.3070

Description description	UBIQUITIN-LIKE PROTEIN DSK2
Molecular weight formula_weight	5214.7 kDa
Source method src_method	man
Copy count entity_count	9

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I
Atom count atom_count	3337

Crystal structure of the UBA domain of Dsk2 from S. cerevisiae

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

UBIQUITIN-LIKE PROTEIN DSK2

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (9 domains)

CATH v4.4 (9 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	SACCHAROMYCES CEREVISIAE
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	ESCHERICHIA COLI

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	150

fit	/app/data/saxs_computation/bw/2bwb/2bwb.fit
pddf	/app/data/pr_computation/bw/2bwb/2bwb.pr.out
profile	/app/data/saxs_computation/bw/2bwb/2bwb.dat