2bwe

The crystal structure of the complex between the UBA and UBL domains of Dsk2

Method: X-RAY DIFFRACTION Dmax: 169.7 Å Quality: GOOD

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

DSK2

SACCHAROMYCES CEREVISIAE

UniProt P48510

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 homooligomer Homooligomer Protein × 10 PDB declaration: decameric(10) Consistent with protein copy count Chain A; UniProt 328–373 Chain B; UniProt 328–373 Chain C; UniProt 328–373 Chain D; UniProt 328–373 Chain E; UniProt 328–373 Chain F; UniProt 328–373 Chain G; UniProt 328–373 Chain H; UniProt 328–373 Chain I; UniProt 328–373 Chain T; UniProt 1–75 Fragment:UBA DOMAIN, RESIDUES 324-327 Fragment:UBL DOMAIN, RESIDUES 1-75 No other associated polymer 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
2 Protein homooligomer Homooligomer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain N; UniProt 328–373 Chain O; UniProt 328–373 Chain P; UniProt 328–373 Chain Q; UniProt 328–373 Chain R; UniProt 328–373 Chain U; UniProt 1–75 Fragment:UBA DOMAIN, RESIDUES 324-327 Fragment:UBL DOMAIN, RESIDUES 1-75 No other associated polymer 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
3 Protein homooligomer Homooligomer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain J; UniProt 328–373 Chain K; UniProt 328–373 Chain L; UniProt 328–373 Chain M; UniProt 328–373 Chain S; UniProt 1–75 Fragment:UBA DOMAIN, RESIDUES 324-327 Fragment:UBL DOMAIN, RESIDUES 1-75 No other associated polymer 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

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.

5 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DSK2_YEAST
Isoform
PDB entities 1, 2
Chains and sequence ranges Author chain A; PDBConstruct 5–50; UniProt 328–373 Author chain B; PDBConstruct 5–50; UniProt 328–373 Author chain C; PDBConstruct 5–50; UniProt 328–373 Author chain D; PDBConstruct 5–50; UniProt 328–373 Author chain E; PDBConstruct 5–50; UniProt 328–373 Author chain F; PDBConstruct 5–50; UniProt 328–373 Author chain G; PDBConstruct 5–50; UniProt 328–373 Author chain H; PDBConstruct 5–50; UniProt 328–373 Author chain I; PDBConstruct 5–50; UniProt 328–373 Author chain J; PDBConstruct 5–50; UniProt 328–373 Author chain K; PDBConstruct 5–50; UniProt 328–373 Author chain L; PDBConstruct 5–50; UniProt 328–373 Author chain M; PDBConstruct 5–50; UniProt 328–373 Author chain N; PDBConstruct 5–50; UniProt 328–373 Author chain O; PDBConstruct 5–50; UniProt 328–373 Author chain P; PDBConstruct 5–50; UniProt 328–373 Author chain Q; PDBConstruct 5–50; UniProt 328–373 Author chain R; PDBConstruct 5–50; UniProt 328–373 Author chain S; PDBConstruct 3–77; UniProt 1–75 Author chain T; PDBConstruct 3–77; UniProt 1–75 Author chain U; PDBConstruct 3–77; UniProt 1–75

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

SAXS profile for 2bwe

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2bwe
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2bwe
Deposition date deposition_date2005-07-13
Structure title titleThe crystal structure of the complex between the UBA and UBL domains of Dsk2
Keywords keywordsUBIQUITIN, UBIQUITIN-LIKE PROTEINS, PROTEIN/PROTEIN INTERACTION, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier49.94
Radius of gyration Rg (electron density) rg_electron50.20
Forward intensity I(0) i0234948000.00
Molecular weight molecular_weight117700.0 kDa
Excluded volume excluded_volume144020 ų
Envelope volume envelope_volume233140 ų
Hydration-shell volume shell_volume42437 ų
Envelope diameter envelope_diameter172.2
Shell Rg shell_rg47.92
Envelope Rg envelope_rg49.51
Shape Rg shape_rg50.22
Total Rg total_rg50.04
Total atoms total_atoms8306
Residues n_residues1047
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

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

Maximum dimension Dmax dmax169.7
Rg (real space) rg_real50.32
Rg uncertainty (real space) rg_real_error1.97
I(0) (real space) i0_real2.3490e+08
I(0) uncertainty (real space) i0_real_error4.5820e+06
Rg (reciprocal space) rg_reciprocal49.94
I(0) (reciprocal space) i0_reciprocal234800000.0000
Solution quality estimate total_estimate0.8623
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary42.4
Skewness Skewness skewness0.277
Kurtosis Kurtosis kurtosis-0.752
Angular range angular_range— – 0.1600 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha7796000.0000
Real-space data points n_real_points33
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.871; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.778; Smooth: 0.814

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 42 domains

SCOP 2.08 (21 domains)

Domain ID domain_idd2bwea1
Class classa — All alpha proteins
Fold Fold folda.5 — RuvA C-terminal domain-like
Superfamily Superfamily superfamilya.5.2 — UBA-like
Family Family familya.5.2.1 — UBA domain
Domain ID domain_idd2bweb_
Class classa — All alpha proteins
Fold Fold folda.5 — RuvA C-terminal domain-like
Superfamily Superfamily superfamilya.5.2 — UBA-like
Family Family familya.5.2.1 — UBA domain
Domain ID domain_idd2bwec_
Class classa — All alpha proteins
Fold Fold folda.5 — RuvA C-terminal domain-like
Superfamily Superfamily superfamilya.5.2 — UBA-like
Family Family familya.5.2.1 — UBA domain
Domain ID domain_idd2bwed_
Class classa — All alpha proteins
Fold Fold folda.5 — RuvA C-terminal domain-like
Superfamily Superfamily superfamilya.5.2 — UBA-like
Family Family familya.5.2.1 — UBA domain
Domain ID domain_idd2bwee_
Class classa — All alpha proteins
Fold Fold folda.5 — RuvA C-terminal domain-like
Superfamily Superfamily superfamilya.5.2 — UBA-like
Family Family familya.5.2.1 — UBA domain
Domain ID domain_idd2bwef_
Class classa — All alpha proteins
Fold Fold folda.5 — RuvA C-terminal domain-like
Superfamily Superfamily superfamilya.5.2 — UBA-like
Family Family familya.5.2.1 — UBA domain
Domain ID domain_idd2bweg_
Class classa — All alpha proteins
Fold Fold folda.5 — RuvA C-terminal domain-like
Superfamily Superfamily superfamilya.5.2 — UBA-like
Family Family familya.5.2.1 — UBA domain
Domain ID domain_idd2bweh_
Class classa — All alpha proteins
Fold Fold folda.5 — RuvA C-terminal domain-like
Superfamily Superfamily superfamilya.5.2 — UBA-like
Family Family familya.5.2.1 — UBA domain
Domain ID domain_idd2bwei_
Class classa — All alpha proteins
Fold Fold folda.5 — RuvA C-terminal domain-like
Superfamily Superfamily superfamilya.5.2 — UBA-like
Family Family familya.5.2.1 — UBA domain
Domain ID domain_idd2bwej_
Class classa — All alpha proteins
Fold Fold folda.5 — RuvA C-terminal domain-like
Superfamily Superfamily superfamilya.5.2 — UBA-like
Family Family familya.5.2.1 — UBA domain
Domain ID domain_idd2bwek_
Class classa — All alpha proteins
Fold Fold folda.5 — RuvA C-terminal domain-like
Superfamily Superfamily superfamilya.5.2 — UBA-like
Family Family familya.5.2.1 — UBA domain
Domain ID domain_idd2bwel_
Class classa — All alpha proteins
Fold Fold folda.5 — RuvA C-terminal domain-like
Superfamily Superfamily superfamilya.5.2 — UBA-like
Family Family familya.5.2.1 — UBA domain
Domain ID domain_idd2bwem_
Class classa — All alpha proteins
Fold Fold folda.5 — RuvA C-terminal domain-like
Superfamily Superfamily superfamilya.5.2 — UBA-like
Family Family familya.5.2.1 — UBA domain
Domain ID domain_idd2bwen_
Class classa — All alpha proteins
Fold Fold folda.5 — RuvA C-terminal domain-like
Superfamily Superfamily superfamilya.5.2 — UBA-like
Family Family familya.5.2.1 — UBA domain
Domain ID domain_idd2bweo_
Class classa — All alpha proteins
Fold Fold folda.5 — RuvA C-terminal domain-like
Superfamily Superfamily superfamilya.5.2 — UBA-like
Family Family familya.5.2.1 — UBA domain
Domain ID domain_idd2bwep_
Class classa — All alpha proteins
Fold Fold folda.5 — RuvA C-terminal domain-like
Superfamily Superfamily superfamilya.5.2 — UBA-like
Family Family familya.5.2.1 — UBA domain
Domain ID domain_idd2bweq_
Class classa — All alpha proteins
Fold Fold folda.5 — RuvA C-terminal domain-like
Superfamily Superfamily superfamilya.5.2 — UBA-like
Family Family familya.5.2.1 — UBA domain
Domain ID domain_idd2bwer_
Class classa — All alpha proteins
Fold Fold folda.5 — RuvA C-terminal domain-like
Superfamily Superfamily superfamilya.5.2 — UBA-like
Family Family familya.5.2.1 — UBA domain
Domain ID domain_idd2bwes1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.1 — Ubiquitin-related
Domain ID domain_idd2bwet_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.0 — automated matches
Domain ID domain_idd2bweu_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.0 — automated matches

CATH v4.4 (21 domains)

Domain ID domain_id2bweA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily10 — Ubiquitin-associated (UBA) domain
Domain ID domain_id2bweB00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily10 — Ubiquitin-associated (UBA) domain
Domain ID domain_id2bweC00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily10 — Ubiquitin-associated (UBA) domain
Domain ID domain_id2bweD00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily10 — Ubiquitin-associated (UBA) domain
Domain ID domain_id2bweE00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily10 — Ubiquitin-associated (UBA) domain
Domain ID domain_id2bweF00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily10 — Ubiquitin-associated (UBA) domain
Domain ID domain_id2bweG00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily10 — Ubiquitin-associated (UBA) domain
Domain ID domain_id2bweH00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily10 — Ubiquitin-associated (UBA) domain
Domain ID domain_id2bweI00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily10 — Ubiquitin-associated (UBA) domain
Domain ID domain_id2bweJ00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily10 — Ubiquitin-associated (UBA) domain
Domain ID domain_id2bweK00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily10 — Ubiquitin-associated (UBA) domain
Domain ID domain_id2bweL00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily10 — Ubiquitin-associated (UBA) domain
Domain ID domain_id2bweM00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily10 — Ubiquitin-associated (UBA) domain
Domain ID domain_id2bweN00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily10 — Ubiquitin-associated (UBA) domain
Domain ID domain_id2bweO00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily10 — Ubiquitin-associated (UBA) domain
Domain ID domain_id2bweP00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily10 — Ubiquitin-associated (UBA) domain
Domain ID domain_id2bweQ00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily10 — Ubiquitin-associated (UBA) domain
Domain ID domain_id2bweR00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily10 — Ubiquitin-associated (UBA) domain
Domain ID domain_id2bweS00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Domain ID domain_id2bweT00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Domain ID domain_id2bweU00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

8. Citations (1)

9. Files and Curves (10)