SAXSdb — 5v1a

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

Ubiquitin-like-specific protease 2

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain B； UniProt 821–845	Not recorded	Monopolin complex subunit CSM1 × 2 （P25651）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；100 mM M HEPES pH 7.5 and 20% PEG 3350, 25% Glycerol	Resolution 2.14 Å R-free 0.278

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 5V1A	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5LNB Crystal structure of the de-sumoylating protease Deposited 2016-08-03	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 411–710（300 aa）	Not recorded	ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M di-ammonium hydrogen citrate, 20 % PEG 3350, protein concentration 3 mg/ml	Resolution 2.30 Å R-free 0.197

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ULP2_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain B； PDBConstruct 2–26； UniProt 821–845

Monopolin complex subunit CSM1

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P25651

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 69–190	Not recorded	Ubiquitin-like-specific protease 2 × 2 （P40537）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；100 mM M HEPES pH 7.5 and 20% PEG 3350, 25% Glycerol	Resolution 2.14 Å R-free 0.278

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 5V1A	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3N4R Structure of Csm1 C-terminal domain, R3 form Deposited 2010-05-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 69–181（113 aa） Fragment：C-terminal domain (residues 69-181) Chain B 69–181（113 aa） Fragment：C-terminal domain (residues 69-181)	Mutation：L157M Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：L157M Non-standard monomer：Yes (specific site not provided by mmCIF)	1PE PENTAETHYLENE GLYCOL × 2 MLI MALONATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.4；293 K；2.0 M Sodium malonate pH 6.4, 2% PEG 400, VAPOR DIFFUSION, temperature 293K	Resolution 2.60 Å R-free 0.243
3N4R Structure of Csm1 C-terminal domain, R3 form Deposited 2010-05-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 69–181（113 aa） Fragment：C-terminal domain (residues 69-181) Chain D 69–181（113 aa） Fragment：C-terminal domain (residues 69-181)	Mutation：L157M Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：L157M Non-standard monomer：Yes (specific site not provided by mmCIF)	1PE PENTAETHYLENE GLYCOL × 2 MLI MALONATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.4；293 K；2.0 M Sodium malonate pH 6.4, 2% PEG 400, VAPOR DIFFUSION, temperature 293K	Resolution 2.60 Å R-free 0.243
3N4S Structure of Csm1 C-terminal domain, P21212 form Deposited 2010-05-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 69–181（113 aa） Fragment：C-terminal domain (residues 69-181) Chain B 69–181（113 aa） Fragment：C-terminal domain (residues 69-181)	Not recorded	1PE PENTAETHYLENE GLYCOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；293 K；2.0 M Sodium malonate pH 6.4, 2% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.35 Å R-free 0.234
3N4S Structure of Csm1 C-terminal domain, P21212 form Deposited 2010-05-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 69–181（113 aa） Fragment：C-terminal domain (residues 69-181) Chain D 69–181（113 aa） Fragment：C-terminal domain (residues 69-181)	Not recorded	1PE PENTAETHYLENE GLYCOL × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；293 K；2.0 M Sodium malonate pH 6.4, 2% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.35 Å R-free 0.234
3N4X Structure of Csm1 full-length Deposited 2010-05-23	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–190（190 aa） Chain B 1–190（190 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；150 mM lithium chloride, 12% PEG 2000, 4% 1,4-butanediol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.41 Å R-free 0.282
3N4X Structure of Csm1 full-length Deposited 2010-05-23	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–190（190 aa） Chain D 1–190（190 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；150 mM lithium chloride, 12% PEG 2000, 4% 1,4-butanediol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.41 Å R-free 0.282
3N7N Structure of Csm1/Lrs4 complex Deposited 2010-05-27	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–190（190 aa） Chain B 1–190（190 aa） Chain C 1–190（190 aa） Chain D 1–190（190 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；0.1 M Tris-HCl pH 8.5, 120 mM MgCl2, 16% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.90 Å R-free 0.355
5KTB Structure of a complex between S. cerevisiae Csm1 and Mam1 Deposited 2016-07-11	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–190（190 aa） Chain B 1–190（190 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；100 mM HEPES, pH 7.5, 100 mM magnesium chloride, 6% PEG4000	Resolution 3.05 Å R-free 0.241
5V3N Structure of S. cerevisiae Ulp2-Tof2-Csm1 complex Deposited 2017-03-07	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 69–181（113 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M Ammonium Acetate, 0.1 M HEPES pH 7.5 and 25% PEG 3350 and 25% Glycerol	Resolution 1.30 Å R-free 0.217
6DEI Structure of Dse3-Csm1 complex Deposited 2018-05-12	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 69–181（113 aa） Chain B 69–181（113 aa）	Not recorded	PGE TRIETHYLENE GLYCOL × 2 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M NaOAc, 0.1M HEPES pH 7.5, 22% PEG 4000	Resolution 1.70 Å R-free 0.221

7 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CSM1_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–122； UniProt 69–190

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	5v1a
Deposition date deposition_date	2017-03-01
Structure title title	Structure of S. cerevisiae Ulp2:Csm1 complex
Keywords keywords	monopolin, rDNA silencing, SUMO isopeptidase, cohibin, HYDROLASE; HYDROLASE
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	16.41 Å
Radius of gyration Rg (electron density) rg_electron	15.25 Å
Forward intensity I(0) i0	3738720.00
Molecular weight molecular_weight	14108.0 kDa
Excluded volume excluded_volume	17905 Å³
Envelope volume envelope_volume	21590 Å³
Hydration-shell volume shell_volume	12375 Å³
Envelope diameter envelope_diameter	59.8 Å
Shell Rg shell_rg	20.81 Å
Envelope Rg envelope_rg	16.24 Å
Shape Rg shape_rg	15.25 Å
Total Rg total_rg	16.47 Å
Total atoms total_atoms	999
Residues n_residues	124
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	60.7 Å
Rg (real space) rg_real	16.45 Å
Rg uncertainty (real space) rg_real_error	0.47 Å
I(0) (real space) i0_real	3.7390e+06
I(0) uncertainty (real space) i0_real_error	5.0030e+04
Rg (reciprocal space) rg_reciprocal	16.44 Å
I(0) (reciprocal space) i0_reciprocal	3739000.0000
Solution quality estimate total_estimate	0.7375
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.0 Å
Skewness Skewness skewness	0.507
Kurtosis Kurtosis kurtosis	0.365
Angular range angular_range	— – 0.4850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	724900.0000
Real-space data points n_real_points	79
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.548; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.938; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Ubiquitin-like-specific protease 2
Molecular weight formula_weight	2892.2 kDa
EC 编号 ec_number	3.4.22.68
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B
Atom count atom_count	1019

AEFTSPYFGRPSLKTRAKQFEGVSSP

来源 Source

来源生物 organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
通用名 common_name	;Baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Monopolin complex subunit CSM1
Molecular weight formula_weight	14139.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

ENSEVIKDLYEYLCNVRVHKSYEDDSGLWFDISQGTHSGGSSDDYSIMDYKLGFVKGQAQVTEVIYAPVLKQRSTEELYSLQSKLPEYLFETLSFPLSSLNQFYNKIAKSLNKKREKKDETE

来源 Source

来源生物 organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
通用名 common_name	;Baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 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	20

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	5v1aA00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily	80 —

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8. Citations (1)

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Unit-cell length a length_a	46.737 Å
Unit-cell length b length_b	46.737 Å
Unit-cell length c length_c	124.638 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	8

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.140 Å
Low-resolution limit resolution_low	43.761 Å
R factor r_factor	0.2391
R_work r_work	0.2345
R_free r_free	0.2782

fit	/app/data/saxs_computation/v1/5v1a/5v1a.fit
pddf	/app/data/pr_computation/v1/5v1a/5v1a.pr.out
profile	/app/data/saxs_computation/v1/5v1a/5v1a.dat

Structure of S. cerevisiae Ulp2:Csm1 complex

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

Ubiquitin-like-specific protease 2

State in the Current Structure

Other States of the Same Protein in the Database

Monopolin complex subunit CSM1

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)