SAXSdb — 5v3n

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

Monopolin complex subunit CSM1

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	Insufficient information Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 69–181	Not recorded	Ulp2p,Topoisomerase 1-associated factor 2 chimera × 2 （H0GHZ9,Q02208）	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

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 5V3N	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
5V1A Structure of S. cerevisiae Ulp2:Csm1 complex Deposited 2017-03-01	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 69–190（122 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 M HEPES pH 7.5 and 20% PEG 3350, 25% Glycerol	Resolution 2.14 Å R-free 0.278
6DEI Structure of Dse3-Csm1 complex Deposited 2018-05-12	Different construct Different mutation/modification Different oligomeric state 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	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–113； UniProt 69–181

Ulp2p,Topoisomerase 1-associated factor 2 chimera

Saccharomyces cerevisiae

UniProt H0GHZ9

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Insufficient information Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain B； UniProt 825–844	Not recorded	Monopolin complex subunit CSM1 × 2 （P25651）	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

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	H0GHZ9_SACCK
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 4–23； UniProt 825–844

Ulp2p,Topoisomerase 1-associated factor 2 chimera

Saccharomyces cerevisiae

UniProt Q02208

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Insufficient information Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain B； UniProt 384–398	Not recorded	Monopolin complex subunit CSM1 × 2 （P25651）	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

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 5V3N	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5HOI Crystal structure of the carboxy-terminal domain of yeast Ctf4 bound to Tof2. Deposited 2016-01-19	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 D 497–517（21 aa） Fragment：UNP residues 497-517 Chain E 497–517（21 aa） Fragment：UNP residues 497-517 Chain F 497–517（21 aa） Fragment：UNP residues 497-517	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；0.2 M tri-sodium citrate pH 6.2, 7-9% PEG 8000 and 0.45-0.9 M NaCl	Resolution 3.30 Å R-free 0.224

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

View Construct and Data Evidence

UniProt name	TOF2_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 24–38； UniProt 384–398

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	5v3n
Deposition date deposition_date	2017-03-07
Structure title title	Structure of S. cerevisiae Ulp2-Tof2-Csm1 complex
Keywords keywords	monopolin, cohibin, rDNA silencing, desumoylation, 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	16.55 Å
Radius of gyration Rg (electron density) rg_electron	15.35 Å
Forward intensity I(0) i0	4913840.00
Molecular weight molecular_weight	16054.0 kDa
Excluded volume excluded_volume	20212 Å³
Envelope volume envelope_volume	24005 Å³
Hydration-shell volume shell_volume	13376 Å³
Envelope diameter envelope_diameter	59.6 Å
Shell Rg shell_rg	21.07 Å
Envelope Rg envelope_rg	15.95 Å
Shape Rg shape_rg	15.34 Å
Total Rg total_rg	16.55 Å
Total atoms total_atoms	2226
Residues n_residues	142
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	57.5 Å
Rg (real space) rg_real	16.48 Å
Rg uncertainty (real space) rg_real_error	0.46 Å
I(0) (real space) i0_real	4.9140e+06
I(0) uncertainty (real space) i0_real_error	6.2570e+04
Rg (reciprocal space) rg_reciprocal	16.49 Å
I(0) (reciprocal space) i0_reciprocal	4914000.0000
Solution quality estimate total_estimate	0.7691
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	21.6 Å
Skewness Skewness skewness	0.283
Kurtosis Kurtosis kurtosis	-0.055
Angular range angular_range	— – 0.4800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	866900.0000
Real-space data points n_real_points	78
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.670; Stabil: 0.996; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; 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	Monopolin complex subunit CSM1
Molecular weight formula_weight	12991.4 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	2354

ENSEVIKDLYEYLCNVRVHKSYEDDSGLWFDISQGTHSGGSSDDYSIMDYKLGFVKGQAQVTEVIYAPVLKQRSTEELYSLQSKLPEYLFETLSFPLSSLNQFYNKIAKSLNK

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	Ulp2p,Topoisomerase 1-associated factor 2 chimera
Molecular weight formula_weight	4269.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

SNAPYFGRPSLKTRAKQFEGVSSKDIGENCRRIEAFSD

来源 Source

来源生物 organism	Saccharomyces cerevisiae
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	85

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	5v3nA00
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	71.684 Å
Unit-cell length b length_b	56.933 Å
Unit-cell length c length_c	40.992 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	121.06 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.300 Å
Low-resolution limit resolution_low	35.115 Å
R factor r_factor	0.1934
R_work r_work	0.1920
R_free r_free	0.2171

fit	/app/data/saxs_computation/v3/5v3n/5v3n.fit
pddf	/app/data/pr_computation/v3/5v3n/5v3n.pr.out
profile	/app/data/saxs_computation/v3/5v3n/5v3n.dat

Structure of S. cerevisiae Ulp2-Tof2-Csm1 complex

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

Monopolin complex subunit CSM1

State in the Current Structure

Other States of the Same Protein in the Database

Ulp2p,Topoisomerase 1-associated factor 2 chimera

State in the Current Structure

Other States of the Same Protein in the Database

Ulp2p,Topoisomerase 1-associated factor 2 chimera

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)