SAXSdb — 6dei

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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	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 69–181 Chain B； UniProt 69–181	Not recorded	Protein DSE3 × 2 （Q08729） 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

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 6DEI	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 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 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 ligand/ion 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 oligomeric state Different ligand/ion 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 mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 69–190（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
5V3N Structure of S. cerevisiae Ulp2-Tof2-Csm1 complex Deposited 2017-03-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion 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

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 Author chain B； PDBConstruct 1–113； UniProt 69–181

Protein DSE3

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt Q08729

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 C； UniProt 60–80 Chain D； UniProt 60–80	Not recorded	Monopolin complex subunit CSM1 × 2 （P25651） 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

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	DSE3_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 4–24； UniProt 60–80 Author chain D； PDBConstruct 4–24； UniProt 60–80

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	6dei
Deposition date deposition_date	2018-05-12
Structure title title	Structure of Dse3-Csm1 complex
Keywords keywords	monopolin, daughter cell-specific protein, Protein Binding-Cell Cycle complex; Protein Binding/Cell Cycle
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	20.44 Å
Radius of gyration Rg (electron density) rg_electron	19.31 Å
Forward intensity I(0) i0	14251700.00
Molecular weight molecular_weight	29413.0 kDa
Excluded volume excluded_volume	37317 Å³
Envelope volume envelope_volume	44717 Å³
Hydration-shell volume shell_volume	19540 Å³
Envelope diameter envelope_diameter	79.0 Å
Shell Rg shell_rg	25.50 Å
Envelope Rg envelope_rg	20.10 Å
Shape Rg shape_rg	19.33 Å
Total Rg total_rg	20.24 Å
Total atoms total_atoms	4124
Residues n_residues	253
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	75.2 Å
Rg (real space) rg_real	20.43 Å
Rg uncertainty (real space) rg_real_error	0.70 Å
I(0) (real space) i0_real	1.4250e+07
I(0) uncertainty (real space) i0_real_error	1.9360e+05
Rg (reciprocal space) rg_reciprocal	20.43 Å
I(0) (reciprocal space) i0_reciprocal	14250000.0000
Solution quality estimate total_estimate	0.7482
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	23.6 Å
Skewness Skewness skewness	0.438
Kurtosis Kurtosis kurtosis	0.142
Angular range angular_range	— – 0.3900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3981000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.588; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.958; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4368

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	Protein DSE3
Molecular weight formula_weight	2705.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

SNAFGGTLKLKKRLESVPELFLHD

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 non-polymer

Description description	TRIETHYLENE GLYCOL
Molecular weight formula_weight	150.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	232

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	6deiA00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily	80 —

Domain ID domain_id	6deiB00
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	41.442 Å
Unit-cell length b length_b	51.235 Å
Unit-cell length c length_c	117.848 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 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.699 Å
Low-resolution limit resolution_low	39.095 Å
R factor r_factor	0.1911
R_work r_work	0.1887
R_free r_free	0.2214

fit	/app/data/saxs_computation/de/6dei/6dei.fit
pddf	/app/data/pr_computation/de/6dei/6dei.pr.out
profile	/app/data/saxs_computation/de/6dei/6dei.dat

Structure of Dse3-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

Protein DSE3

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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)