SAXSdb — 3n7n

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

Monopolin complex subunit CSM1

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 heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain A； UniProt 1–190 Chain B； UniProt 1–190 Chain C； UniProt 1–190 Chain D； UniProt 1–190	Not recorded	Monopolin complex subunit LRS4 × 2 （Q04087）	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

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 3N7N	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
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 mutation/modification 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
5V3N Structure of S. cerevisiae Ulp2-Tof2-Csm1 complex Deposited 2017-03-07	Different construct Different mutation/modification 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 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 1–190； UniProt 1–190 Author chain B； PDBConstruct 1–190； UniProt 1–190 Author chain C； PDBConstruct 1–190； UniProt 1–190 Author chain D； PDBConstruct 1–190； UniProt 1–190

Monopolin complex subunit LRS4

Saccharomyces cerevisiae

UniProt Q04087

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 × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain E； UniProt 1–102 Chain F； UniProt 1–102	Fragment：UNP Residues 1-102, delta 38-44	Monopolin complex subunit CSM1 × 4 （P25651）	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

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	LRS4_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 1–95； UniProt 1–102 Author chain F； PDBConstruct 1–95； UniProt 1–102

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	3n7n
Deposition date deposition_date	2010-05-27
Structure title title	Structure of Csm1/Lrs4 complex
Keywords keywords	meiosis, rDNA, REPLICATION; REPLICATION
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	50.00 Å
Radius of gyration Rg (electron density) rg_electron	49.98 Å
Forward intensity I(0) i0	86137900.00
Molecular weight molecular_weight	77827.0 kDa
Excluded volume excluded_volume	98120 Å³
Envelope volume envelope_volume	178320 Å³
Hydration-shell volume shell_volume	32092 Å³
Envelope diameter envelope_diameter	149.7 Å
Shell Rg shell_rg	50.67 Å
Envelope Rg envelope_rg	46.23 Å
Shape Rg shape_rg	50.03 Å
Total Rg total_rg	49.83 Å
Total atoms total_atoms	5496
Residues n_residues	704
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	137.0 Å
Rg (real space) rg_real	49.90 Å
Rg uncertainty (real space) rg_real_error	1.52 Å
I(0) (real space) i0_real	8.6140e+07
I(0) uncertainty (real space) i0_real_error	1.7890e+06
Rg (reciprocal space) rg_reciprocal	50.00 Å
I(0) (reciprocal space) i0_reciprocal	86150000.0000
Solution quality estimate total_estimate	0.6995
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	84.0 Å
Skewness Skewness skewness	-0.123
Kurtosis Kurtosis kurtosis	-1.040
Angular range angular_range	— – 0.1550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4521000.0000
Real-space data points n_real_points	32
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.422; Stabil: 0.995; Sysdev: 1.000; Positv: 1.000; Valcen: 0.837; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Monopolin complex subunit CSM1
Molecular weight formula_weight	21776.4 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	5496

MDPLTVYKNSVKQQIDSADLLVANLVNENFVLSEKLDTKATEIKQLQKQIDSLNAQVKELKTQTSQQAENSEVIKDLYEYLCNVRVHKSYEDDSGLWFDISQGTHSGGSSDDYSIMDYKLGFVKGQAQVTEVIYAPVLKQRSTEELYSLQSKLPEYLFETLSFPLSSLNQFYNKIAKSLNKKREKKDETE

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;brewer's yeast,lager beer yeast,yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Monopolin complex subunit LRS4
Molecular weight formula_weight	11240.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F

MTTLLQLLSNYYKAKLDSERIYNEYVQSQYEFASLDKPKKVVDETLFLQRQIAQLNKQLQLSFQENEKLLSVQKNQKALYQSKLSSKDAFIDDLK

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;brewer's yeast,lager beer yeast,yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

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7. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	3n7nA01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	340 —

Domain ID domain_id	3n7nA02
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	3n7nB01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	340 —

Domain ID domain_id	3n7nB02
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	3n7nC01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	340 —

Domain ID domain_id	3n7nC02
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	3n7nD01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	340 —

Domain ID domain_id	3n7nD02
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	152.624 Å
Unit-cell length b length_b	152.624 Å
Unit-cell length c length_c	118.794 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	P 3 2 1
Space-group number int_tables_number	150
Crystal system crystal_system	—

Resolution resolution	3.900 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	—
R_work r_work	0.3330
R_free r_free	0.3550

fit	/app/data/saxs_computation/n7/3n7n/3n7n.fit
pddf	/app/data/pr_computation/n7/3n7n/3n7n.pr.out
profile	/app/data/saxs_computation/n7/3n7n/3n7n.dat

Structure of Csm1/Lrs4 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

Monopolin complex subunit LRS4

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 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)