SAXSdb — 5o9e

▼

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

Putative U3 small nucleolar ribonucleoprotein

Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 75–274	Not recorded	Putative U3 small nucleolar ribonucleoprotein protein × 1 （G0S9I7） EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291 K；20-30 % Ethylene glycol	Resolution 1.88 Å R-free 0.219

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 5O9E	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5JPQ Cryo-EM structure of the 90S pre-ribosome Deposited 2016-05-04	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 56-meric	Chain c 1–297（297 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.30 Å
5OQL Cryo-EM structure of the 90S pre-ribosome from Chaetomium thermophilum Deposited 2017-08-12	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 55-meric	Chain b 1–297（297 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
6RXT Cryo-EM structure of the 90S pre-ribosome (Kre33-Noc4) from Chaetomium thermophilum, state A Deposited 2019-06-10	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 57-meric	Chain CK 1–297（297 aa）	Not recorded	ZN ZINC ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.00 Å
6RXU Cryo-EM structure of the 90S pre-ribosome (Kre33-Noc4) from Chaetomium thermophilum, state B1 Deposited 2019-06-10	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 64 PDB declaration: 66-meric	Chain CK 1–297（297 aa）	Not recorded	ZN ZINC ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
6RXV Cryo-EM structure of the 90S pre-ribosome (Kre33-Noc4) from Chaetomium thermophilum, state B2 Deposited 2019-06-10	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 66 PDB declaration: 68-meric	Chain CK 1–297（297 aa）	Not recorded	ZN ZINC ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
6RXX Cryo-EM structure of the 90S pre-ribosome (Kre33-Noc4) from Chaetomium thermophilum, state C, Poly-Ala Deposited 2019-06-10	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 66 PDB declaration: 68-meric	Chain CK 1–297（297 aa）	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.10 Å
6RXY Cryo-EM structure of the 90S pre-ribosome (Kre33-Noc4) from Chaetomium thermophilum, state a Deposited 2019-06-10	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 57 PDB declaration: 59-meric	Chain CK 1–297（297 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.70 Å
6RXZ Cryo-EM structure of the 90S pre-ribosome (Kre33-Noc4) from Chaetomium thermophilum, state b Deposited 2019-06-10	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 66 PDB declaration: 68-meric	Chain CK 1–297（297 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.40 Å

8 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	G0SE90_CHATD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–201； UniProt 75–274

Putative U3 small nucleolar ribonucleoprotein protein

Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)

UniProt G0S9I7

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 433–562	Not recorded	Putative U3 small nucleolar ribonucleoprotein × 1 （G0SE90） EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291 K；20-30 % Ethylene glycol	Resolution 1.88 Å R-free 0.219

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 5O9E	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5OQL Cryo-EM structure of the 90S pre-ribosome from Chaetomium thermophilum Deposited 2017-08-12	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 55-meric	Chain c 1–785（785 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
6RXT Cryo-EM structure of the 90S pre-ribosome (Kre33-Noc4) from Chaetomium thermophilum, state A Deposited 2019-06-10	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 57-meric	Chain CL 1–785（785 aa）	Not recorded	ZN ZINC ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.00 Å
6RXU Cryo-EM structure of the 90S pre-ribosome (Kre33-Noc4) from Chaetomium thermophilum, state B1 Deposited 2019-06-10	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 64 PDB declaration: 66-meric	Chain CL 1–785（785 aa）	Not recorded	ZN ZINC ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
6RXV Cryo-EM structure of the 90S pre-ribosome (Kre33-Noc4) from Chaetomium thermophilum, state B2 Deposited 2019-06-10	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 66 PDB declaration: 68-meric	Chain CL 1–785（785 aa）	Not recorded	ZN ZINC ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
6RXX Cryo-EM structure of the 90S pre-ribosome (Kre33-Noc4) from Chaetomium thermophilum, state C, Poly-Ala Deposited 2019-06-10	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 66 PDB declaration: 68-meric	Chain CL 1–785（785 aa）	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.10 Å
6RXY Cryo-EM structure of the 90S pre-ribosome (Kre33-Noc4) from Chaetomium thermophilum, state a Deposited 2019-06-10	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 57 PDB declaration: 59-meric	Chain CL 1–785（785 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.70 Å
6RXZ Cryo-EM structure of the 90S pre-ribosome (Kre33-Noc4) from Chaetomium thermophilum, state b Deposited 2019-06-10	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 66 PDB declaration: 68-meric	Chain CL 1–785（785 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.40 Å

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

View Construct and Data Evidence

UniProt name	G0S9I7_CHATD
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 2–131； UniProt 433–562

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	5o9e
Deposition date deposition_date	2017-06-19
Structure title title	Crystal structure of the Imp4-Mpp10 complex from Chaetomium thermophilum
Keywords keywords	Ribosome biogenesis, RIBOSOME, BRIX; RIBOSOME
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	21.58 Å
Radius of gyration Rg (electron density) rg_electron	20.54 Å
Forward intensity I(0) i0	18024500.00
Molecular weight molecular_weight	31961.0 kDa
Excluded volume excluded_volume	40098 Å³
Envelope volume envelope_volume	48719 Å³
Hydration-shell volume shell_volume	20630 Å³
Envelope diameter envelope_diameter	89.4 Å
Shell Rg shell_rg	26.16 Å
Envelope Rg envelope_rg	21.32 Å
Shape Rg shape_rg	20.52 Å
Total Rg total_rg	21.39 Å
Total atoms total_atoms	2248
Residues n_residues	281
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

▼

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

Maximum dimension Dmax dmax	87.2 Å
Rg (real space) rg_real	21.70 Å
Rg uncertainty (real space) rg_real_error	0.86 Å
I(0) (real space) i0_real	1.8020e+07
I(0) uncertainty (real space) i0_real_error	2.5960e+05
Rg (reciprocal space) rg_reciprocal	21.67 Å
I(0) (reciprocal space) i0_reciprocal	18020000.0000
Solution quality estimate total_estimate	0.5838
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.9 Å
Skewness Skewness skewness	0.689
Kurtosis Kurtosis kurtosis	0.918
Angular range angular_range	— – 0.3700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3633000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.336; Stabil: 1.000; Sysdev: 0.281; Positv: 1.000; Valcen: 0.733; Smooth: 0.998

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Putative U3 small nucleolar ribonucleoprotein
Molecular weight formula_weight	22800.3 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	2392

MDEYSELSGIVDPRVLVTTSRDPSSRLMAFSKEIRLMFPTAIRLNRGNLILPDLVMSAQRERLSDIILLHEHRGTPTAITISHFPHGPTLMASLHNVVLRADIPKSIKGTVSESYPHLIFEGFRTPLGQRVVKILKHLFPPRDPTNNAKSGNRVITFVNQDDCIEVRHHVYVRTNYNSVELSEVGPRFTMRPFSITMGTLE

来源 Source

来源生物 organism	Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
NCBI Class编号 ncbi_taxonomy_id	759272
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Putative U3 small nucleolar ribonucleoprotein protein
Molecular weight formula_weight	14787.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MDADVERAEQDVRRDLFDDLSEHEDSEDALSDASAGDPKSRKSAHERRQAKIAEQIRKLEAELVAKRAWTLAGEATAADRPVNSLLGEDMEFDHVGKPVPVVTEEVSESIEELIKRRILAGEFDEVLRRRP

来源 Source

来源生物 organism	Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
NCBI Class编号 ncbi_taxonomy_id	759272
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	136

▶

8. Citations (1)

▶

Unit-cell length a length_a	112.890 Å
Unit-cell length b length_b	112.890 Å
Unit-cell length c length_c	44.000 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	6

Space group space_group	P 64
Space-group number int_tables_number	172
Crystal system crystal_system	—

Resolution resolution	1.884 Å
Low-resolution limit resolution_low	48.883 Å
R factor r_factor	0.1853
R_work r_work	0.1836
R_free r_free	0.2192

fit	/app/data/saxs_computation/o9/5o9e/5o9e.fit
pddf	/app/data/pr_computation/o9/5o9e/5o9e.pr.out
profile	/app/data/saxs_computation/o9/5o9e/5o9e.dat

Crystal structure of the Imp4-Mpp10 complex from Chaetomium thermophilum

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

Putative U3 small nucleolar ribonucleoprotein

State in the Current Structure

Other States of the Same Protein in the Database

Putative U3 small nucleolar ribonucleoprotein protein

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 (4)

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 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)