← Back to search
5wyl

Crystal structure of Chaetomium thermophilum Utp10 N-terminal domain in complex with Utp17 C-terminal helices

Method: X-RAY DIFFRACTION Dmax: 101.2 Å Quality: EXCELLENT
▼

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

Putative uncharacterized protein

Chaetomium thermophilum var. thermophilum DSM 1495

UniProt G0S5L1

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 1–471 Fragment：N-terminal domain, UNP residues 1-471 Putative uncharacterized protein × 1 （G0SCS8） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M Hepes-Na, 20% w/v PEG 8000 Resolution 2.64 Å R-free 0.267
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain C； UniProt 1–471 Fragment：N-terminal domain, UNP residues 1-471 Putative uncharacterized protein × 1 （G0SCS8） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M Hepes-Na, 20% w/v PEG 8000 Resolution 2.64 Å R-free 0.267

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 5WYL 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 experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 56-meric
Chain G 1–1802（1802 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 G 1–1802（1802 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
5WY3 Crystal structure of Chaetomium thermophilum Utp10 middle domain Deposited 2017-01-10 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 472–872（401 aa） Fragment：UNP residues 472-872
Chain B 472–872（401 aa） Fragment：UNP residues 472-872
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Hepes-Na, 2.0 M ammonium sulfate
Resolution 3.20 Å R-free 0.266
5WY4 Crystal structure of Chaetomium thermophilum Utp10 N-terminal domain Deposited 2017-01-10 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–471（471 aa） Fragment：N-terminal domain, UNP residues 1-471
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；0.1 M sodium citrate, 1.0 M ammonium dihydrogen phosphate
Resolution 2.50 Å R-free 0.264
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 UJ 1–1802（1802 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 UJ 1–1802（1802 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 UJ 1–1802（1802 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 UJ 1–1802（1802 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 UJ 1–1802（1802 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 UJ 1–1802（1802 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

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

View Construct and Data Evidence
UniProt name G0S5L1_CHATD
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–471； UniProt 1–471 Author chain C； PDBConstruct 1–471； UniProt 1–471

Putative uncharacterized protein

Chaetomium thermophilum var. thermophilum DSM 1495

UniProt G0SCS8

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 907–960 Fragment：C-terminal domain, UNP residues 907-960 Putative uncharacterized protein × 1 （G0S5L1） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M Hepes-Na, 20% w/v PEG 8000 Resolution 2.64 Å R-free 0.267
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain D； UniProt 907–960 Fragment：C-terminal domain, UNP residues 907-960 Putative uncharacterized protein × 1 （G0S5L1） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M Hepes-Na, 20% w/v PEG 8000 Resolution 2.64 Å R-free 0.267

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 5WYL 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 M 1–960（960 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 UQ 1–960（960 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 UQ 1–960（960 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 UQ 1–960（960 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 UQ 1–960（960 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 UQ 1–960（960 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 UQ 1–960（960 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 G0SCS8_CHATD
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–54； UniProt 907–960 Author chain D； PDBConstruct 1–54； UniProt 907–960

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.

SAXS scattering curve SAXS Profile

SAXS profile for 5wyl

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5wyl
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id5wyl
Deposition date deposition_date2017-01-13
Structure title titleCrystal structure of Chaetomium thermophilum Utp10 N-terminal domain in complex with Utp17 C-terminal helices
Keywords keywordsnucleolar protein, protein complex, components of 90S preribosome, RIBOSOMAL PROTEIN-NUCLEAR PROTEIN complex; RIBOSOMAL PROTEIN/NUCLEAR PROTEIN
Experimental Method methodX-RAY DIFFRACTION
▼

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

Radius of gyration Rg (Guinier) rg_guinier33.99 Å
Radius of gyration Rg (electron density) rg_electron33.04 Å
Forward intensity I(0) i0144835000.00
Molecular weight molecular_weight99849.0 kDa
Excluded volume excluded_volume126780 ų
Envelope volume envelope_volume162770 ų
Hydration-shell volume shell_volume40880 ų
Envelope diameter envelope_diameter108.1 Å
Shell Rg shell_rg39.87 Å
Envelope Rg envelope_rg32.67 Å
Shape Rg shape_rg33.07 Å
Total Rg total_rg33.52 Å
Total atoms total_atoms7031
Residues n_residues909
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
▼

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

Maximum dimension Dmax dmax101.2 Å
Rg (real space) rg_real33.86 Å
Rg uncertainty (real space) rg_real_error0.74 Å
I(0) (real space) i0_real1.4480e+08
I(0) uncertainty (real space) i0_real_error2.1570e+06
Rg (reciprocal space) rg_reciprocal33.94 Å
I(0) (reciprocal space) i0_reciprocal144800000.0000
Solution quality estimate total_estimate0.9056
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary47.4 Å
Skewness Skewness skewness0.102
Kurtosis Kurtosis kurtosis-0.653
Angular range angular_range— – 0.2350 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha45850000.0000
Real-space data points n_real_points48
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.979; Stabil: 0.996; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.844
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

▶

8. Citations (1)

▶

9. Files and Curves (10)