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6emg

Crystal structure of Rrp1 from Chaetomium thermophilum in space group P6322

Method: X-RAY DIFFRACTION Dmax: 87.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

G0S4M2

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

UniProt G0S4M2

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–282 Not recorded PO4 PHOSPHATE ION × 2 EDO 1,2-ETHANEDIOL × 7 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；0.8M K-H2PO4 0.8M Na-H2PO4 Resolution 2.24 Å R-free 0.207
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 1–282 Not recorded PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；0.8M K-H2PO4 0.8M Na-H2PO4 Resolution 2.24 Å R-free 0.207

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 6EMG Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6EMF Crystal structure of Rrp1 from Chaetomium thermophilum in space group C2 Deposited 2017-10-02 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–282（282 aa）
Not recorded EDO 1,2-ETHANEDIOL × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；200 mM Proline 100 mM HEPES pH 7.5 10% PEG3350
Resolution 2.65 Å R-free 0.232
6EMF Crystal structure of Rrp1 from Chaetomium thermophilum in space group C2 Deposited 2017-10-02 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–282（282 aa）
Not recorded EDO 1,2-ETHANEDIOL × 2 PRO PROLINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；200 mM Proline 100 mM HEPES pH 7.5 10% PEG3350
Resolution 2.65 Å R-free 0.232
8I9P Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - State Mak16 Deposited 2023-02-07 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 31 PDB declaration: 33-meric
Chain Cc 1–282（282 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8I9R Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - State 5S RNP Deposited 2023-02-07 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain Cc 1–282（282 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8I9T Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - State Dbp10-1 Deposited 2023-02-07 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 55-meric
Chain Cc 1–282（282 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8I9V Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - State Dbp10-2 Deposited 2023-02-07 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: 56-meric
Chain Cc 1–282（282 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å

5 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name G0S4M2_CHATD
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–282； UniProt 1–282 Author chain B； PDBConstruct 1–282； UniProt 1–282

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 6emg

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6emg
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6emg
Deposition date deposition_date2017-10-02
Structure title titleCrystal structure of Rrp1 from Chaetomium thermophilum in space group P6322
Keywords keywordsRibosome biogenesis, RIBOSOME, translation; RIBOSOME
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier26.19 Å
Radius of gyration Rg (electron density) rg_electron25.38 Å
Forward intensity I(0) i047268900.00
Molecular weight molecular_weight53567.0 kDa
Excluded volume excluded_volume67291 ų
Envelope volume envelope_volume82789 ų
Hydration-shell volume shell_volume27801 ų
Envelope diameter envelope_diameter92.3 Å
Shell Rg shell_rg32.12 Å
Envelope Rg envelope_rg25.62 Å
Shape Rg shape_rg25.36 Å
Total Rg total_rg26.21 Å
Total atoms total_atoms3757
Residues n_residues458
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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax87.8 Å
Rg (real space) rg_real26.25 Å
Rg uncertainty (real space) rg_real_error0.82 Å
I(0) (real space) i0_real4.7270e+07
I(0) uncertainty (real space) i0_real_error7.1350e+05
Rg (reciprocal space) rg_reciprocal26.23 Å
I(0) (reciprocal space) i0_reciprocal47270000.0000
Solution quality estimate total_estimate0.8715
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.8 Å
Skewness Skewness skewness0.453
Kurtosis Kurtosis kurtosis-0.248
Angular range angular_range— – 0.3050 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha11520000.0000
Real-space data points n_real_points62
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.798; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.972; Smooth: 0.965
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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8. Citations (1)

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9. Files and Curves (10)