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8ptw

Chaetomium thermophilum Rix1-complex

Method: ELECTRON MICROSCOPY Dmax: 113.2 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Pre-rRNA-processing protein IPI3

OrganismNot specified

UniProt G0S1T5

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 CT； UniProt 1–437 Chain CU； UniProt 1–437 Not recorded Pre-rRNA-processing protein RIX1 × 2 （G0S5R0） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 2.91 Å

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 8PTW Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
8PV4 Chaetomium thermophilum pre-60S State 2 - pre-5S rotation with Rix1 complex - composite structure Deposited 2023-07-17 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 62 PDB declaration: 66-meric
Chain CT 1–437（437 aa）
Chain CU 1–437（437 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
8PV6 Chaetomium thermophilum pre-60S State 3 - post-5S rotation with Rix1 complex with Foot - composite structure Deposited 2023-07-17 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 60 PDB declaration: 64-meric
Chain CT 1–437（437 aa）
Chain CU 1–437（437 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.94 Å
8PV8 Chaetomium thermophilum pre-60S State 4 - post-5S rotation with Rix1 complex without Foot - composite structure Deposited 2023-07-17 Different oligomeric state Different ligand/ion Assembly 1 Protein–RNA Heteromer；Protein × 57 PDB declaration: 60-meric
Chain CT 1–437（437 aa）
Chain CU 1–437（437 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.91 Å

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name G0S1T5_CHATD
Isoform —
PDB entities 1
Chains and sequence ranges Author chain CT； PDBConstruct 1–437； UniProt 1–437 Author chain CU； PDBConstruct 1–437； UniProt 1–437

Pre-rRNA-processing protein RIX1

OrganismNot specified

UniProt G0S5R0

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 CV； UniProt 1–781 Chain CW； UniProt 1–781 Not recorded Pre-rRNA-processing protein IPI3 × 2 （G0S1T5） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 2.91 Å

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 8PTW Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
8PV4 Chaetomium thermophilum pre-60S State 2 - pre-5S rotation with Rix1 complex - composite structure Deposited 2023-07-17 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 62 PDB declaration: 66-meric
Chain CV 1–781（781 aa）
Chain CW 1–781（781 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
8PV6 Chaetomium thermophilum pre-60S State 3 - post-5S rotation with Rix1 complex with Foot - composite structure Deposited 2023-07-17 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 60 PDB declaration: 64-meric
Chain CV 1–781（781 aa）
Chain CW 1–781（781 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.94 Å
8PV8 Chaetomium thermophilum pre-60S State 4 - post-5S rotation with Rix1 complex without Foot - composite structure Deposited 2023-07-17 Different oligomeric state Different ligand/ion Assembly 1 Protein–RNA Heteromer；Protein × 57 PDB declaration: 60-meric
Chain CV 1–781（781 aa）
Chain CW 1–781（781 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.91 Å

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name G0S5R0_CHATD
Isoform —
PDB entities 2
Chains and sequence ranges Author chain CV； PDBConstruct 1–781； UniProt 1–781 Author chain CW； PDBConstruct 1–781； UniProt 1–781

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 8ptw

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8ptw
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8ptw
Deposition date deposition_date2023-07-15
Structure title titleChaetomium thermophilum Rix1-complex
Keywords keywordsbiogenesis, pre-60S, 5S RNP, RIBOSOME; RIBOSOME
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier38.84 Å
Radius of gyration Rg (electron density) rg_electron37.63 Å
Forward intensity I(0) i0591649000.00
Molecular weight molecular_weight202400.0 kDa
Excluded volume excluded_volume255150 ų
Envelope volume envelope_volume337630 ų
Hydration-shell volume shell_volume71649 ų
Envelope diameter envelope_diameter119.2 Å
Shell Rg shell_rg46.58 Å
Envelope Rg envelope_rg36.63 Å
Shape Rg shape_rg37.63 Å
Total Rg total_rg38.15 Å
Total atoms total_atoms14242
Residues n_residues1878
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 dmax113.2 Å
Rg (real space) rg_real38.47 Å
Rg uncertainty (real space) rg_real_error0.71 Å
I(0) (real space) i0_real5.9160e+08
I(0) uncertainty (real space) i0_real_error1.0080e+07
Rg (reciprocal space) rg_reciprocal38.70 Å
I(0) (reciprocal space) i0_reciprocal591800000.0000
Solution quality estimate total_estimate0.9061
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary52.5 Å
Skewness Skewness skewness-0.021
Kurtosis Kurtosis kurtosis-0.654
Angular range angular_range— – 0.2050 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha101100000.0000
Real-space data points n_real_points42
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.964; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.971; Smooth: 0.912
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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9. Files and Curves (10)