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4zoz

Crystal structure of the Chaetomium thermophilum Sqt1 bound to the N-terminus of the ribosomal protein L10

Method: X-RAY DIFFRACTION Dmax: 104.0 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Sqt1

Chaetomium thermophilum

UniProt G0S0R0

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 54–533 Fragment：UNP residues 54-533 60S ribosomal protein L10-like protein × 1 （G0SEI1） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M sodium chloride, 0.1 M Na/K-phosphate pH 6.2, 40% PEG400 Resolution 1.70 Å R-free 0.216
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 54–533 Fragment：UNP residues 54-533 60S ribosomal protein L10-like protein × 1 （G0SEI1） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M sodium chloride, 0.1 M Na/K-phosphate pH 6.2, 40% PEG400 Resolution 1.70 Å R-free 0.216

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 4ZOZ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4ZN4 Crystal structure of Sqt1 from Chaetomium thermophilum solved by MR Deposited 2015-05-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–533（533 aa）
Not recorded GOL GLYCEROL × 2 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；1.6M (NH4)2SO4 and 100 mM MES pH 6
Resolution 1.94 Å R-free 0.205
4ZN4 Crystal structure of Sqt1 from Chaetomium thermophilum solved by MR Deposited 2015-05-04 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–533（533 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；1.6M (NH4)2SO4 and 100 mM MES pH 6
Resolution 1.94 Å R-free 0.205
4ZOY Crystal structure of the Chaetomium thermophilum Sqt1 Deposited 2015-05-07 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 52–533（482 aa） Fragment：UNP residues 52-533
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M Tris pH 8.5, 20% (v/v) EtOH
Resolution 1.50 Å R-free 0.202

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

View Construct and Data Evidence
UniProt name G0S0R0_CHATD
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–480； UniProt 54–533 Author chain B； PDBConstruct 1–480； UniProt 54–533

60S ribosomal protein L10-like protein

Chaetomium thermophilum

UniProt G0SEI1

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 Y； UniProt 1–20 Not recorded Sqt1 × 1 （G0S0R0） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M sodium chloride, 0.1 M Na/K-phosphate pH 6.2, 40% PEG400 Resolution 1.70 Å R-free 0.216
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain C； UniProt 1–20 Not recorded Sqt1 × 1 （G0S0R0） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M sodium chloride, 0.1 M Na/K-phosphate pH 6.2, 40% PEG400 Resolution 1.70 Å R-free 0.216

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 4ZOZ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7OLC Thermophilic eukaryotic 80S ribosome at idle POST state Deposited 2021-05-19 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 84-meric
Chain LI 1–219（219 aa）
Not recorded MG MAGNESIUM ION × 571 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
7OLD Thermophilic eukaryotic 80S ribosome at pe/E (TI)-POST state Deposited 2021-05-19 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 85-meric
Chain LI 1–219（219 aa）
Not recorded MG MAGNESIUM ION × 3 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7Z3N Cryo-EM structure of the ribosome-associated RAC complex on the 80S ribosome - RAC-1 conformation Deposited 2022-03-02 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 82 PDB declaration: 86-meric
Chain LI 1–219（219 aa）
Not recorded MG MAGNESIUM ION × 455 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7Z3O Cryo-EM structure of the ribosome-associated RAC complex on the 80S ribosome - RAC-2 conformation Deposited 2022-03-02 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 82 PDB declaration: 86-meric
Chain LI 1–219（219 aa）
Not recorded MG MAGNESIUM ION × 472 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8OO0 Chaetomium thermophilum Methionine Aminopeptidase 2 autoproteolysis product at the 80S ribosome Deposited 2023-04-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 85-meric
Chain LI 1–219（219 aa）
Not recorded ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9I1W High resolution structure of the thermophilic 60S ribosomal subunit of Chaetomium thermophilum Deposited 2025-01-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 51-meric
Chain LI 1–219（219 aa）
Not recorded SPD SPERMIDINE × 2 SPM SPERMINE × 2 MG MAGNESIUM ION × 239 K POTASSIUM ION × 188 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.38 Å
9I78 Cryo-EM structure of Chaetomium thermophilum ribosome-bound SND3 translocon Deposited 2025-01-31 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 50-meric
Chain LI 1–219（219 aa）
Not recorded MG MAGNESIUM ION × 379 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；waiting time: 15 s blot force: 0
Resolution 2.20 Å

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

View Construct and Data Evidence
UniProt name G0SEI1_CHATD
Isoform —
PDB entities 2
Chains and sequence ranges Author chain C； PDBConstruct 1–20； UniProt 1–20 Author chain Y； PDBConstruct 1–20； UniProt 1–20

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 4zoz

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4zoz
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4zoz
Deposition date deposition_date2015-05-07
Structure title titleCrystal structure of the Chaetomium thermophilum Sqt1 bound to the N-terminus of the ribosomal protein L10
Keywords keywordsChaperone, ribosomal biogenesis, WD40 - repeat; CHAPERONE
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_guinier31.99 Å
Radius of gyration Rg (electron density) rg_electron31.29 Å
Forward intensity I(0) i0117758000.00
Molecular weight molecular_weight85382.0 kDa
Excluded volume excluded_volume106320 ų
Envelope volume envelope_volume130030 ų
Hydration-shell volume shell_volume35573 ų
Envelope diameter envelope_diameter104.5 Å
Shell Rg shell_rg37.40 Å
Envelope Rg envelope_rg31.15 Å
Shape Rg shape_rg31.29 Å
Total Rg total_rg31.78 Å
Total atoms total_atoms6026
Residues n_residues812
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 dmax104.0 Å
Rg (real space) rg_real32.16 Å
Rg uncertainty (real space) rg_real_error0.77 Å
I(0) (real space) i0_real1.1780e+08
I(0) uncertainty (real space) i0_real_error1.7540e+06
Rg (reciprocal space) rg_reciprocal32.09 Å
I(0) (reciprocal space) i0_reciprocal117800000.0000
Solution quality estimate total_estimate0.8650
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary31.2 Å
Skewness Skewness skewness0.418
Kurtosis Kurtosis kurtosis-0.577
Angular range angular_range— – 0.2500 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha23340000.0000
Real-space data points n_real_points51
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.815; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.942; Smooth: 0.852
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id4zozA00
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily10 — YVTN repeat-like/Quinoprotein amine dehydrogenase
Domain ID domain_id4zozB00
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily10 — YVTN repeat-like/Quinoprotein amine dehydrogenase
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8. Citations (1)

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9. Files and Curves (10)