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4gmo

Crystal structure of Syo1

Method: X-RAY DIFFRACTION Dmax: 98.2 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Putative uncharacterized protein

Chaetomium thermophilum var. thermophilum DSM 1495

UniProt G0S5S6

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 1–676 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 4.7；291 K；0.2 M potassium acetate, 20% (v/v) PEG 3350, pH 4.7, VAPOR DIFFUSION, SITTING DROP, temperature 291K Resolution 2.10 Å R-free 0.256

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 4GMO Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4GMN Structural basis of Rpl5 recognition by Syo1 Deposited 2012-08-16 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–676（676 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；0.1 M succinic acid pH 7.0, 20% (v/v) PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Resolution 2.95 Å R-free 0.259
5AFF Symportin 1 chaperones 5S RNP assembly during ribosome biogenesis by occupying an essential rRNA binding site Deposited 2015-01-21 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 24–676（653 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions 0.1 M SODIUM ACETATE, 8% (V/V) PEG 4000
Resolution 3.40 Å R-free 0.300
7OZS Structure of the hexameric 5S RNP from C. thermophilum Deposited 2021-06-28 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 6 PDB declaration: heptameric
Chain F 1–676（676 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å

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

View Construct and Data Evidence
UniProt name G0S5S6_CHATD
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–676； UniProt 1–676

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 4gmo

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id4gmo
Deposition date deposition_date2012-08-16
Structure title titleCrystal structure of Syo1
Keywords keywordsARM, HEAT, solenoid, nuclear transport, chaperone, Rpl5, Rpl11, Kap104, nucleus; 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_guinier29.72 Å
Radius of gyration Rg (electron density) rg_electron29.03 Å
Forward intensity I(0) i057306300.00
Molecular weight molecular_weight61393.0 kDa
Excluded volume excluded_volume77700 ų
Envelope volume envelope_volume100540 ų
Hydration-shell volume shell_volume29422 ų
Envelope diameter envelope_diameter101.1 Å
Shell Rg shell_rg35.99 Å
Envelope Rg envelope_rg28.50 Å
Shape Rg shape_rg29.04 Å
Total Rg total_rg29.68 Å
Total atoms total_atoms4327
Residues n_residues556
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 dmax98.2 Å
Rg (real space) rg_real29.76 Å
Rg uncertainty (real space) rg_real_error0.69 Å
I(0) (real space) i0_real5.7310e+07
I(0) uncertainty (real space) i0_real_error8.8430e+05
Rg (reciprocal space) rg_reciprocal29.74 Å
I(0) (reciprocal space) i0_reciprocal57310000.0000
Solution quality estimate total_estimate0.8912
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary31.5 Å
Skewness Skewness skewness0.330
Kurtosis Kurtosis kurtosis-0.478
Angular range angular_range— – 0.2650 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha12010000.0000
Real-space data points n_real_points54
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.911; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.952; Smooth: 0.898
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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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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id4gmoA00
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology10 — Leucine-rich Repeat Variant
Homologous superfamily homologous superfamily10 — Leucine-rich Repeat Variant
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8. Citations (1)

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9. Files and Curves (10)