9y4g

Structure of tuco-tuco ribosome (rotated, tRNAs, and mRNA)

Method: ELECTRON MICROSCOPY Dmax: 237.8 Å Quality: EXCELLENT

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

No usable UniProt protein identity is available for this entry.

七张关系表仍保留该条目的 assembly 与组成信息,但缺少统一蛋白身份时,不能可靠建立跨 PDB 的同蛋白Chain接。

Assembly Composition of the Current Entry

Assembly Oligomeric State 实体与Construct证据 Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–RNA Heteromer 蛋白 75 / DNA 0 / RNA 8 / 其他Polymer 0 PDB declaration: 83-meric Entity 1:Guanine nucleotide-binding protein subunit beta-2-like 1 × 1 Entity 2:40S ribosomal protein S20 × 1 Entity 3:40S ribosomal protein S10 × 1 Entity 4:40S ribosomal protein S12 × 1 Entity 5:40S ribosomal protein S18 × 1 Entity 6:40S ribosomal protein S29 × 1 Entity 7:40S ribosomal protein S17 × 1 Entity 8:40S ribosomal protein S15 × 1 Entity 9:40S ribosomal protein S19 × 1 Entity 10:40S ribosomal protein S25 × 1 Entity 11:40S ribosomal protein S28 × 1 Entity 12:40S ribosomal protein S3 × 1 Entity 13:40S ribosomal protein S27a × 1 Entity 14:40S ribosomal protein S5 × 1 Entity 15:40S ribosomal protein S16 × 1 Entity 16:18S ribosomal RNA × 1 Entity 17:40S ribosomal protein S14 × 1 Entity 18:40S ribosomal protein S23 × 1 Entity 19:40S ribosomal protein S13 × 1 Entity 20:40S ribosomal protein S11 × 1 Entity 21:40S ribosomal protein S3a × 1 Entity 22:40S ribosomal protein SA × 1 Entity 23:40S ribosomal protein S21 × 1 Entity 24:40S ribosomal protein S24 × 1 Entity 25:40S ribosomal protein S26 × 1 Entity 26:40S ribosomal protein S27 × 1 Entity 27:40S ribosomal protein S30 × 1 Entity 28:40S ribosomal protein S9 × 1 Entity 29:40S ribosomal protein S4, X isoform × 1 Entity 30:40S ribosomal protein S2 × 1 Entity 31:40S ribosomal protein S6 × 1 Entity 32:40S ribosomal protein S7 × 1 Entity 33:40S ribosomal protein S15a × 1 Entity 34:40S ribosomal protein S8 × 1 Entity 35:60S ribosomal protein L19 × 1 Entity 36:60S ribosomal protein L24 × 1 Entity 37:60S ribosomal protein L10a × 1 Entity 38:60S ribosomal protein L13a × 1 Entity 39:60S ribosomal protein L13 × 1 Entity 40:60S ribosomal protein L23 × 1 Entity 41:60S ribosomal protein L14 × 1 Entity 42:60S ribosomal protein L27a × 1 Entity 43:60S ribosomal protein L15 × 1 Entity 44:60S ribosomal protein L10-like × 1 Entity 45:60S ribosomal protein L5 × 1 Entity 46:60S ribosomal protein L18 × 1 Entity 47:60S ribosomal protein L8 × 1 Entity 48:60S ribosomal protein L18a × 1 Entity 49:60S ribosomal protein L21 × 1 Entity 50:60S ribosomal protein L17 × 1 Entity 51:60S ribosomal protein L22 × 1 Entity 52:60S ribosomal protein L23a × 1 Entity 53:60S ribosomal protein L26 × 1 Entity 54:60S ribosomal protein L27 × 1 Entity 55:60S ribosomal protein L28 × 1 Entity 56:60S ribosomal protein L35 × 1 Entity 57:60S ribosomal protein L29 × 1 Entity 58:60S ribosomal protein L3 × 1 Entity 59:60S ribosomal protein L7 × 1 Entity 60:60S ribosomal protein L31 × 1 Entity 61:60S ribosomal protein L32 × 1 Entity 62:60S ribosomal protein L35a × 1 Entity 63:60S ribosomal protein L34 × 1 Entity 64:60S ribosomal protein L36 × 1 Entity 65:60S ribosomal protein L37 × 1 Entity 66:60S ribosomal protein L38 × 1 Entity 67:60S ribosomal protein L39 × 1 Entity 68:60S ribosomal protein L4 × 1 Entity 69:60S ribosomal protein L40 × 1 Entity 70:60S ribosomal protein L41 × 1 Entity 71:60S ribosomal protein L37a × 1 Entity 72:60S ribosomal protein L36a × 1 Entity 73:60S ribosomal protein L11 × 1 Entity 74:60S ribosomal protein L9 × 1 Entity 75:60S ribosomal protein L6 × 1 Entity 76:60S ribosomal protein L7a × 1 Entity 77:LSU-alpha rRNA × 1 Entity 78:5S ribosomal RNA × 1 Entity 79:5.8S rRNA (157-MER) × 1 Entity 80:tRNA (78-MER) × 1 Entity 81:tRNA (77-MER) × 1 Entity 82:;RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U*(MG))-3') ; × 1 Entity 83:LSU-beta rRNA (2108-MER) × 1 缺少 UniProt 身份时不显示参考序列区间 Non-standard monomer:Yes (specific site not provided by mmCIF) MG MAGNESIUM ION × 3 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5cryo-EM vitrification conditions:Cryogen ETHANE-PROPANE Resolution 3.30 Å

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 9y4g

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9y4g
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9y4g
Deposition date deposition_date2025-09-03
Structure title titleStructure of tuco-tuco ribosome (rotated, tRNAs, and mRNA)
Keywords keywordsTuco tuco Ribosome, RIBOSOME; RIBOSOME
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier93.15
Radius of gyration Rg (electron density) rg_electron94.19
Forward intensity I(0) i0304147000000.00
Molecular weight molecular_weight3242200.0 kDa
Excluded volume excluded_volume3452700 ų
Envelope volume envelope_volume5740900 ų
Hydration-shell volume shell_volume456480 ų
Envelope diameter envelope_diameter310.2
Shell Rg shell_rg111.80
Envelope Rg envelope_rg93.99
Shape Rg shape_rg94.21
Total Rg total_rg94.18
Total atoms total_atoms219311
Residues n_residues17468
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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 dmax237.8
Rg (real space) rg_real90.51
Rg uncertainty (real space) rg_real_error0.36
I(0) (real space) i0_real2.9140e+11
I(0) uncertainty (real space) i0_real_error4.9230e+09
Rg (reciprocal space) rg_reciprocal94.84
I(0) (reciprocal space) i0_reciprocal305800000000.0000
Solution quality estimate total_estimate0.9129
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary111.9
Skewness Skewness skewness0.114
Kurtosis Kurtosis kurtosis-0.604
Angular range angular_range— – 0.0850 −1
Current regularization parameter α current_alpha0.7170
Highest regularization parameter α highest_alpha21360000000.0000
Real-space data points n_real_points18
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.997; Stabil: 0.969; Sysdev: 1.000; Positv: 1.000; Valcen: 0.976; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (85)

8. Citations (1)

9. Files and Curves (10)