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1t0k

Joint X-ray and NMR Refinement of Yeast L30e-mRNA complex

Method: X-RAY DIFFRACTION Dmax: 105.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Maltose-binding periplasmic protein

Escherichia coli

UniProt P02928

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–RNA Heteromer Protein × 2 RNA 2 其他Polymer 1 PDB declaration: tetrameric（4） Count mismatch; review required Chain A； UniProt 27–392 Not recorded 5'-R(*GP*AP*CP*CP*GP*GP*AP*GP*UP*GP*UP*CP*C)-3' × 1 5'-R(*G*GP*AP*CP*GP*CP*AP*GP*AP*GP*AP*UP*GP*GP*UP*C)-3' × 1 60S ribosomal protein L30 × 1 （P14120） alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6；295 K；Lithium Sulfate, Sodium Cacodylate, Magnesium Chloride, Jeffamine, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 295K Resolution 3.24 Å R-free 0.320

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 1T0K Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1A7L DOMINANT B-CELL EPITOPE FROM THE PRES2 REGION OF HEPATITIS B VIRUS IN THE FORM OF AN INSERTED PEPTIDE SEGMENT IN MALTODEXTRIN-BINDING PROTEIN Deposited 1998-03-16 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 27–389（363 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；PROTEIN CONCENTRATION 3.0MG/ML, BUFFER 0.1M TRIS-HCL PH 8.5 WITH 0.2 M MGCL2, 1 MM MALTOSE, 26% PEG 4000.
Resolution 2.90 Å R-free 0.286
1A7L DOMINANT B-CELL EPITOPE FROM THE PRES2 REGION OF HEPATITIS B VIRUS IN THE FORM OF AN INSERTED PEPTIDE SEGMENT IN MALTODEXTRIN-BINDING PROTEIN Deposited 1998-03-16 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain B 27–389（363 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；PROTEIN CONCENTRATION 3.0MG/ML, BUFFER 0.1M TRIS-HCL PH 8.5 WITH 0.2 M MGCL2, 1 MM MALTOSE, 26% PEG 4000.
Resolution 2.90 Å R-free 0.286
1A7L DOMINANT B-CELL EPITOPE FROM THE PRES2 REGION OF HEPATITIS B VIRUS IN THE FORM OF AN INSERTED PEPTIDE SEGMENT IN MALTODEXTRIN-BINDING PROTEIN Deposited 1998-03-16 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 3 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain C 27–389（363 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；PROTEIN CONCENTRATION 3.0MG/ML, BUFFER 0.1M TRIS-HCL PH 8.5 WITH 0.2 M MGCL2, 1 MM MALTOSE, 26% PEG 4000.
Resolution 2.90 Å R-free 0.286
1A7L DOMINANT B-CELL EPITOPE FROM THE PRES2 REGION OF HEPATITIS B VIRUS IN THE FORM OF AN INSERTED PEPTIDE SEGMENT IN MALTODEXTRIN-BINDING PROTEIN Deposited 1998-03-16 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 4 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 27–389（363 aa）
Chain B 27–389（363 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；PROTEIN CONCENTRATION 3.0MG/ML, BUFFER 0.1M TRIS-HCL PH 8.5 WITH 0.2 M MGCL2, 1 MM MALTOSE, 26% PEG 4000.
Resolution 2.90 Å R-free 0.286
1ANF MALTODEXTRIN BINDING PROTEIN WITH BOUND MALTOSE Deposited 1997-06-25 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 27–396（370 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.2；PROTEIN WAS CRYSTALLIZED FROM 18% PEG 8000, 10 MM CITRATE, PH 6.2
Resolution 1.67 Å
1DMB REFINED 1.8 ANGSTROMS STRUCTURE REVEALS THE MECHANISM OF BINDING OF A CYCLIC SUGAR, BETA-CYCLODEXTRIN, TO THE MALTODEXTRIN BINDING PROTEIN Deposited 1993-06-10 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 27–396（370 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.80 Å
1EZ9 STRUCTURE OF MALTOTETRAITOL BOUND TO OPEN-FORM MALTODEXTRIN BINDING PROTEIN IN P1 CRYSTAL FORM Deposited 2000-05-10 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 27–396（370 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；298 K；PEG 3350, MES, sodium azide, maltotetraitol, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 1.90 Å R-free 0.235
1EZ9 STRUCTURE OF MALTOTETRAITOL BOUND TO OPEN-FORM MALTODEXTRIN BINDING PROTEIN IN P1 CRYSTAL FORM Deposited 2000-05-10 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain B 27–396（370 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；298 K；PEG 3350, MES, sodium azide, maltotetraitol, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 1.90 Å R-free 0.235
1EZO GLOBAL FOLD OF MALTODEXTRIN BINDING PROTEIN COMPLEXED WITH BETA-CYCLODEXTRIN Deposited 2000-05-11 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 27–396（370 aa）
Mutation：I28T No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.2；310 K；Pressure ambient
NMR sample composition 1.4 mM maltodextrin binding protein U-15N,13C,2H, with 1H amide and methyl on Val, Leu, and Ile(delta1) 2mM beta-cyclodextrin, 20 mM sodium phosphate pH 7.2, 3uM NaN3, 100uM EDTA. | 90% H2O/10% D2O
Resolution not provided
1EZP GLOBAL FOLD OF MALTODEXTRIN BINDING PROTEIN COMPLEXED WITH BETA-CYCLODEXTRIN USING PEPTIDE ORIENTATIONS FROM DIPOLAR COUPLINGS Deposited 2000-05-11 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 27–396（370 aa）
Mutation：I28T No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.2；310 K；Pressure ambient
NMR measurement conditions pH 7.2；310 K；Pressure ambient
NMR sample composition 1.4 mM maltodextrin binding protein U-15N,13C,2H, with 1H amide and methyl on Val, Leu, and Ile(delta1) 2mM beta-cyclodextrin, 20 mM sodium phosphate pH 7.2, 3uM NaN3, 100uM EDTA. | 90% H2O/10% D2O
NMR sample composition 1.4 mM maltodextrin binding protein U-15N,13C,2H, with 1H amide and methyl on Val, Leu, and Ile(delta1) 2mM beta-cyclodextrin, 20 mM sodium phosphate pH 7.2, 3uM NaN3, 100uM EDTA. ~19mg/ml pf1 bacteriophage | 90% H2O/10% D2O
Resolution not provided
1FQA STRUCTURE OF MALTOTETRAITOL BOUND TO OPEN-FORM MALTODEXTRIN BINDING PROTEIN IN P2(1)CRYSTAL FORM Deposited 2000-09-04 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 27–396（370 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；273 K；PEG 3350, NaN3, MES, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 273.0K
Resolution 1.90 Å R-free 0.215
1FQB STRUCTURE OF MALTOTRIOTOL BOUND TO OPEN-FORM MALTODEXTRIN BINDING PROTEIN IN P2(1)CRYSTAL FORM Deposited 2000-09-04 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 27–396（370 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；273 K；PEG 3350, NaN3, MES, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 273K
Resolution 1.90 Å R-free 0.218
1FQC CRYSTAL STRUCTURE OF MALTOTRIOTOL BOUND TO CLOSED-FORM MALTODEXTRIN BINDING PROTEIN Deposited 2000-09-04 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 27–396（370 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；293 K；PEG 6000, Mes, NaN3, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.30 Å R-free 0.246
1FQD CRYSTAL STRUCTURE OF MALTOTETRAITOL BOUND TO CLOSED-FORM MALTODEXTRIN BINDING PROTEIN Deposited 2000-09-04 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 27–396（370 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；293 K；PEG 6000, Mes, NaN3, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.30 Å R-free 0.244
1IUD MALTODEXTRIN-BINDING PROTEIN INSERTION/DELETION MUTANT WITH AN INSERTED B-CELL EPITOPE FROM THE PRES2 REGION OF HEPATITIS B VIRUS Deposited 1996-05-29 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 27–396（370 aa）
Mutation：INSERTED B-CELL EPITOPE FROM THE PRES2 REGION OF HEPATITIS B VIRUS No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.70 Å R-free 0.281
1JVX Maltodextrin-binding protein variant D207C/A301GS/P316C cross-linked in crystal Deposited 2001-08-31 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 27–396（370 aa）
Mutation：D207C/A301GS/P316C No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；277 K；PEG 6000, sodium MES, maltose, sodium azide, beta-mercaptoethanol, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.50 Å R-free 0.304
1JVY Maltodextrin-binding protein variant D207C/A301GS/P316C with beta-mercaptoethanol mixed disulfides Deposited 2001-08-31 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 27–396（370 aa）
Mutation：D207C/A301GS/P316C Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；277 K；PEG 6000, sodium MES, maltose, sodium azide, beta-mercaptoethanol, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.90 Å R-free 0.273
1JW4 Structure of ligand-free maltodextrin-binding protein Deposited 2001-09-02 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 27–396（370 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；298 K；PEG 20k, Mes, sodium azide, pH 6.2, VAPOR DIFFUSION, HANGING DROP
Resolution 2.00 Å R-free 0.260
1JW5 Structure of Maltose Bound to Open-form Maltodextrin-binding Protein in P1 Crystal Deposited 2001-09-02 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 27–396（370 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；PEG 20k, Mes, sodium azide, pH 6.2, VAPOR DIFFUSION, HANGING DROP
Resolution 2.00 Å R-free 0.253
1LAX CRYSTAL STRUCTURE OF MALE31, A DEFECTIVE FOLDING MUTANT OF MALTOSE-BINDING PROTEIN Deposited 2002-03-29 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 27–396（370 aa） Fragment：MALE31
Mutation：G32D I33P No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；290 K；PEG 4000, TRIS/HCl, ISOPROPANOL, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 1.85 Å R-free 0.202
1LAX CRYSTAL STRUCTURE OF MALE31, A DEFECTIVE FOLDING MUTANT OF MALTOSE-BINDING PROTEIN Deposited 2002-03-29 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain C 27–396（370 aa） Fragment：MALE31
Mutation：G32D I33P No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；290 K；PEG 4000, TRIS/HCl, ISOPROPANOL, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 1.85 Å R-free 0.202
1LLS CRYSTAL STRUCTURE OF UNLIGANDED MALTOSE BINDING PROTEIN WITH XENON Deposited 2002-04-30 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 27–396（370 aa）
Not recorded XE XENON × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；298 K；10 mM Sodium Citrate, 23% PEG 8000, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.80 Å R-free 0.226
1MDP REFINED STRUCTURES OF TWO INSERTION(SLASH)DELETION MUTANTS PROBE FUNCTION OF THE MALTODEXTRIN BINDING PROTEIN Deposited 1994-08-10 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain 1 27–396（370 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.30 Å
1MDP REFINED STRUCTURES OF TWO INSERTION(SLASH)DELETION MUTANTS PROBE FUNCTION OF THE MALTODEXTRIN BINDING PROTEIN Deposited 1994-08-10 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain 2 27–396（370 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.30 Å
1MDQ REFINED STRUCTURES OF TWO INSERTION(SLASH)DELETION MUTANTS PROBE FUNCTION OF THE MALTODEXTRIN BINDING PROTEIN Deposited 1994-08-10 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 27–396（370 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.90 Å
1MG1 HTLV-1 GP21 ECTODOMAIN/MALTOSE-BINDING PROTEIN CHIMERA Deposited 1999-03-01 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 31–387（357 aa） Fragment：GP21 ECTODOMAIN (GP62 RESIDUES 338-425)
Not recorded CL CHLORIDE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.7；pH 4.7
Resolution 2.50 Å R-free 0.305
1MH3 maltose binding-a1 homeodomain protein chimera, crystal form I Deposited 2002-08-19 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 27–392（366 aa）
Mutation：E359A, K362A, D363A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；298 K；amonium sulfate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.10 Å R-free 0.262
1MH4 maltose binding-a1 homeodomain protein chimera, crystal form II Deposited 2002-08-19 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 27–392（366 aa）
Mutation：E359A, K362A, D363A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；PEG 6000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.30 Å R-free 0.293
1MPB MALTODEXTRIN-BINDING PROTEIN (MALTOSE-BINDING PROTEIN) MUTANT, WITH ARGININE REPLACING TRYPTOPHAN AT POSITION 230 (TRP-230-ARG) Deposited 1995-07-25 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 27–396（370 aa）
Mutation：W230R No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.00 Å
1MPC MALTODEXTRIN-BINDING PROTEIN (MALTOSE-BINDING PROTEIN) MUTANT, WITH ARGININE REPLACING TRYPTOPHAN AT POSITION 230 (TRP-230-ARG) Deposited 1995-07-25 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 27–396（370 aa）
Mutation：W230R No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.10 Å
1MPD MALTODEXTRIN-BINDING PROTEIN (MALTOSE-BINDING PROTEIN) MUTANT, WITH ARGININE REPLACING TRYPTOPHAN AT POSITION 230 (TRP-230-ARG), COMPLEXED WITH MALTOSE Deposited 1995-07-25 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 27–396（370 aa）
Mutation：W230R No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.30 Å
1N3W Engineered High-Affinity Maltose-Binding Protein Deposited 2002-10-29 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 27–396（370 aa）
Mutation：Deletion of residues 172,173,175,176 No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；290 K；PEG 4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 2.60 Å R-free 0.295
1N3X Ligand-free High-Affinity Maltose-Binding Protein Deposited 2002-10-29 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 27–396（370 aa）
Mutation：Deletion of residues 172,173,175,176. No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；290 K；PEG 4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 2.50 Å R-free 0.241
1NL5 Engineered High-affinity Maltose-Binding Protein Deposited 2003-01-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 27–396（370 aa）
Mutation：M321A Q325A, deletion of residues 172,173,175,176 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；PEG 3350, Zinc Chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 100K
Resolution 2.10 Å R-free 0.290
1NMU MBP-L30 Deposited 2003-01-10 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 27–392（366 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；Sodium Citrate, Tris, Sodium Chloride, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.31 Å R-free 0.254
1NMU MBP-L30 Deposited 2003-01-10 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 27–392（366 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；Sodium Citrate, Tris, Sodium Chloride, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.31 Å R-free 0.254
1OMP CRYSTALLOGRAPHIC EVIDENCE OF A LARGE LIGAND-INDUCED HINGE-TWIST MOTION BETWEEN THE TWO DOMAINS OF THE MALTODEXTRIN-BINDING PROTEIN INVOLVED IN ACTIVE TRANSPORT AND CHEMOTAXIS Deposited 1992-09-14 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 27–396（370 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.80 Å
1PEB LIGAND-FREE HIGH-AFFINITY MALTOSE-BINDING PROTEIN Deposited 2003-05-21 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 27–396（370 aa）
Mutation：M321A, Q325A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；312 K；PEG 3500, cacodylic acid, zinc acetate, sodium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 312K
Resolution 2.60 Å R-free 0.242
1R6Z The Crystal Structure of the Argonaute2 PAZ domain (as a MBP fusion) Deposited 2003-10-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 27–392（366 aa） Fragment：MBP (residues 28-392) fused with Argonaute2 PAZ domain (residues 591-726)
Chain P 27–392（366 aa） Fragment：MBP (residues 28-392) fused with Argonaute2 PAZ domain (residues 591-726)
Chain Z 27–392（366 aa） Fragment：MBP (residues 28-392) fused with Argonaute2 PAZ domain (residues 591-726)
Not recorded NI NICKEL (II) ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；290 K；PEG2KMME, NiCl2, TrisHCl, NaF, meso-erythritol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 2.80 Å R-free 0.281
1R6Z The Crystal Structure of the Argonaute2 PAZ domain (as a MBP fusion) Deposited 2003-10-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain P 27–392（366 aa） Fragment：MBP (residues 28-392) fused with Argonaute2 PAZ domain (residues 591-726)
Not recorded NI NICKEL (II) ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；290 K；PEG2KMME, NiCl2, TrisHCl, NaF, meso-erythritol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 2.80 Å R-free 0.281
1R6Z The Crystal Structure of the Argonaute2 PAZ domain (as a MBP fusion) Deposited 2003-10-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 27–392（366 aa） Fragment：MBP (residues 28-392) fused with Argonaute2 PAZ domain (residues 591-726)
Not recorded NI NICKEL (II) ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；290 K；PEG2KMME, NiCl2, TrisHCl, NaF, meso-erythritol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 2.80 Å R-free 0.281
1R6Z The Crystal Structure of the Argonaute2 PAZ domain (as a MBP fusion) Deposited 2003-10-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain Z 27–392（366 aa） Fragment：MBP (residues 28-392) fused with Argonaute2 PAZ domain (residues 591-726)
Not recorded NI NICKEL (II) ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；290 K；PEG2KMME, NiCl2, TrisHCl, NaF, meso-erythritol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 2.80 Å R-free 0.281
1SVX Crystal structure of a designed selected Ankyrin Repeat protein in complex with the Maltose Binding Protein Deposited 2004-03-30 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 29–392（364 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；30% PEG 6000, 0.1M Tris, 0.1M NaCl, pH 8-9, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.24 Å R-free 0.249
1Y4C Designed Helical Protein fusion MBP Deposited 2004-11-30 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 27–392（366 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.90 Å R-free 0.225
1YTV Maltose-binding protein fusion to a C-terminal fragment of the V1a vasopressin receptor Deposited 2005-02-11 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 27–392（366 aa） Fragment：c-terminal residues 27-392
Chain B 27–392（366 aa） Fragment：c-terminal residues 27-392
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；0.2M Ammonium sulfate, 25%(v/v)PEG 400 and 25%(v/v) glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.80 Å R-free 0.225
1ZIU Crystal Structure of nickel-bound engineered Maltose Binding Protein Deposited 2005-04-27 Different construct Different mutation/modification 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 27–396（370 aa） Fragment：residues 27-396
Mutation：A63H, R66H, E111M, Y155E, W340E NI NICKEL (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；PEG 2000 MME, sodium acetate, nickel chloride, Tris-HCl, sodium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.00 Å R-free 0.243
1ZJL Crystal structure of zinc-bound engineered maltose binding protein Deposited 2005-04-29 Different construct Different mutation/modification 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 27–396（370 aa） Fragment：residues 27-396
Mutation：A63H, R66H, E111M, Y155E, W340E ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；PEG 2000 MME, sodium acetate, zinc acetate, HEPES, sodium chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.00 Å R-free 0.232
1ZKB Zinc-free Engineered maltose binding protein Deposited 2005-05-02 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 27–396（370 aa） Fragment：RESIDUES 27-396
Mutation：A66H, R63H, E111M, Y155E, W340E No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；PEG 2000 MME, sodium acetate, Tris-HcL, sodium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.20 Å R-free 0.285
1ZMG Crystal structure of copper-bound engineered maltose binding protein Deposited 2005-05-10 Different construct Different mutation/modification 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 27–396（370 aa） Fragment：RESIDUES 27-396
Mutation：A63H, R66H, E111M, Y155E, W340E CU COPPER (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；PEG 2000 MME, copper sulphate, sodium acetate, Tris-HCl, sodium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.50 Å R-free 0.268
3MBP MALTODEXTRIN-BINDING PROTEIN WITH BOUND MALTOTRIOSE Deposited 1997-06-25 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 27–396（370 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.2；PROTEIN WAS CRYSTALLIZED FROM 18% PEG 8000, 10 MM CITRATE, PH 6.2
Resolution 1.70 Å
4MBP MALTODEXTRIN BINDING PROTEIN WITH BOUND MALTETROSE Deposited 1997-08-17 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 27–396（370 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.2；PROTEIN WAS CRYSTALLIZED FROM 18% PEG 8000, 10 MM CITRATE, PH 6.2
Resolution 1.70 Å

41 other PDB entries and 51 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MALE_ECOLI
Isoform —
PDB entities 3
Chains and sequence ranges Author chain A； PDBConstruct 2–367； UniProt 27–392

60S ribosomal protein L30

Saccharomyces cerevisiae

UniProt P14120

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–RNA Heteromer Protein × 2 RNA 2 其他Polymer 1 PDB declaration: tetrameric（4） Count mismatch; review required Chain B； UniProt 0–104 Not recorded 5'-R(*GP*AP*CP*CP*GP*GP*AP*GP*UP*GP*UP*CP*C)-3' × 1 5'-R(*G*GP*AP*CP*GP*CP*AP*GP*AP*GP*AP*UP*GP*GP*UP*C)-3' × 1 Maltose-binding periplasmic protein × 1 （P02928） alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6；295 K；Lithium Sulfate, Sodium Cacodylate, Magnesium Chloride, Jeffamine, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 295K Resolution 3.24 Å R-free 0.320

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 1T0K Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1CK2 YEAST (SACCHAROMYCES CEREVISIAE) RIBOSOMAL PROTEIN L30 Deposited 1999-04-26 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–104（104 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；288 K；Ionic strength (raw mmCIF value) 300 mM；Pressure 1
NMR sample composition 10% WATER/90% D2O
Resolution not provided
1CN7 Yeast ribosomal protein L30 Deposited 1999-05-26 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–105（104 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；283 K；Ionic strength (raw mmCIF value) 300 mM；Pressure 1
NMR sample composition 10% WATER/90% D2O
Resolution not provided
1NMU MBP-L30 Deposited 2003-01-10 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–104（104 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；Sodium Citrate, Tris, Sodium Chloride, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.31 Å R-free 0.254
1NMU MBP-L30 Deposited 2003-01-10 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–104（104 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；Sodium Citrate, Tris, Sodium Chloride, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.31 Å R-free 0.254
3J6X S. cerevisiae 80S ribosome bound with Taura syndrome virus (TSV) IRES, 5 degree rotation (Class II) Deposited 2014-04-16 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain 70 1–105（105 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 45 mM HEPES/KOH, 10 mM MgCl2, 100 mM KCl, 2.5 mM spermine, 2 mM BME, 0.5 U/uL RNasin；pH 7.5；45 mM HEPES/KOH, 10 mM MgCl2, 100 mM KCl, 2.5 mM spermine, 2 mM BME, 0.5 U/uL RNasin
cryo-EM vitrification conditions Fresh glow discharge, 7 second blot；Cryogen ETHANE；Fresh glow discharge, 7 second blot before plunging into liquid ehtane (FEI VITROBOT MARK II).
Resolution 6.10 Å
3J6Y S. cerevisiae 80S ribosome bound with Taura syndrome virus (TSV) IRES, 2 degree rotation (Class I) Deposited 2014-04-16 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain 70 1–105（105 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 45 mM HEPES/KOH, 10 mM MgCl2, 100 mM KCl, 2.5 mM spermine, 2 mM BME, 0.5 U/uL RNasin；pH 7.5；45 mM HEPES/KOH, 10 mM MgCl2, 100 mM KCl, 2.5 mM spermine, 2 mM BME, 0.5 U/uL RNasin
cryo-EM vitrification conditions Fresh glow discharge, 7 second blot；Cryogen ETHANE；Fresh glow discharge, 7 second blot before plunging into liquid ehtane (FEI VITROBOT MARK II).
Resolution 6.10 Å
3J77 Structures of yeast 80S ribosome-tRNA complexes in the rotated and non-rotated conformations (Class II - rotated ribosome with 1 tRNA) Deposited 2014-05-29 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 83-meric
Chain 80 1–105（105 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 20 mM Tris-HCl, 50 mM NH4Cl, 20 mM MgCl2；pH 7.5；20 mM Tris-HCl, 50 mM NH4Cl, 20 mM MgCl2
cryo-EM vitrification conditions Cryogen ETHANE；Plunged into liquid ethane (FEI VITROBOT MARK II)
Resolution 6.20 Å
3J78 Structures of yeast 80S ribosome-tRNA complexes in the rotated and non-rotated conformations (Class I - non-rotated ribosome with 2 tRNAs) Deposited 2014-05-29 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain 80 1–105（105 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 20 mM Tris-HCl, 50 mM NH4Cl, 20 mM MgCl2；pH 7.5；20 mM Tris-HCl, 50 mM NH4Cl, 20 mM MgCl2
cryo-EM vitrification conditions Cryogen ETHANE；Plunged into liquid ethane (FEI VITROBOT MARK II)
Resolution 6.30 Å
3JCT Cryo-em structure of eukaryotic pre-60S ribosomal subunits Deposited 2016-03-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 58-meric
Chain c 1–105（105 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.08 Å
4U3M Crystal structure of Anisomycin bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain O0 2–105（104 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 ANM ANISOMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.245
4U3M Crystal structure of Anisomycin bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain o0 2–105（104 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 ANM ANISOMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.245
4U3N Crystal structure of CCA trinucleotide bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain O0 2–105（104 aa）
Not recorded MG MAGNESIUM ION × 677 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.237
4U3N Crystal structure of CCA trinucleotide bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 84-meric
Chain o0 2–105（104 aa）
Not recorded MG MAGNESIUM ION × 731 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.237
4U3U Crystal structure of Cycloheximide bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain O0 2–105（104 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 2.90 Å R-free 0.245
4U3U Crystal structure of Cycloheximide bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain o0 2–105（104 aa）
Not recorded MG MAGNESIUM ION × 730 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 2.90 Å R-free 0.245
4U4N Crystal structure of Edeine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain O0 2–105（104 aa）
Not recorded MG MAGNESIUM ION × 676 OHX osmium (III) hexammine × 557 EDE EDEINE B × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
4U4N Crystal structure of Edeine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain o0 2–105（104 aa）
Not recorded MG MAGNESIUM ION × 730 OHX osmium (III) hexammine × 574 EDE EDEINE B × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
4U4O Crystal structure of Geneticin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain O0 2–105（104 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 556 GET GENETICIN × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.60 Å R-free 0.267
4U4O Crystal structure of Geneticin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain o0 2–105（104 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.60 Å R-free 0.267
4U4Q Crystal structure of Homoharringtonine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain O0 2–105（104 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 HMT (3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.255
4U4Q Crystal structure of Homoharringtonine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain o0 2–105（104 aa）
Not recorded MG MAGNESIUM ION × 733 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 HMT (3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.255
4U4R Crystal structure of Lactimidomycin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain O0 2–105（104 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 3H3 4-{(2R,5S,6E)-2-hydroxy-5-methyl-7-[(2R,3S,4E,6Z,10E)-3-methyl-12-oxooxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl}piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 2.80 Å R-free 0.246
4U4R Crystal structure of Lactimidomycin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain o0 2–105（104 aa）
Not recorded MG MAGNESIUM ION × 730 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 3H3 4-{(2R,5S,6E)-2-hydroxy-5-methyl-7-[(2R,3S,4E,6Z,10E)-3-methyl-12-oxooxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl}piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 2.80 Å R-free 0.246
4U4U Crystal structure of Lycorine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-MERIC
Chain O0 2–105（104 aa）
Not recorded MG MAGNESIUM ION × 679 OHX osmium (III) hexammine × 557 ZN ZINC ION × 8 3KD (1S,2S,12bS,12cS)-2,4,5,7,12b,12c-hexahydro-1H-[1,3]dioxolo[4,5-j]pyrrolo[3,2,1-de]phenanthridine-1,2-diol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.259
4U4U Crystal structure of Lycorine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-MERIC
Chain o0 2–105（104 aa）
Not recorded MG MAGNESIUM ION × 733 OHX osmium (III) hexammine × 576 ZN ZINC ION × 8 3KD (1S,2S,12bS,12cS)-2,4,5,7,12b,12c-hexahydro-1H-[1,3]dioxolo[4,5-j]pyrrolo[3,2,1-de]phenanthridine-1,2-diol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.259
4U4Y Crystal structure of Pactamycin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain O0 2–105（104 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 556 PCY Pactamycin × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.245
4U4Y Crystal structure of Pactamycin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 85-meric
Chain o0 2–105（104 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 574 PCY Pactamycin × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.245
4U4Z Crystal structure of Phyllanthoside bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain O0 2–105（104 aa）
Not recorded MG MAGNESIUM ION × 677 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 3K5 3-O-acetyl-2-O-(3-O-acetyl-6-deoxy-beta-D-glucopyranosyl)-6-deoxy-1-O-{[(2R,2'S,3a'R,4''S,5''R,6'S,7a'S)-5''-methyl-4''-{[(2E)-3-phenylprop-2-enoyl]oxy}decahydrodispiro[oxirane-2,3'-[1]benzofuran-2',2''-pyran]-6'-yl]carbonyl}-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
4U4Z Crystal structure of Phyllanthoside bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 95-meric
Chain o0 2–105（104 aa）
Not recorded MG MAGNESIUM ION × 731 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 3K5 3-O-acetyl-2-O-(3-O-acetyl-6-deoxy-beta-D-glucopyranosyl)-6-deoxy-1-O-{[(2R,2'S,3a'R,4''S,5''R,6'S,7a'S)-5''-methyl-4''-{[(2E)-3-phenylprop-2-enoyl]oxy}decahydrodispiro[oxirane-2,3'-[1]benzofuran-2',2''-pyran]-6'-yl]carbonyl}-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
4U50 Crystal structure of Verrucarin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain O0 2–105（104 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 556 ZN ZINC ION × 8 3L2 (4S,5R,10E,12Z,16R,16aS,17S,18R,19aR,23aR)-4-hydroxy-5,16a,21-trimethyl-4,5,6,7,16,16a,22,23-octahydro-3H,18H,19aH-spiro[16,18-methano[1,6,12]trioxacyclooctadecino[3,4-d]chromene-17,2'-oxirane]-3,9,14-trione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.262
4U50 Crystal structure of Verrucarin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain o0 2–105（104 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 576 ZN ZINC ION × 8 3L2 (4S,5R,10E,12Z,16R,16aS,17S,18R,19aR,23aR)-4-hydroxy-5,16a,21-trimethyl-4,5,6,7,16,16a,22,23-octahydro-3H,18H,19aH-spiro[16,18-methano[1,6,12]trioxacyclooctadecino[3,4-d]chromene-17,2'-oxirane]-3,9,14-trione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.262
4U51 Crystal structure of Narciclasine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain O0 2–105（104 aa）
Not recorded MG MAGNESIUM ION × 676 OHX osmium (III) hexammine × 557 ZN ZINC ION × 8 3KF (2S,3R,4S,4aR)-2,3,4,7-tetrahydroxy-3,4,4a,5-tetrahydro[1,3]dioxolo[4,5-j]phenanthridin-6(2H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.253
4U51 Crystal structure of Narciclasine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain o0 2–105（104 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 572 ZN ZINC ION × 8 3KF (2S,3R,4S,4aR)-2,3,4,7-tetrahydroxy-3,4,4a,5-tetrahydro[1,3]dioxolo[4,5-j]phenanthridin-6(2H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.253
4U52 Crystal structure of Nagilactone C bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain O0 2–105（104 aa）
Not recorded MG MAGNESIUM ION × 679 OHX osmium (III) hexammine × 556 ZN ZINC ION × 8 3J2 Nagilactone C × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.258
4U52 Crystal structure of Nagilactone C bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain o0 2–105（104 aa）
Not recorded MG MAGNESIUM ION × 734 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 3J2 Nagilactone C × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.258
4U53 Crystal structure of Deoxynivalenol bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain O0 2–105（104 aa）
Not recorded MG MAGNESIUM ION × 676 OHX osmium (III) hexammine × 556 ZN ZINC ION × 8 3J6 (3beta,7alpha)-3,7,15-trihydroxy-12,13-epoxytrichothec-9-en-8-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.30 Å R-free 0.255
4U53 Crystal structure of Deoxynivalenol bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain o0 2–105（104 aa）
Not recorded MG MAGNESIUM ION × 730 OHX osmium (III) hexammine × 574 ZN ZINC ION × 8 3J6 (3beta,7alpha)-3,7,15-trihydroxy-12,13-epoxytrichothec-9-en-8-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.30 Å R-free 0.255
4U55 Crystal structure of Cryptopleurine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-MERIC
Chain O0 2–105（104 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 557 3K8 (14aR)-2,3,6-trimethoxy-11,12,13,14,14a,15-hexahydro-9H-dibenzo[f,h]pyrido[1,2-b]isoquinoline × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.246
4U55 Crystal structure of Cryptopleurine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-MERIC
Chain o0 2–105（104 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 574 3K8 (14aR)-2,3,6-trimethoxy-11,12,13,14,14a,15-hexahydro-9H-dibenzo[f,h]pyrido[1,2-b]isoquinoline × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.246
4U56 Crystal structure of Blasticidin S bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain O0 2–105（104 aa）
Not recorded MG MAGNESIUM ION × 675 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 BLS BLASTICIDIN S × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.45 Å R-free 0.260
4U56 Crystal structure of Blasticidin S bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 85-meric
Chain o0 2–105（104 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 574 ZN ZINC ION × 8 BLS BLASTICIDIN S × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.45 Å R-free 0.260
4U6F Crystal structure of T-2 toxin bound to the yeast 80S ribosome Deposited 2014-07-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain O0 2–105（104 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 557 ZN ZINC ION × 8 ZBA 12,13-Epoxytrichothec-9-ene-3,4,8,15-tetrol-4,15-diacetate-8-isovalerate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.247
4U6F Crystal structure of T-2 toxin bound to the yeast 80S ribosome Deposited 2014-07-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain o0 2–105（104 aa）
Not recorded MG MAGNESIUM ION × 731 OHX osmium (III) hexammine × 574 ZN ZINC ION × 8 ZBA 12,13-Epoxytrichothec-9-ene-3,4,8,15-tetrol-4,15-diacetate-8-isovalerate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.247
4V6I Localization of the small subunit ribosomal proteins into a 6.1 A cryo-EM map of Saccharomyces cerevisiae translating 80S ribosome Deposited 2010-10-12 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 86-meric
Chain Bf 1–105（105 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.80 Å
4V7F Arx1 pre-60S particle. Deposited 2013-12-10 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain b 1–105（105 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.70 Å
4V7R Yeast 80S ribosome. Deposited 2010-07-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 69 PDB declaration: 73-meric
Chain BZ 1–105（105 aa）
Not recorded OHX osmium (III) hexammine × 355 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；297 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine, pH 7, VAPOR DIFFUSION, temperature 297K
Resolution 4.00 Å R-free 0.341
4V7R Yeast 80S ribosome. Deposited 2010-07-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 62 PDB declaration: 66-meric
Chain DZ 1–105（105 aa）
Not recorded OHX osmium (III) hexammine × 360 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；297 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine, pH 7, VAPOR DIFFUSION, temperature 297K
Resolution 4.00 Å R-free 0.341
4V88 The structure of the eukaryotic ribosome at 3.0 A resolution. Deposited 2011-10-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain Bc 1–105（105 aa）
Not recorded OHX osmium (III) hexammine × 657 MG MAGNESIUM ION × 1035 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.00 Å R-free 0.229
4V88 The structure of the eukaryotic ribosome at 3.0 A resolution. Deposited 2011-10-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain Dc 1–105（105 aa）
Not recorded OHX osmium (III) hexammine × 688 MG MAGNESIUM ION × 1170 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.00 Å R-free 0.229
4V8T Cryo-EM Structure of the 60S Ribosomal Subunit in Complex with Arx1 and Rei1 Deposited 2012-08-07 Different construct 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: 50-meric
Chain c 1–105（105 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer 20 MM HEPES-NAOH PH 8.0, 50 MM NACL, 5 MM BETA- MERCAPTOETHANOL, 5 MM MGCL2；pH 8；20 MM HEPES-NAOH PH 8.0, 50 MM NACL, 5 MM BETA- MERCAPTOETHANOL, 5 MM MGCL2
cryo-EM vitrification conditions Cryogen ETHANE；PLUNGE FREEZING IN LIQUID ETHANE AFTER MANUAL BLOTTING USING A MANUAL PLUNGE FREEZING DEVICE
Resolution 8.10 Å
4V8Y Cryo-EM reconstruction of the 80S-eIF5B-Met-itRNAMet Eukaryotic Translation Initiation Complex Deposited 2013-07-20 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: 87-meric
Chain Bc 2–105（104 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 191 OHX osmium (III) hexammine × 197 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer 3MM HEPES-KOH, 6.6 MM TRIS-ACETATE PH 7.2, 3 MM NH4CL, 6.6 MM NH4- ACETATE, 48 MM K-ACETATE, 4 MM MG-ACETATE, 2.4 MM DTT；pH 7.2；3MM HEPES-KOH, 6.6 MM TRIS-ACETATE PH 7.2, 3 MM NH4CL, 6.6 MM NH4- ACETATE, 48 MM K-ACETATE, 4 MM MG-ACETATE, 2.4 MM DTT
cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 90, INSTRUMENT- FEI VITROBOT MARK II, METHOD- BLOT 2.5 SECONDS BEFORE PLUNGING,
Resolution 4.30 Å
4V8Z Cryo-EM reconstruction of the 80S-eIF5B-Met-itRNAMet Eukaryotic Translation Initiation Complex Deposited 2013-07-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 79 PDB declaration: 85-meric
Chain Bc 2–105（104 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 226 OHX osmium (III) hexammine × 210 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer 3MM HEPES-KOH, 6.6 MM TRIS-ACETATE PH 7.2, 3 MM NH4CL, 6.6 MM NH4- ACETATE, 48 MM K-ACETATE, 4 MM MG-ACETATE, 2.4 MM DTT；pH 7.2；3MM HEPES-KOH, 6.6 MM TRIS-ACETATE PH 7.2, 3 MM NH4CL, 6.6 MM NH4- ACETATE, 48 MM K-ACETATE, 4 MM MG-ACETATE, 2.4 MM DTT
cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 90, INSTRUMENT- FEI VITROBOT MARK II, METHOD- BLOT 2.5 SECONDS BEFORE PLUNGING,
Resolution 6.60 Å
5APN Structure of the yeast 60S ribosomal subunit in complex with Arx1, Alb1 and N-terminally tagged Rei1 Deposited 2015-09-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain c 1–105（105 aa）
Not recorded MG MAGNESIUM ION × 280 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer 20MM；pH 8；20MM
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；PLUNGE-FROZEN
Resolution 3.91 Å
5APO Structure of the yeast 60S ribosomal subunit in complex with Arx1, Alb1 and C-terminally tagged Rei1 Deposited 2015-09-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain c 1–105（105 aa）
Not recorded MG MAGNESIUM ION × 280 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer 20MM HEPES-KOH, 100mM NACL, 5mM MGCL2, 5mM BETA-MERCAPTOETHANOL；pH 8；20MM HEPES-KOH, 100mM NACL, 5mM MGCL2, 5mM BETA-MERCAPTOETHANOL
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；PLUNGE-FROZEN
Resolution 3.41 Å
5DAT Complex of yeast 80S ribosome with hypusine-containing eIF5A Deposited 2015-08-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 86-MERIC
Chain o0 2–105（104 aa）
Not recorded MG MAGNESIUM ION × 580 OHX osmium (III) hexammine × 601 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.15 Å R-free 0.252
5DAT Complex of yeast 80S ribosome with hypusine-containing eIF5A Deposited 2015-08-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 86-MERIC
Chain O0 2–105（104 aa）
Not recorded MG MAGNESIUM ION × 528 OHX osmium (III) hexammine × 565 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.15 Å R-free 0.252
5DC3 Complex of yeast 80S ribosome with non-modified eIF5A Deposited 2015-08-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-meric
Chain O0 2–105（104 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.25 Å R-free 0.301
5DC3 Complex of yeast 80S ribosome with non-modified eIF5A Deposited 2015-08-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 80 PDB declaration: 81-meric
Chain o0 2–105（104 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.25 Å R-free 0.301
5DGE Coping with proline stalling: structural basis of hypusine-induced protein synthesis by the eukaryotic ribosome Deposited 2015-08-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 155 PDB declaration: 165-meric
Chain O0 2–105（104 aa）
Chain o0 2–105（104 aa）
Not recorded MG MAGNESIUM ION × 1093 OHX osmium (III) hexammine × 1169 ZN ZINC ION × 16 SPS SPARSOMYCIN × 2 PRO PROLINE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.45 Å R-free 0.263
5DGF Complex of yeast 80S ribosome with hypusine-containing/non-modified eIF5A and/or a peptidyl-tRNA analog Deposited 2015-08-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: TRIMERIC
Chain O0 2–105（104 aa）
Not recorded ZN ZINC ION × 8 SPS SPARSOMYCIN × 1 MG MAGNESIUM ION × 4 OHX osmium (III) hexammine × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.30 Å R-free 0.310
5DGF Complex of yeast 80S ribosome with hypusine-containing/non-modified eIF5A and/or a peptidyl-tRNA analog Deposited 2015-08-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 80 PDB declaration: TRIMERIC
Chain o0 2–105（104 aa）
Not recorded ZN ZINC ION × 8 SPS SPARSOMYCIN × 1 MG MAGNESIUM ION × 8 OHX osmium (III) hexammine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.30 Å R-free 0.310
5DGV Complex of yeast 80S ribosome with hypusine-containing/non-modified eIF5A and/or a peptidyl-tRNA analog Deposited 2015-08-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 81-MERIC
Chain o0 2–105（104 aa）
Not recorded ZN ZINC ION × 8 SPS SPARSOMYCIN × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.10 Å R-free 0.284
5DGV Complex of yeast 80S ribosome with hypusine-containing/non-modified eIF5A and/or a peptidyl-tRNA analog Deposited 2015-08-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-MERIC
Chain O0 2–105（104 aa）
Not recorded ZN ZINC ION × 8 SPS SPARSOMYCIN × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.10 Å R-free 0.284
5FCI Structure of the vacant uL3 W255C mutant 80S yeast ribosome Deposited 2015-12-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain O0 2–105（104 aa）
Not recorded OHX osmium (III) hexammine × 874 MG MAGNESIUM ION × 994 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-Acetate pH 7.0, KSCN, Mg-Acetate, Glycerol, Spermidine, PEG20000
Resolution 3.40 Å R-free 0.284
5FCI Structure of the vacant uL3 W255C mutant 80S yeast ribosome Deposited 2015-12-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain o0 2–105（104 aa）
Not recorded OHX osmium (III) hexammine × 561 MG MAGNESIUM ION × 626 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-Acetate pH 7.0, KSCN, Mg-Acetate, Glycerol, Spermidine, PEG20000
Resolution 3.40 Å R-free 0.284
5FCJ Structure of the anisomycin-containing uL3 W255C mutant 80S yeast ribosome Deposited 2015-12-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 82-meric
Chain o0 2–105（104 aa）
Not recorded MG MAGNESIUM ION × 517 OHX osmium (III) hexammine × 534 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；Tris-Acetate pH7.0, KSCN, Mg-Acetate, Glycerol, Spermidine, PEG20000
Resolution 3.10 Å R-free 0.291
5FCJ Structure of the anisomycin-containing uL3 W255C mutant 80S yeast ribosome Deposited 2015-12-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain O0 2–105（104 aa）
Not recorded MG MAGNESIUM ION × 462 OHX osmium (III) hexammine × 500 ZN ZINC ION × 8 ANM ANISOMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；Tris-Acetate pH7.0, KSCN, Mg-Acetate, Glycerol, Spermidine, PEG20000
Resolution 3.10 Å R-free 0.291
5GAK Yeast 60S ribosomal subunit with A-site tRNA, P-site tRNA and eIF-5A Deposited 2015-12-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 49-meric
Chain e 1–105（105 aa）
Not recorded 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Details can be retrieved from EMD-3227
Resolution 3.88 Å
5H4P Structural snapshot of cytoplasmic pre-60S ribosomal particles bound with Nmd3, Lsg1, Tif6 and Reh1 Deposited 2016-11-01 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 41 PDB declaration: 44-meric
Chain c 1–105（105 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.07 Å
5I4L Crystal structure of Amicoumacin A bound to the yeast 80S ribosome Deposited 2016-02-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain O0 6–105（100 aa）
Not recorded OHX osmium (III) hexammine × 481 MG MAGNESIUM ION × 493 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.251
5I4L Crystal structure of Amicoumacin A bound to the yeast 80S ribosome Deposited 2016-02-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain o0 6–105（100 aa）
Not recorded OHX osmium (III) hexammine × 512 MG MAGNESIUM ION × 526 ZN ZINC ION × 8 UAM Amicoumacin A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.251
5JCS CRYO-EM STRUCTURE OF THE RIX1-REA1 PRE-60S PARTICLE Deposited 2016-04-15 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain c 1–105（105 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.50 Å
5JUO Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure I (fully rotated 40S subunit) Deposited 2016-05-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain HA 1–105（105 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
5JUP Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure II (mid-rotated 40S subunit) Deposited 2016-05-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain HA 1–105（105 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
5JUS Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure III (mid-rotated 40S subunit) Deposited 2016-05-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain HA 1–105（105 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
Resolution 4.20 Å
5JUT Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure IV (almost non-rotated 40S subunit) Deposited 2016-05-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain HA 1–105（105 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
5JUU Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure V (least rotated 40S subunit) Deposited 2016-05-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain HA 1–105（105 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
5LYB Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCPmn Deposited 2016-09-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain O0 6–105（100 aa）
Not recorded MG MAGNESIUM ION × 1026 OHX osmium (III) hexammine × 659 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；277 K；Tris-Acetate pH 7.0, KSCN, MgOAc2, glycerol, spermidine, PEG20K
Resolution 3.25 Å R-free 0.249
5LYB Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCPmn Deposited 2016-09-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 84-meric
Chain o0 6–105（100 aa）
Not recorded MG MAGNESIUM ION × 1166 OHX osmium (III) hexammine × 686 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；277 K；Tris-Acetate pH 7.0, KSCN, MgOAc2, glycerol, spermidine, PEG20K
Resolution 3.25 Å R-free 0.249
5M1J Nonstop ribosomal complex bound with Dom34 and Hbs1 Deposited 2016-10-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain c5 9–105（97 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1058 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 5CR N-acetyl-L-phenylalanine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
5MC6 Cryo-EM structure of a native ribosome-Ski2-Ski3-Ski8 complex from S. cerevisiae Deposited 2016-11-09 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 87-meric
Chain AY 1–105（105 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
5MEI Crystal structure of Agelastatin A bound to the 80S ribosome Deposited 2016-11-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 78-meric
Chain AD 9–105（97 aa）
Not recorded OHX osmium (III) hexammine × 517 MG MAGNESIUM ION × 673 7MB Agelastatin A × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.50 Å R-free 0.239
5MEI Crystal structure of Agelastatin A bound to the 80S ribosome Deposited 2016-11-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain DE 9–105（97 aa）
Not recorded OHX osmium (III) hexammine × 553 MG MAGNESIUM ION × 733 7MB Agelastatin A × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.50 Å R-free 0.239
5NDG Crystal structure of geneticin (G418) bound to the yeast 80S ribosome Deposited 2017-03-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain O0 6–105（100 aa）
Not recorded MG MAGNESIUM ION × 597 GET GENETICIN × 9 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.70 Å R-free 0.253
5NDG Crystal structure of geneticin (G418) bound to the yeast 80S ribosome Deposited 2017-03-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain o0 6–105（100 aa）
Not recorded MG MAGNESIUM ION × 624 GET GENETICIN × 12 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.70 Å R-free 0.253
5NDV Crystal structure of Paromomycin bound to the yeast 80S ribosome Deposited 2017-03-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain o0 6–105（100 aa）
Not recorded PAR PAROMOMYCIN × 40 MG MAGNESIUM ION × 1006 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.30 Å R-free 0.250
5NDV Crystal structure of Paromomycin bound to the yeast 80S ribosome Deposited 2017-03-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain O0 6–105（100 aa）
Not recorded PAR PAROMOMYCIN × 47 MG MAGNESIUM ION × 1133 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.30 Å R-free 0.250
5NDW Crystal structure of aminoglycoside TC007 bound to the yeast 80S ribosome Deposited 2017-03-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain o0 6–105（100 aa）
Not recorded MG MAGNESIUM ION × 671 8UZ TC007 × 10 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.70 Å R-free 0.235
5NDW Crystal structure of aminoglycoside TC007 bound to the yeast 80S ribosome Deposited 2017-03-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain O0 6–105（100 aa）
Not recorded MG MAGNESIUM ION × 694 8UZ TC007 × 15 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.70 Å R-free 0.235
5OBM Crystal structure of Gentamicin bound to the yeast 80S ribosome Deposited 2017-06-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-MERIC
Chain O0 6–105（100 aa）
Not recorded MG MAGNESIUM ION × 855 LLL (2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDR OXYCYCLOHEXYLOXY)-5-METHYL-4-(METHYLAMINO)-TETRAHYDRO-2H-PYRAN-3,5-DIOL × 22 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.40 Å R-free 0.238
5OBM Crystal structure of Gentamicin bound to the yeast 80S ribosome Deposited 2017-06-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 78 PDB declaration: 82-MERIC
Chain o0 6–105（100 aa）
Not recorded MG MAGNESIUM ION × 1211 LLL (2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDR OXYCYCLOHEXYLOXY)-5-METHYL-4-(METHYLAMINO)-TETRAHYDRO-2H-PYRAN-3,5-DIOL × 47 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.40 Å R-free 0.238
5ON6 Crystal structure of haemanthamine bound to the 80S ribosome Deposited 2017-08-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 78-meric
Chain AD 9–105（97 aa）
Not recorded OHX osmium (III) hexammine × 515 MG MAGNESIUM ION × 703 HN8 Haemanthamine × 1 GOL GLYCEROL × 2 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
5ON6 Crystal structure of haemanthamine bound to the 80S ribosome Deposited 2017-08-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 77 PDB declaration: 80-meric
Chain DE 9–105（97 aa）
Not recorded OHX osmium (III) hexammine × 549 MG MAGNESIUM ION × 758 HN8 Haemanthamine × 1 GOL GLYCEROL × 3 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
5T62 Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis: 60S-Nmd3-Tif6-Lsg1 Complex Deposited 2016-09-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain p 1–105（105 aa）
Not recorded MG MAGNESIUM ION × 160 K POTASSIUM ION × 2 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
5T6R Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis: 60S-Nmd3 Complex Deposited 2016-09-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 42 PDB declaration: 45-meric
Chain p 1–105（105 aa）
Not recorded MG MAGNESIUM ION × 86 K POTASSIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
5TBW Crystal structure of chlorolissoclimide bound to the yeast 80S ribosome Deposited 2016-09-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain AD 9–105（97 aa）
Not recorded OHX osmium (III) hexammine × 518 MG MAGNESIUM ION × 666 7AL Chlorolissoclimide × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.00 Å R-free 0.227
5TBW Crystal structure of chlorolissoclimide bound to the yeast 80S ribosome Deposited 2016-09-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain DE 9–105（97 aa）
Not recorded OHX osmium (III) hexammine × 556 MG MAGNESIUM ION × 728 7AL Chlorolissoclimide × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.00 Å R-free 0.227
5TGA Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCA-Pro Deposited 2016-09-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain O0 6–105（100 aa）
Not recorded OHX osmium (III) hexammine × 659 MG MAGNESIUM ION × 1026 ZN ZINC ION × 8 PRO PROLINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；PEG20000
Resolution 3.30 Å R-free 0.265
5TGA Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCA-Pro Deposited 2016-09-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 84-meric
Chain o0 6–105（100 aa）
Not recorded OHX osmium (III) hexammine × 686 MG MAGNESIUM ION × 1166 ZN ZINC ION × 8 PRO PROLINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；PEG20000
Resolution 3.30 Å R-free 0.265
5TGM Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCA-Pro Deposited 2016-09-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 154 PDB declaration: 164-meric
Chain O0 6–105（100 aa）
Chain o0 6–105（100 aa）
Not recorded OHX osmium (III) hexammine × 1095 MG MAGNESIUM ION × 1191 ZN ZINC ION × 16 PHE PHENYLALANINE × 2 LEU LEUCINE × 2 SPS SPARSOMYCIN × 2 8AN 3'-amino-3'-deoxyadenosine 5'-(dihydrogen phosphate) × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG20000
Resolution 3.50 Å R-free 0.312
6CB1 Yeast nucleolar pre-60S ribosomal subunit (state 3) Deposited 2018-02-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 37 PDB declaration: 40-meric
Chain c 1–105（105 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
6ELZ State E (TAP-Flag-Ytm1 E80A) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-09-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 54-meric
Chain c 1–105（105 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
6EM5 State D architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric
Chain c 1–105（105 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6FT6 Structure of the Nop53 pre-60S particle bound to the exosome nuclear cofactors Deposited 2018-02-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric
Chain c 1–105（105 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.90 Å
6GQ1 Cryo-EM reconstruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GMPPCP/sordarin) Deposited 2018-06-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 83-meric
Chain c 9–105（97 aa）
Not recorded ZN ZINC ION × 8 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blot force 4, blot waiting time 30 s
Resolution 4.40 Å
6GQB Cryo-EM reconstruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GDP+AlF4/sordarin) Deposited 2018-06-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 84-meric
Chain c 9–105（97 aa）
Not recorded ZN ZINC ION × 8 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ALF TETRAFLUOROALUMINATE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blot force 4, blot waiting time 30 s
Resolution 3.90 Å
6GQV Cryo-EM recosntruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GMPPCP) Deposited 2018-06-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 84-meric
Chain c 9–105（97 aa）
Not recorded ZN ZINC ION × 8 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blot force 4, blot waiting time 30 s
Resolution 4.00 Å
6HD7 Cryo-EM structure of the ribosome-NatA complex Deposited 2018-08-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 51-meric
Chain e 1–105（105 aa）
Not recorded 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6HHQ Crystal structure of compound C45 bound to the yeast 80S ribosome Deposited 2018-08-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain AD 1–105（105 aa）
Not recorded OHX osmium (III) hexammine × 513 MG MAGNESIUM ION × 717 G5B (3~{R})-3-[(1~{S})-2-[(1~{S},4~{a}~{R},6~{S},7~{S},8~{a}~{R})-6,7-bis(chloranyl)-5,5,8~{a}-trimethyl-2-methylidene-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.264
6HHQ Crystal structure of compound C45 bound to the yeast 80S ribosome Deposited 2018-08-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain DE 1–105（105 aa）
Not recorded OHX osmium (III) hexammine × 544 MG MAGNESIUM ION × 792 G5B (3~{R})-3-[(1~{S})-2-[(1~{S},4~{a}~{R},6~{S},7~{S},8~{a}~{R})-6,7-bis(chloranyl)-5,5,8~{a}-trimethyl-2-methylidene-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 ZN ZINC ION × 8 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.264
6I7O The structure of a di-ribosome (disome) as a unit for RQC and NGD quality control pathways recognition. Deposited 2018-11-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 150 PDB declaration: 163-meric
Chain AY 6–105（100 aa）
Chain XY 6–105（100 aa）
Not recorded ZN ZINC ION × 15 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.30 Å
6M62 Cryo-Em structure of eukaryotic pre-60S ribosome subunit from Saccharomyces cerevisiae rpf2 delta 255-344 strain, C4 state. Deposited 2020-03-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 58-meric
Chain c 1–105（105 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6N8J Cryo-EM structure of late nuclear (LN) pre-60S ribosomal subunit Deposited 2018-11-29 Different construct 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 c 1–105（105 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6N8K Cryo-EM structure of early cytoplasmic-immediate (ECI) pre-60S ribosomal subunit Deposited 2018-11-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain c 1–105（105 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6N8L Cryo-EM structure of early cytoplasmic-late (ECL) pre-60S ribosomal subunit Deposited 2018-11-29 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain c 1–105（105 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6N8M Cryo-EM structure of pre-Lsg1 (PL) pre-60S ribosomal subunit Deposited 2018-11-29 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain p 1–105（105 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
6N8N Cryo-EM structure of Lsg1-engaged (LE) pre-60S ribosomal subunit Deposited 2018-11-29 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain p 1–105（105 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6N8O Cryo-EM structure of Rpl10-inserted (RI) pre-60S ribosomal subunit Deposited 2018-11-29 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain p 1–105（105 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
6OIG Subunit joining exposes nascent pre-40S rRNA for processing and quality control Deposited 2019-04-09 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain c 9–105（97 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6Q8Y Cryo-EM structure of the mRNA translating and degrading yeast 80S ribosome-Xrn1 nuclease complex Deposited 2018-12-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain AY 9–105（97 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6QIK Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-01-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain c 1–105（105 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6QT0 Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-02-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 42 PDB declaration: 45-meric
Chain c 1–105（105 aa）
Not recorded ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6QTZ Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-02-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain c 1–105（105 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6R84 Yeast Vms1 (Q295L)-60S ribosomal subunit complex (pre-state with Arb1) Deposited 2019-03-31 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 50-meric
Chain e 9–105（97 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6R86 Yeast Vms1-60S ribosomal subunit complex (post-state) Deposited 2019-03-31 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 47-meric
Chain e 9–105（97 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6R87 Yeast Vms1 (Q295L)-60S ribosomal subunit complex (pre-state without Arb1) Deposited 2019-03-31 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 49-meric
Chain e 9–105（97 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6RI5 Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-04-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain c 1–105（105 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
6RZZ Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-06-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain c 1–105（105 aa）
Not recorded ZN ZINC ION × 10 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6S05 Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-06-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain c 1–105（105 aa）
Not recorded ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6S47 Saccharomyces cerevisiae 80S ribosome bound with ABCF protein New1 Deposited 2019-06-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain Ae 2–105（104 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.28 Å
6SNT Yeast 80S ribosome stalled on SDD1 mRNA. Deposited 2019-08-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-meric
Chain an 1–105（105 aa）
Not recorded MG MAGNESIUM ION × 87 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
6SV4 The cryo-EM structure of SDD1-stalled collided trisome. Deposited 2019-09-17 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 225 PDB declaration: 242-meric
Chain AY 1–105（105 aa）
Chain XY 1–105（105 aa）
Chain zY 1–105（105 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
6T4Q Structure of yeast 80S ribosome stalled on the CGA-CCG inhibitory codon combination. Deposited 2019-10-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain Lc 9–104（96 aa）
Not recorded MG MAGNESIUM ION × 291 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
6T7I Structure of yeast 80S ribosome stalled on the CGA-CGA inhibitory codon combination. Deposited 2019-10-22 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 81-meric
Chain Lc 1–105（105 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6T7T Structure of yeast 80S ribosome stalled on poly(A) tract. Deposited 2019-10-23 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain Lc 9–104（96 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6T83 Structure of yeast disome (di-ribosome) stalled on poly(A) tract. Deposited 2019-10-24 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 149 PDB declaration: 159-meric
Chain N 1–105（105 aa）
Chain cy 1–105（105 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
6TB3 yeast 80S ribosome in complex with the Not5 subunit of the CCR4-NOT complex Deposited 2019-10-31 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 83-meric
Chain AY 9–104（96 aa）
Not recorded MG MAGNESIUM ION × 327 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
6TNU Yeast 80S ribosome in complex with eIF5A and decoding A-site and P-site tRNAs. Deposited 2019-12-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain AY 9–104（96 aa）
Not recorded ZN ZINC ION × 7 SPD SPERMIDINE × 1 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6WOO CryoEM structure of yeast 80S ribosome with Met-tRNAiMet, eIF5B, and GDP Deposited 2020-04-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 84-meric
Chain c 9–105（97 aa）
Not recorded ZN ZINC ION × 6 GDP GUANOSINE-5'-DIPHOSPHATE × 1 U6A N-carboxy-L-threonine × 1 MET METHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
6XIQ Cryo-EM Structure of K63R Ubiquitin Mutant Ribosome under Oxidative Stress Deposited 2020-06-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain c 1–105（105 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
6XIR Cryo-EM Structure of K63 Ubiquitinated Yeast Translocating Ribosome under Oxidative Stress Deposited 2020-06-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 70 PDB declaration: 76-meric
Chain c 1–105（105 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6YLG Rix1-Rea1 pre-60S particle - 60S core, body 1 (rigid body refinement) Deposited 2020-04-07 Different construct 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 n 1–105（105 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
6YLH Rix1-Rea1 pre-60S particle - full composite structure Deposited 2020-04-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 57 PDB declaration: 60-meric
Chain n 1–105（105 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6YLX pre-60S State NE1 (TAP-Flag-Nop53) Deposited 2020-04-07 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain c 1–105（105 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6YLY pre-60S State NE2 (TAP-Flag-Nop53) Deposited 2020-04-07 Different construct 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 c 1–105（105 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6Z6J Cryo-EM structure of yeast Lso2 bound to 80S ribosomes under native condition Deposited 2020-05-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain Lc 1–105（105 aa）
Not recorded ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6Z6K Cryo-EM structure of yeast reconstituted Lso2 bound to 80S ribosomes Deposited 2020-05-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain Lc 1–105（105 aa）
Not recorded ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7B7D Yeast 80S ribosome bound to eEF3 and A/A- and P/P-tRNAs Deposited 2020-12-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain LY 9–104（96 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.30 Å
7BT6 Cryo-EM structure of pre-60S ribosome from Saccharomyces cerevisiae rpl4delta63-87 strain at 3.12 Angstroms resolution(state R1) Deposited 2020-03-31 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain c 1–105（105 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.12 Å
7BTB Cryo-EM structure of pre-60S ribosome from Saccharomyces cerevisiae rpl4delta63-87 strain at 3.22 Angstroms resolution(state R2) Deposited 2020-04-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 53-meric
Chain c 1–105（105 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.22 Å
7MPI Stm1 bound vacant 80S structure isolated from cbf5-D95A Deposited 2021-05-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain Ac 9–105（97 aa）
Not recorded MG MAGNESIUM ION × 366 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
7MPJ Stm1 bound vacant 80S structure isolated from wild-type Deposited 2021-05-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain Ac 9–105（97 aa）
Not recorded MG MAGNESIUM ION × 745 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
7N8B Cycloheximide bound vacant 80S structure isolated from cbf5-D95A Deposited 2021-06-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain Ac 9–105（97 aa）
Not recorded 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 MG MAGNESIUM ION × 374 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
7NAC State E2 nucleolar 60S ribosomal biogenesis intermediate - Composite model Deposited 2021-06-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 58-meric
Chain c 1–105（105 aa）
Not recorded ZN ZINC ION × 2 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
7NAD State E2 nucleolar 60S ribosomal biogenesis intermediate - Spb4 local refinement model Deposited 2021-06-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain c 1–105（105 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
7NRC Structure of the yeast Gcn1 bound to a leading stalled 80S ribosome with Rbg2, Gir2, A- and P-tRNA and eIF5A Deposited 2021-03-03 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 86-meric
Chain Le 9–104（96 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.90 Å
7NRD Structure of the yeast Gcn1 bound to a colliding stalled 80S ribosome with MBF1, A/P-tRNA and P/E-tRNA Deposited 2021-03-03 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain Le 9–104（96 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.36 Å
7OF1 Nog1-TAP associated immature ribosomal particle population A from S. cerevisiae Deposited 2021-05-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 39 PDB declaration: 42-meric
Chain c 1–105（105 aa）
Not recorded MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7OH3 Nog1-TAP associated immature ribosomal particle population B from S. cerevisiae Deposited 2021-05-08 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 c 1–105（105 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7OHQ Nog1-TAP associated immature ribosomal particle population C from S. cerevisiae Deposited 2021-05-11 Different construct 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: 56-meric
Chain c 1–105（105 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7OHR Nog1-TAP associated immature ribosomal particle population E from S. cerevisiae Deposited 2021-05-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 51-meric
Chain c 1–105（105 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.72 Å
7R72 State E1 nucleolar 60S ribosome biogenesis intermediate - Spb4 local model Deposited 2021-06-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 22 PDB declaration: 24-meric
Chain c 1–105（105 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.07 Å
7R7A State E1 nucleolar 60S ribosome biogenesis intermediate - Composite model Deposited 2021-06-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric
Chain c 1–105（105 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
7RR5 Structure of ribosomal complex bound with Rbg1/Tma46 Deposited 2021-08-09 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: 87-meric
Chain Lc 1–105（105 aa）
Not recorded MG MAGNESIUM ION × 286 ASP ASPARTIC ACID × 1 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.23 Å
7TOO Yeast 80S ribosome bound with the ALS/FTD-associated dipeptide repeat protein GR20 Deposited 2022-01-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 48-meric
Chain AL30 1–105（105 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
7TOP Yeast 80S ribosome bound with the ALS/FTD-associated dipeptide repeat protein PR20 Deposited 2022-01-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 48-meric
Chain AL30 1–105（105 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
7U0H State NE1 nucleolar 60S ribosome biogenesis intermediate - Overall model Deposited 2022-02-18 Different construct 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 c 1–105（105 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.76 Å
7UG6 Cryo-EM structure of pre-60S ribosomal subunit, unmethylated G2922 Deposited 2022-03-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 52-meric
Chain 7 1–105（105 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；One blotting step of 2 seconds at force 0
Resolution 2.90 Å
7UOO Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state Deposited 2022-04-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain c 1–105（105 aa）
Not recorded MG MAGNESIUM ION × 81 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.34 Å
7UQB Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a SPB1-D52A strain with AlF4 Deposited 2022-04-19 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain c 1–105（105 aa）
Not recorded B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 MG MAGNESIUM ION × 81 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 2 ALF TETRAFLUOROALUMINATE ION × 1 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.43 Å
7UQZ Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a SPB1 D52A strain Deposited 2022-04-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain c 1–105（105 aa）
Not recorded MG MAGNESIUM ION × 81 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 2 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.44 Å
7V08 Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a Spb1 D52A suppressor 3 strain Deposited 2022-05-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain c 1–105（105 aa）
Not recorded MG MAGNESIUM ION × 81 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 2 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.36 Å
7Z34 Structure of pre-60S particle bound to DRG1(AFG2). Deposited 2022-03-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 58-meric
Chain c 1–105（105 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 11 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7ZPQ Structure of the RQT-bound 80S ribosome from S. cerevisiae (C1) Deposited 2022-04-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain Bb 9–104（96 aa）
Not recorded MG MAGNESIUM ION × 86 ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.47 Å
7ZRS Structure of the RQT-bound 80S ribosome from S. cerevisiae (C2) - composite map Deposited 2022-05-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain Bb 9–104（96 aa）
Not recorded MG MAGNESIUM ION × 4 ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
7ZS5 Structure of 60S ribosomal subunit from S. cerevisiae with eIF6 and tRNA Deposited 2022-05-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 42 PDB declaration: 45-meric
Chain Bd 9–105（97 aa）
Not recorded MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7ZUW Structure of RQT (C1) bound to the stalled ribosome in a disome unit from S. cerevisiae Deposited 2022-05-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain Bb 9–104（96 aa）
Not recorded MG MAGNESIUM ION × 86 ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
7ZUX Collided ribosome in a disome unit from S. cerevisiae Deposited 2022-05-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 80-meric
Chain Eb 9–104（96 aa）
Not recorded MG MAGNESIUM ION × 86 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
7ZW0 FAP-80S Complex - Rotated state Deposited 2022-05-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 86-meric
Chain Lf 1–105（105 aa）
Not recorded MG MAGNESIUM ION × 324 SPD SPERMIDINE × 1 ZN ZINC ION × 34 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
8AAF Yeast RQC complex in state G Deposited 2022-07-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 54-meric
Chain P 1–105（105 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
8AGT Yeast RQC complex in state F Deposited 2022-07-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 54-meric
Chain P 1–105（105 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8AGU Yeast RQC complex in state E Deposited 2022-07-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 53-meric
Chain P 1–105（105 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8AGV Yeast RQC complex in state H Deposited 2022-07-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 54-meric
Chain P 1–105（105 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8AGW Yeast RQC complex in state D Deposited 2022-07-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 53-meric
Chain P 1–105（105 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8AGX Yeast RQC complex in state with the RING domain of Ltn1 in the IN position Deposited 2022-07-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 52-meric
Chain P 1–105（105 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
8AGZ Yeast RQC complex in state with the RING domain of Ltn1 in the OUT position Deposited 2022-07-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 54-meric
Chain P 1–105（105 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8BIP Structure of a yeast 80S ribosome-bound N-Acetyltransferase B complex Deposited 2022-11-02 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain Lc 9–104（96 aa）
Not recorded MG MAGNESIUM ION × 206 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8BJQ Structure of a yeast 80S ribosome-bound N-Acetyltransferase B complex Deposited 2022-11-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain Lc 9–104（96 aa）
Not recorded MG MAGNESIUM ION × 206 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8BN3 Yeast 80S, ES7s delta, eIF5A, Stm1 containing Deposited 2022-11-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 81-meric
Chain O0 9–105（97 aa）
Not recorded MG MAGNESIUM ION × 220 K POTASSIUM ION × 72 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 SPD SPERMIDINE × 3 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.40 Å
8BQD Yeast 80S ribosome in complex with Map1 (conformation 1) Deposited 2022-11-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain AY 9–104（96 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8BQX Yeast 80S ribosome in complex with Map1 (conformation 2) Deposited 2022-11-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain AY 9–104（96 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8CCS 80S S. cerevisiae ribosome with ligands in hybrid-1 pre-translocation (PRE-H1) complex Deposited 2023-01-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain O 1–105（105 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 281 K POTASSIUM ION × 22 SPD SPERMIDINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.97 Å
8CDL 80S S. cerevisiae ribosome with ligands in hybrid-2 pre-translocation (PRE-H2) complex Deposited 2023-01-31 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain O 1–105（105 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 258 K POTASSIUM ION × 21 SPD SPERMIDINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.72 Å
8CDR Translocation intermediate 2 (TI-2) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-01-31 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain O 1–105（105 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 267 SPD SPERMIDINE × 4 K POTASSIUM ION × 21 GDP GUANOSINE-5'-DIPHOSPHATE × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.04 Å
8CEH Translocation intermediate 4 (TI-4) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-02-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain O 1–105（105 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 262 K POTASSIUM ION × 21 SPD SPERMIDINE × 3 GDP GUANOSINE-5'-DIPHOSPHATE × 1 PO4 PHOSPHATE ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.05 Å
8CF5 Translocation intermediate 1 (TI-1) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-02-02 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain O 1–105（105 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 241 K POTASSIUM ION × 21 SPD SPERMIDINE × 11 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.71 Å
8CG8 Translocation intermediate 3 (TI-3) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-02-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain O 1–105（105 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 241 SPD SPERMIDINE × 8 K POTASSIUM ION × 19 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.57 Å
8CGN Non-rotated 80S S. cerevisiae ribosome with ligands Deposited 2023-02-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain O 1–105（105 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 263 K POTASSIUM ION × 19 SPD SPERMIDINE × 4 MET METHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.28 Å
8CIV Translocation intermediate 5 (TI-5) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-02-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain O 1–105（105 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 251 K POTASSIUM ION × 21 SPD SPERMIDINE × 3 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.47 Å
8CKU Translocation intermediate 1 (TI-1*) of 80S S. cerevisiae ribosome with ligands and eEF2 in the absence of sordarin Deposited 2023-02-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain O 1–105（105 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 205 K POTASSIUM ION × 16 SPD SPERMIDINE × 3 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.11 Å
8CMJ Translocation intermediate 4 (TI-4*) of 80S S. cerevisiae ribosome with eEF2 in the absence of sordarin Deposited 2023-02-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain O 1–105（105 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 153 K POTASSIUM ION × 10 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.79 Å
8EUB Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2 and GDP, Structure I Deposited 2022-10-18 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain Ac 1–105（105 aa）
Not recorded MG MAGNESIUM ION × 255 ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.52 Å
8EVP Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), Structure I Deposited 2022-10-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain Ac 1–105（105 aa）
Not recorded MG MAGNESIUM ION × 256 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.38 Å
8EVQ Hypopseudouridylated Ribosome bound with TSV IRES, eEF2, GDP, and sordarin, Structure I Deposited 2022-10-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain Ac 1–105（105 aa）
Not recorded MG MAGNESIUM ION × 241 ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.72 Å
8EVR Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure II Deposited 2022-10-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain Ac 1–105（105 aa）
Not recorded MG MAGNESIUM ION × 217 ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 W9C (1S,3S,3aR,4S,4aR,7R,7aR,8aS)-8a-{[(6-deoxy-4-O-methyl-alpha-D-altropyranosyl)oxy]methyl}-4-formyl-7-methyl-3-(propan-2-yl)decahydro-1,4-methano-s-indacene-3a(1H)-carboxylate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.87 Å
8EVS Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2 and GDP, Structure II Deposited 2022-10-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain Ac 1–105（105 aa）
Not recorded MG MAGNESIUM ION × 254 ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.62 Å
8EVT Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES) refined against a composite map Deposited 2022-10-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain Ac 1–105（105 aa）
Not recorded MG MAGNESIUM ION × 272 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.20 Å
8EWB Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2 and GDP, Structure III Deposited 2022-10-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain Ac 1–105（105 aa）
Not recorded MG MAGNESIUM ION × 242 ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.87 Å
8EWC Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), Structure II Deposited 2022-10-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain Ac 1–105（105 aa）
Not recorded MG MAGNESIUM ION × 247 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.45 Å
8HFR NPC-trapped pre-60S particle Deposited 2022-11-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 58 PDB declaration: 61-meric
Chain cC 1–105（105 aa）
Not recorded MG MAGNESIUM ION × 237 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.64 Å
8K2D Cryo-EM structure of the yeast 80S ribosome with tigecycline, eEF2, Stm1 and eIF5A Deposited 2023-07-12 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 Lc 1–105（105 aa）
Not recorded ZN ZINC ION × 9 T1C TIGECYCLINE × 6 MG MAGNESIUM ION × 4 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8K82 Cryo-EM structure of the yeast 80S ribosome with tigecycline, Not5 and P-site tRNA Deposited 2023-07-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 85-meric
Chain Lc 1–105（105 aa）
Not recorded MG MAGNESIUM ION × 316 T1C TIGECYCLINE × 6 SPD SPERMIDINE × 1 ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8P4V 80S yeast ribosome in complex with HaterumaimideQ Deposited 2023-05-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain AD 1–105（105 aa）
Not recorded OHX osmium (III) hexammine × 461 MG MAGNESIUM ION × 711 K POTASSIUM ION × 2 SPD SPERMIDINE × 1 X1K (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},8~{a}~{S})-5,5,8~{a}-trimethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 ZN ZINC ION × 8 OS OSMIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 3.16 Å R-free 0.251
8P4V 80S yeast ribosome in complex with HaterumaimideQ Deposited 2023-05-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain DE 1–105（105 aa）
Not recorded OHX osmium (III) hexammine × 492 MG MAGNESIUM ION × 766 K POTASSIUM ION × 5 SPD SPERMIDINE × 1 X1K (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},8~{a}~{S})-5,5,8~{a}-trimethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 ZN ZINC ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 3.16 Å R-free 0.251
8P85 80S yeast ribosome in complex with Fluorolissoclimide Deposited 2023-08-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain AD 1–105（105 aa）
Not recorded OHX osmium (III) hexammine × 484 MG MAGNESIUM ION × 717 K POTASSIUM ION × 2 SPD SPERMIDINE × 1 VDU fluorolissoclimide × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 2.90 Å R-free 0.223
8P85 80S yeast ribosome in complex with Fluorolissoclimide Deposited 2023-08-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain DE 1–105（105 aa）
Not recorded OHX osmium (III) hexammine × 519 MG MAGNESIUM ION × 785 K POTASSIUM ION × 2 SPD SPERMIDINE × 1 VDU fluorolissoclimide × 1 ZN ZINC ION × 9 5XU (2~{S})-2-azanylpropanal × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 2.90 Å R-free 0.223
8P8M Yeast 60S ribosomal subunit, RPL39 deletion Deposited 2023-06-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain RC 1–105（105 aa）
Not recorded MG MAGNESIUM ION × 156 SPM SPERMINE × 1 SPD SPERMIDINE × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.66 Å
8P8N Mouse RPL39 integrated into the yeast 60S ribosomal subunit Deposited 2023-06-02 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain RC 1–105（105 aa）
Not recorded MG MAGNESIUM ION × 152 CL CHLORIDE ION × 20 SPD SPERMIDINE × 1 SPM SPERMINE × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.15 Å
8P8U Yeast 60S ribosomal subunit Deposited 2023-06-02 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain RC 1–105（105 aa）
Not recorded MG MAGNESIUM ION × 129 CL CHLORIDE ION × 24 SPM SPERMINE × 1 SPD SPERMIDINE × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.23 Å
8P9A 80S yeast ribosome in complex with Methyllissoclimide Deposited 2023-06-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 150 PDB declaration: 158-meric
Chain AD 1–105（105 aa）
Chain DE 1–105（105 aa）
Not recorded OHX osmium (III) hexammine × 930 MG MAGNESIUM ION × 1464 SPD SPERMIDINE × 2 XBI (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},7~{S},8~{a}~{S})-5,5,7,8~{a}-tetramethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 2 ZN ZINC ION × 18 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 2.90 Å
8PFR Mouse RPL39L integrated into the yeast 60S ribosomal subunit Deposited 2023-06-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain RC 1–105（105 aa）
Not recorded MG MAGNESIUM ION × 170 CL CHLORIDE ION × 24 SPM SPERMINE × 1 SPD SPERMIDINE × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；50mM Hepes pH 7.6, 200 mM KCl, 10 mM MgCl2, 5 mM EDTA, 2 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；30s pre-blot incubation
Resolution 2.15 Å
8PNN 80S yeast ribosome in complex with Bromolissoclimide Deposited 2023-06-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain AD 1–105（105 aa）
Not recorded OHX osmium (III) hexammine × 456 MG MAGNESIUM ION × 707 ZN ZINC ION × 8 K POTASSIUM ION × 1 ZWB (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},7~{S},8~{a}~{S})-7-bromanyl-5,5,8~{a}-trimethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 SPD SPERMIDINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 2.90 Å R-free 0.230
8PNN 80S yeast ribosome in complex with Bromolissoclimide Deposited 2023-06-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain DE 1–105（105 aa）
Not recorded OHX osmium (III) hexammine × 479 MG MAGNESIUM ION × 783 ZN ZINC ION × 7 K POTASSIUM ION × 3 ZWB (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},7~{S},8~{a}~{S})-7-bromanyl-5,5,8~{a}-trimethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 SPD SPERMIDINE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 2.90 Å R-free 0.230
8T2X Hypomethylated yeast 80S bound with cycloheximide, P-site tRNA, A-site tRNA, messenger RNA and eIF5A, PRE Deposited 2023-06-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain Ac 1–105（105 aa）
Not recorded MG MAGNESIUM ION × 181 K POTASSIUM ION × 23 SPD SPERMIDINE × 1 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.46 Å
8T2Y Hypomethylated yeast 80S bound with cycloheximide, P-site tRNA, and A-site tRNA, messenger RNA, PRE Deposited 2023-06-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 81-meric
Chain Ac 1–105（105 aa）
Not recorded MG MAGNESIUM ION × 197 SPD SPERMIDINE × 1 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.20 Å
8T2Z Hypomethylated yeast 80S bound with cycloheximide, P-site tRNA, and A-site tRNA, messenger RNA, POST Deposited 2023-06-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 81-meric
Chain Ac 1–105（105 aa）
Not recorded SPD SPERMIDINE × 1 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
8T30 Hypomethylated yeast 80S bound with cycloheximide, unmodified U2921, mid rotated Deposited 2023-06-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain Ac 1–105（105 aa）
Not recorded SPD SPERMIDINE × 1 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.88 Å
8T3A Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, sordarin, and hibernating factor Los2 Deposited 2023-06-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain Ac 1–105（105 aa）
Not recorded ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.86 Å
8T3B Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure I Deposited 2023-06-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 81-meric
Chain Ac 1–105（105 aa）
Not recorded ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.08 Å
8T3C Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure II Deposited 2023-06-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 81-meric
Chain Ac 1–105（105 aa）
Not recorded ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.86 Å
8T3D Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure III Deposited 2023-06-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 81-meric
Chain Ac 1–105（105 aa）
Not recorded ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.95 Å
8T3E Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure IV Deposited 2023-06-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 81-meric
Chain Ac 1–105（105 aa）
Not recorded ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
8T3F Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure V Deposited 2023-06-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 81-meric
Chain Ac 1–105（105 aa）
Not recorded ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.09 Å
8UT0 Eukaryotic 80S ribosome with Reh1, eIF5A and A/P site tRNA Deposited 2023-10-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain Le 9–104（96 aa）
Not recorded 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.22 Å
8UTI Eukaryotic 80S ribosome with Reh1 and A/P site tRNA Deposited 2023-10-31 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain Le 9–104（96 aa）
Not recorded 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.13 Å
8V87 60S ribosome biogenesis intermediate (Dbp10 post-catalytic structure - Overall map) Deposited 2023-12-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 56-meric
Chain c 1–105（105 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 1 K POTASSIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.66 Å
8XU8 State 2c(S2c) of yeast 80S ribosome bound to compact eEF2 and 2 tRNAs during peptidyl transferation Deposited 2024-01-12 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-meric
Chain e 9–104（96 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 4.5；YPD
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8Y0U dormant ribosome with STM1 Deposited 2024-01-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 73 PDB declaration: 77-meric
Chain Lc 1–105（105 aa）
Not recorded MG MAGNESIUM ION × 281 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；50mM HEPES, pH7.5, 100mM KOAc, 5mM Mg(OAc)2, 1mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.59 Å
8YLD State 4a (S4a) of yeast 80S ribosome bound to 2 tRNAs and open eEF3 and eEF2 during translocation Deposited 2024-03-06 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain e 9–104（96 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 4.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8YLR State 6 (S6) of yeast 80S ribosome bound to 2 tRNAs and eEF2 and eEF3 during tranlocation Deposited 2024-03-06 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain e 9–104（96 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 4.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8Z70 State 1 (S1) of yeast 80S ribosome bound to 2 tRNAs during mRNA decoding Deposited 2024-04-19 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-meric
Chain e 9–104（96 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 4.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8Z71 State 1a (S1a) of yeast 80S ribosome bound to open eEF3 and 2 tRNAs and eEF1A during mRNA decoding Deposited 2024-04-19 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain e 9–104（96 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 4.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8ZGR 80S ribosome with A/A tRNA and mRNA of WNV Deposited 2024-05-09 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 79-meric
Chain Le 9–104（96 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8ZGY 80S ribosome with P/E tRNA and mRNA of WNV Deposited 2024-05-10 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 80-meric
Chain Le 9–104（96 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
8ZH3 80S ribosome with A/P-P/E tRNA and mRNA of WNV Deposited 2024-05-10 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 81-meric
Chain Le 9–104（96 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8ZHB 80S ribosome with A/A P/E tRNA and mRNA of WNV Deposited 2024-05-10 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 81-meric
Chain Le 9–104（96 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8ZHC pre-frameshift complex of yeast 80S ribosome with eRF1 and mRNA of WNV Deposited 2024-05-10 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain Le 9–104（96 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.30 Å
9DOV Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES) and hygromycin B Deposited 2024-09-19 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain Ac 1–105（105 aa）
Not recorded MG MAGNESIUM ION × 257 HYG HYGROMYCIN B × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.49 Å
9DP7 Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES) and hygromycin B, Class II Deposited 2024-09-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain Ac 1–105（105 aa）
Not recorded MG MAGNESIUM ION × 247 HYG HYGROMYCIN B × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.38 Å
9F58 Gcn2 dimer bound to the 60S ribosomal subunit Deposited 2024-04-28 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 N 1–105（105 aa）
Not recorded ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.10 Å
9F9S Yeast SDD1 Disome with Mbf1 Deposited 2024-05-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 152 PDB declaration: 164-meric
Chain Lo 1–105（105 aa）
Chain Mo 1–105（105 aa）
Not recorded MG MAGNESIUM ION × 295 ZN ZINC ION × 13 K POTASSIUM ION × 16 SPD SPERMIDINE × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9OFV Consensus reconstruction of the eukaryotic Ribosome-associated Quality Control complex Deposited 2025-04-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 59 PDB declaration: 64-meric
Chain P 1–105（105 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 9 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ZN ZINC ION × 7 MG MAGNESIUM ION × 12 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.16 Å
9PN5 Composite map of hypomethylated 80S ribosome treated with hygromycin B Deposited 2025-07-19 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain Ac 1–105（105 aa）
Not recorded MG MAGNESIUM ION × 174 K POTASSIUM ION × 27 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.75 Å
9R9O Yeast 80S with nascent chain in complex with Ssb1-ADP in the S1 state Deposited 2025-05-20 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 73 PDB declaration: 79-meric
Chain Lc 1–105（105 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9R9P Yeast 80S with nascent chain in complex with Ssb1-ADP in the S2 state Deposited 2025-05-20 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 73 PDB declaration: 79-meric
Chain Lc 1–105（105 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å

215 other PDB entries and 255 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RL30_YEAST
Isoform —
PDB entities 4
Chains and sequence ranges Author chain B； PDBConstruct 1–105； UniProt 0–104

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 1t0k

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1t0k
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1t0k
Deposition date deposition_date2004-04-09
Structure title titleJoint X-ray and NMR Refinement of Yeast L30e-mRNA complex
Keywords keywordsJoint NMR and X-ray refinement, Ribosomal Protein L30e, MBP fusion protein, RIBOSOME; 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_guinier31.56 Å
Radius of gyration Rg (electron density) rg_electron29.74 Å
Forward intensity I(0) i066639800.00
Molecular weight molecular_weight59921.0 kDa
Excluded volume excluded_volume73114 ų
Envelope volume envelope_volume94753 ų
Hydration-shell volume shell_volume28563 ų
Envelope diameter envelope_diameter104.7 Å
Shell Rg shell_rg34.50 Å
Envelope Rg envelope_rg29.59 Å
Shape Rg shape_rg29.61 Å
Total Rg total_rg30.55 Å
Total atoms total_atoms4194
Residues n_residues489
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 dmax105.8 Å
Rg (real space) rg_real31.82 Å
Rg uncertainty (real space) rg_real_error1.33 Å
I(0) (real space) i0_real6.6640e+07
I(0) uncertainty (real space) i0_real_error1.1100e+06
Rg (reciprocal space) rg_reciprocal31.72 Å
I(0) (reciprocal space) i0_reciprocal66630000.0000
Solution quality estimate total_estimate0.8512
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary27.5 Å
Skewness Skewness skewness0.429
Kurtosis Kurtosis kurtosis-0.604
Angular range angular_range— – 0.2500 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha7057000.0000
Real-space data points n_real_points51
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.809; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.771; Smooth: 0.865
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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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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd1t0ka1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.94 — Periplasmic binding protein-like II
Superfamily Superfamily superfamilyc.94.1 — Periplasmic binding protein-like II
Family Family familyc.94.1.1 — Phosphate binding protein-like
Domain ID domain_idd1t0ka2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd1t0kb_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamilyd.79.3 — L30e-like
Family Family familyd.79.3.1 — L30e/L7ae ribosomal proteins

CATH v4.4 (3 domains)

Domain ID domain_id1t0kA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily10 — Periplasmic binding protein-like II
Domain ID domain_id1t0kA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily10 — Periplasmic binding protein-like II
Domain ID domain_id1t0kB00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily30 — Ribosomal protein L30/S12
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8. Citations (1)

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9. Files and Curves (10)