Current Protein Identity：P0CH08
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Difference tags compare only the current result set; every original PDB and assembly record remains separate.
Related-Structure Differences
Each row represents one biological assembly in one PDB entry; multiple monomers of the same protein are listed separately.
| PDB Entry | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Experimental Method | Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 3J6X S. cerevisiae 80S ribosome bound with Taura syndrome virus (TSV) IRES, 5 degree rotation (Class II) Deposited 2014-04-16 | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric（80） Consistent with all polymers |
Chain 80
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric（80） Consistent with all polymers |
Chain 80
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 83-meric（83） Consistent with all polymers |
Chain 90
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric（84） Consistent with all polymers |
Chain 90
1–128（128 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 |
| 4U3M Crystal structure of Anisomycin bound to the yeast 80S ribosome Deposited 2014-07-22 | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric（79） Consistent with all polymers |
Chain Q0
77–128（52 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 | Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric（83） Consistent with all polymers |
Chain q0
77–128（52 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 | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric（80） Consistent with all polymers |
Chain Q0
77–128（52 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 | Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 84-meric（84） Consistent with all polymers |
Chain q0
77–128（52 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 | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric（79） Consistent with all polymers |
Chain Q0
77–128（52 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 | Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric（83） Consistent with all polymers |
Chain q0
77–128（52 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 | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric（79） Consistent with all polymers |
Chain Q0
77–128（52 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 | Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric（83） Consistent with all polymers |
Chain q0
77–128（52 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 | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric（79） Consistent with all polymers |
Chain Q0
77–128（52 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 | Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric（83） Consistent with all polymers |
Chain q0
77–128（52 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 | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric（79） Consistent with all polymers |
Chain Q0
77–128（52 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 | Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric（83） Consistent with all polymers |
Chain q0
77–128（52 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 | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric（79） Consistent with all polymers |
Chain Q0
77–128（52 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 | Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric（83） Consistent with all polymers |
Chain q0
77–128（52 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 | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-MERIC（79） Consistent with all polymers |
Chain Q0
77–128（52 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 | Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-MERIC（83） Consistent with all polymers |
Chain q0
77–128（52 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 | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric（79） Consistent with all polymers |
Chain Q0
77–128（52 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 | Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 85-meric（85） Review required |
Chain q0
77–128（52 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 | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric（80） Review required |
Chain Q0
77–128（52 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 | Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 95-meric（95） Review required |
Chain q0
77–128（52 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 | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric（79） Consistent with all polymers |
Chain Q0
77–128（52 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 | Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric（83） Consistent with all polymers |
Chain q0
77–128（52 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 | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric（79） Consistent with all polymers |
Chain Q0
77–128（52 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 | Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric（83） Consistent with all polymers |
Chain q0
77–128（52 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 | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric（79） Consistent with all polymers |
Chain Q0
77–128（52 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 | Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric（83） Consistent with all polymers |
Chain q0
77–128（52 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 | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric（79） Consistent with all polymers |
Chain Q0
77–128（52 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 | Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric（83） Consistent with all polymers |
Chain q0
77–128（52 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 | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-MERIC（79） Consistent with all polymers |
Chain Q0
77–128（52 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 | Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-MERIC（83） Consistent with all polymers |
Chain q0
77–128（52 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 | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric（80） Review required |
Chain Q0
77–128（52 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 | Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 85-meric（85） Review required |
Chain q0
77–128（52 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 | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric（79） Consistent with all polymers |
Chain Q0
77–128（52 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 | Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric（83） Consistent with all polymers |
Chain q0
77–128（52 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 | Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 86-meric（86） Consistent with all polymers |
Chain Bp
77–128（52 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 |
| 4V88 The structure of the eukaryotic ribosome at 3.0 A resolution. Deposited 2011-10-11 | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric（79） Consistent with all polymers |
Chain Bm
1–128（128 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 | Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric（83） Consistent with all polymers |
Chain Dm
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 50-meric（50） Consistent with all polymers |
Chain m
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 87-meric（87） Consistent with all polymers |
Chain Bm
1–128（128 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 | Assembly 1 Insufficient information Heteromer；Protein × 79 PDB declaration: 85-meric（85） Consistent with all polymers |
Chain Bm
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric（47） Consistent with all polymers |
Chain m
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric（47） Consistent with all polymers |
Chain m
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 86-MERIC（86） Review required |
Chain q0
77–128（52 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 | Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 86-MERIC（86） Review required |
Chain Q0
77–128（52 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 | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-meric（81） Review required |
Chain Q0
77–128（52 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 | Assembly 2 Protein–RNA Heteromer；Protein × 80 PDB declaration: 81-meric（81） Review required |
Chain q0
77–128（52 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 | Assembly 1 Protein–RNA Heteromer；Protein × 155 PDB declaration: 165-meric（165） Consistent with all polymers |
Chain Q0
77–128（52 aa）
Chain q0
77–128（52 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 | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: TRIMERIC（83） Review required |
Chain Q0
77–128（52 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 | Assembly 2 Protein–RNA Heteromer；Protein × 80 PDB declaration: TRIMERIC（81） Review required |
Chain q0
77–128（52 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 | Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 81-MERIC（81） Review required |
Chain q0
77–128（52 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 | Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-MERIC（81） Review required |
Chain Q0
77–128（52 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 | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric（79） Review required |
Chain Q0
77–128（52 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 | Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric（83） Consistent with all polymers |
Chain q0
77–128（52 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 | Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 82-meric（82） Review required |
Chain q0
77–128（52 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 | Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric（79） Consistent with all polymers |
Chain Q0
77–128（52 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 | Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 49-meric（49） Consistent with all polymers |
Chain o
1–128（128 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 |
| 5I4L Crystal structure of Amicoumacin A bound to the yeast 80S ribosome Deposited 2016-02-12 | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric（79） Consistent with all polymers |
Chain Q0
77–128（52 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 | Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric（83） Consistent with all polymers |
Chain q0
77–128（52 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 |
| 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 | Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric（83） Consistent with all polymers |
Chain RA
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric（83） Consistent with all polymers |
Chain RA
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric（83） Consistent with all polymers |
Chain RA
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric（83） Consistent with all polymers |
Chain RA
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric（83） Consistent with all polymers |
Chain RA
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric（80） Consistent with all polymers |
Chain Q0
77–128（52 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 | Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 84-meric（84） Consistent with all polymers |
Chain q0
77–128（52 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 | Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric（82） Consistent with all polymers |
Chain m5
77–128（52 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 | Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 87-meric（87） Consistent with all polymers |
Chain AO
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 78-meric（78） Review required |
Chain AN
77–128（52 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 | Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric（80） Consistent with all polymers |
Chain DO
77–128（52 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 | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric（79） Consistent with all polymers |
Chain Q0
77–128（52 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 | Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric（80） Consistent with all polymers |
Chain q0
77–128（52 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 | Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric（78） Consistent with all polymers |
Chain q0
77–128（52 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 | Assembly 2 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric（78） Consistent with all polymers |
Chain Q0
77–128（52 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 | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric（79） Consistent with all polymers |
Chain q0
77–128（52 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 | Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric（79） Consistent with all polymers |
Chain Q0
77–128（52 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 | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-MERIC（79） Consistent with all polymers |
Chain Q0
77–128（52 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 | Assembly 2 Protein–RNA Heteromer；Protein × 78 PDB declaration: 82-MERIC（82） Consistent with all polymers |
Chain q0
77–128（52 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 | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 78-meric（79） Consistent with all polymers |
Chain AN
77–128（52 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 | Assembly 2 Protein–RNA Heteromer；Protein × 77 PDB declaration: 80-meric（80） Review required |
Chain DO
77–128（52 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 | Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric（47） Consistent with all polymers |
Chain z
1–128（128 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 | Assembly 1 Insufficient information Heteromer；Protein × 42 PDB declaration: 45-meric（45） Consistent with all polymers |
Chain z
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric（79） Consistent with all polymers |
Chain AN
77–128（52 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 | Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric（80） Consistent with all polymers |
Chain DO
77–128（52 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 | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric（80） Consistent with all polymers |
Chain Q0
77–128（52 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 | Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 84-meric（84） Consistent with all polymers |
Chain q0
77–128（52 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 | Assembly 1 Protein–RNA Heteromer；Protein × 154 PDB declaration: 164-meric（164） Consistent with all polymers |
Chain Q0
77–128（52 aa）
Chain q0
77–128（52 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 |
| 6EF3 Yeast 26S proteasome bound to ubiquitinated substrate (4D motor state) Deposited 2018-08-15 | Assembly 1 Protein heterocomplex Heteromer；Protein × 24 PDB declaration: 24-meric（24） Consistent with protein count |
Chain u
1–128（128 aa）
|
Not recorded | ATP ADENOSINE-5'-TRIPHOSPHATE × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE；specimens were manually blotted with Whatman #1 filter paper
|
Resolution 4.17 Å |
| 6GQ1 Cryo-EM reconstruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GMPPCP/sordarin) Deposited 2018-06-07 | Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 83-meric（83） Consistent with all polymers |
Chain m
77–128（52 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 | Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 84-meric（84） Consistent with all polymers |
Chain m
77–128（52 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 | Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 84-meric（84） Consistent with all polymers |
Chain m
77–128（52 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 | Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 51-meric（51） Consistent with all polymers |
Chain o
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric（79） Consistent with all polymers |
Chain AN
1–128（128 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 | Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric（80） Consistent with all polymers |
Chain DO
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 150 PDB declaration: 163-meric（163） Consistent with all polymers |
Chain AO
77–128（52 aa）
Chain XO
77–128（52 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 |
| 6N8M Cryo-EM structure of pre-Lsg1 (PL) pre-60S ribosomal subunit Deposited 2018-11-29 | Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric（47） Consistent with all polymers |
Chain z
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric（48） Consistent with all polymers |
Chain z
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric（49） Consistent with all polymers |
Chain z
1–128（128 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 |
| 6OA9 Cdc48-Npl4 complex processing poly-ubiquitinated substrate in the presence of ATP Deposited 2019-03-15 | Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric（10） Consistent with protein count |
Chain H
1–76（76 aa）
Chain J
1–76（76 aa）
Chain K
1–76（76 aa）
|
Not recorded | ATP ADENOSINE-5'-TRIPHOSPHATE × 9 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ZN ZINC ION × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE；Waited 20 seconds before blotting for 2.5-3 seconds.
|
Resolution 3.90 Å |
| 6OAA Cdc48-Npl4 complex processing poly-ubiquitinated substrate in the presence of ADP-BeFx, state 1 Deposited 2019-03-15 | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count |
Chain H
1–76（76 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 8 BEF BERYLLIUM TRIFLUORIDE ION × 6 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE；Waited 20 seconds before blotting for 2.5-3 seconds.
|
Resolution 4.10 Å |
| 6OIG Subunit joining exposes nascent pre-40S rRNA for processing and quality control Deposited 2019-04-09 | Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric（48） Consistent with all polymers |
Chain m
77–128（52 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 | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric（82） Consistent with all polymers |
Chain AO
77–128（52 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 | Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric（47） Consistent with all polymers |
Chain t
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 42 PDB declaration: 45-meric（45） Consistent with all polymers |
Chain t
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric（48） Consistent with all polymers |
Chain t
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 50-meric（50） Consistent with all polymers |
Chain o
77–128（52 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 | Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 47-meric（47） Review required |
Chain o
77–128（52 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 | Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 49-meric（49） Consistent with all polymers |
Chain o
77–128（52 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 | Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric（48） Consistent with all polymers |
Chain t
1–128（128 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 |
| 6S47 Saccharomyces cerevisiae 80S ribosome bound with ABCF protein New1 Deposited 2019-06-26 | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric（79） Consistent with all polymers |
Chain Ao
2–128（127 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 | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-meric（81） Consistent with all polymers |
Chain ad
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 225 PDB declaration: 242-meric（242） Consistent with all polymers |
Chain AO
1–128（128 aa）
Chain XO
1–128（128 aa）
Chain zO
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric（82） Consistent with all polymers |
Chain Lm
77–128（52 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 | Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 81-meric（81） Consistent with all polymers |
Chain Lm
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric（82） Consistent with all polymers |
Chain Lm
77–128（52 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 | Assembly 1 Protein–RNA Heteromer；Protein × 149 PDB declaration: 159-meric（159） Consistent with all polymers |
Chain X
1–128（128 aa）
Chain mb
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 83-meric（83） Consistent with all polymers |
Chain AO
77–128（52 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 | Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric（83） Consistent with all polymers |
Chain AO
77–128（52 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 | Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 84-meric（84） Consistent with all polymers |
Chain m
78–128（51 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 | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric（82） Consistent with all polymers |
Chain m
1–128（128 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 |
| 6Z6J Cryo-EM structure of yeast Lso2 bound to 80S ribosomes under native condition Deposited 2020-05-28 | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric（79） Consistent with all polymers |
Chain Lm
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric（79） Consistent with all polymers |
Chain Lm
1–128（128 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 |
| 7AZY Context-specific inhibition of eukaryotic translation by macrolide antibiotics Deposited 2020-11-17 | Assembly 1 Protein–RNA Heteromer；Protein × 39 PDB declaration: 42-meric（42） Consistent with all polymers |
Chain P
1–128（128 aa）
|
Not recorded | TEL TELITHROMYCIN × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.88 Å |
| 7B7D Yeast 80S ribosome bound to eEF3 and A/A- and P/P-tRNAs Deposited 2020-12-10 | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric（82） Consistent with all polymers |
Chain Li
77–128（52 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 |
| 7MPI Stm1 bound vacant 80S structure isolated from cbf5-D95A Deposited 2021-05-04 | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric（79） Consistent with all polymers |
Chain Am
77–128（52 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 | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric（79） Consistent with all polymers |
Chain Am
77–128（52 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 | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric（79） Consistent with all polymers |
Chain Am
77–128（52 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 |
| 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 | Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 86-meric（86） Consistent with all polymers |
Chain Lo
77–128（52 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 | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric（82） Consistent with all polymers |
Chain Lo
77–128（52 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 |
| 7TOO Yeast 80S ribosome bound with the ALS/FTD-associated dipeptide repeat protein GR20 Deposited 2022-01-24 | Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 48-meric（48） Consistent with all polymers |
Chain AL40
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 48-meric（48） Consistent with all polymers |
Chain AL40
1–128（128 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 |
| 7ZPQ Structure of the RQT-bound 80S ribosome from S. cerevisiae (C1) Deposited 2022-04-28 | Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric（82） Consistent with all polymers |
Chain Bl
77–128（52 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 | Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric（82） Consistent with all polymers |
Chain Bl
77–128（52 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 | Assembly 1 Protein–RNA Heteromer；Protein × 42 PDB declaration: 45-meric（45） Review required |
Chain Bn
77–128（52 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 | Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric（82） Consistent with all polymers |
Chain Bl
77–128（52 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 | Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 80-meric（80） Consistent with all polymers |
Chain El
77–128（52 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 | Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 86-meric（86） Consistent with all polymers |
Chain Lp
77–128（52 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 | Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 54-meric（54） Consistent with all polymers |
Chain Z
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 54-meric（54） Consistent with all polymers |
Chain Z
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 53-meric（53） Consistent with all polymers |
Chain Z
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 54-meric（54） Consistent with all polymers |
Chain Z
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 53-meric（53） Consistent with all polymers |
Chain Z
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 52-meric（52） Review required |
Chain Z
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 54-meric（54） Consistent with all polymers |
Chain Z
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric（47） Consistent with all polymers |
Chain Lm
77–128（52 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 | Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric（48） Consistent with all polymers |
Chain Lm
77–128（52 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 | Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 81-meric（81） Consistent with all polymers |
Chain Q0
77–128（52 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 | Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric（80） Consistent with all polymers |
Chain AO
77–128（52 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 | Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric（80） Consistent with all polymers |
Chain AO
77–128（52 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 |
| 8CAH Cryo-EM structure of native Otu2-bound ubiquitinated 43S pre-initiation complex Deposited 2023-01-24 | Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 48-meric（48） Consistent with all polymers |
Chain k
1–76（76 aa）
|
Not recorded | MG MAGNESIUM ION × 80 ZN ZINC ION × 2 SF4 IRON/SULFUR CLUSTER × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 8CAS Cryo-EM structure of native Otu2-bound ubiquitinated 48S initiation complex (partial) Deposited 2023-01-24 | Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 50-meric（50） Consistent with all polymers |
Chain y
1–76（76 aa）
|
Not recorded | ZN ZINC ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 5 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 SF4 IRON/SULFUR CLUSTER × 2 MET METHIONINE × 1 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 8CCS 80S S. cerevisiae ribosome with ligands in hybrid-1 pre-translocation (PRE-H1) complex Deposited 2023-01-27 | Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric（83） Consistent with all polymers |
Chain Y
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric（83） Consistent with all polymers |
Chain Y
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric（84） Consistent with all polymers |
Chain Y
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric（84） Consistent with all polymers |
Chain Y
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric（84） Consistent with all polymers |
Chain Y
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric（84） Consistent with all polymers |
Chain Y
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric（82） Consistent with all polymers |
Chain Y
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric（84） Consistent with all polymers |
Chain Y
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric（83） Consistent with all polymers |
Chain Y
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric（80） Consistent with all polymers |
Chain Y
1–128（128 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 |
| 8DAS Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex bound to two ubiquitin moieties in presence of SUMO-ubiquitin(K48polyUb)-mEOS and ATP, state 1 (intA) Deposited 2022-06-14 | Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric（10） Consistent with protein count |
Chain J
1–76（76 aa）
Chain K
1–76（76 aa）
|
Not recorded | ATP ADENOSINE-5'-TRIPHOSPHATE × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 7 ZN ZINC ION × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 8；20 mM HEPES pH 8.0, 150 mM NaCl, 0.1 mM TCEP, 1 mM MgCl2, 5 mM ATP. Added 0.05% CHAPSO before vitrification.
cryo-EM vitrification conditions
Cryogen ETHANE；8 s wait, 4 s blot before plunging
|
Resolution 3.50 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 | Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric（82） Consistent with all polymers |
Chain Am
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric（80） Consistent with all polymers |
Chain Am
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric（82） Consistent with all polymers |
Chain Am
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric（82） Consistent with all polymers |
Chain Am
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric（82） Consistent with all polymers |
Chain Am
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric（80） Consistent with all polymers |
Chain Am
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric（82） Consistent with all polymers |
Chain Am
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric（80） Consistent with all polymers |
Chain Am
1–128（128 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 |
| 8HTD Crystal structure of an effector from Chromobacterium violaceum in complex with ubiquitin Deposited 2022-12-21 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；100 mM sodium cacodylate, pH 6.5, 200 mM sodium acetate, 28% to 30% PEG 8000
|
Resolution 1.85 Å R-free 0.225 |
| 8HTE Crystal structure of an effector mutant in complex with ubiquitin Deposited 2022-12-21 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
1–76（76 aa）
|
Not recorded | SO4 SULFATE ION × 2 GOL GLYCEROL × 2 NCA NICOTINAMIDE × 1 AR6 [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；289 K；100 mM BIS-TRIS propane, pH 7.0, and 1.5 M ammonium sulfate
|
Resolution 2.31 Å R-free 0.228 |
| 8K2D Cryo-EM structure of the yeast 80S ribosome with tigecycline, eEF2, Stm1 and eIF5A Deposited 2023-07-12 | Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 84-meric（84） Consistent with all polymers |
Chain Lm
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 85-meric（85） Consistent with all polymers |
Chain Lm
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric（79） Consistent with all polymers |
Chain AN
1–128（128 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 | Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric（80） Consistent with all polymers |
Chain DO
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric（78） Consistent with all polymers |
Chain AN
1–128（128 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 | Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric（79） Consistent with all polymers |
Chain DO
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric（43） Consistent with all polymers |
Chain RO
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric（43） Consistent with all polymers |
Chain RO
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric（43） Consistent with all polymers |
Chain RO
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 150 PDB declaration: 158-meric（158） Consistent with all polymers |
Chain AN
1–128（128 aa）
Chain DO
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric（43） Consistent with all polymers |
Chain RO
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric（78） Consistent with all polymers |
Chain AN
1–128（128 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 | Assembly 2 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric（78） Consistent with all polymers |
Chain DO
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric（83） Consistent with all polymers |
Chain Am
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 81-meric（81） Consistent with all polymers |
Chain Am
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 81-meric（81） Consistent with all polymers |
Chain Am
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric（78） Consistent with all polymers |
Chain Am
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric（82） Consistent with all polymers |
Chain Am
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 81-meric（81） Consistent with all polymers |
Chain Am
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 81-meric（81） Consistent with all polymers |
Chain Am
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 81-meric（81） Consistent with all polymers |
Chain Am
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 81-meric（81） Consistent with all polymers |
Chain Am
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 81-meric（81） Consistent with all polymers |
Chain Am
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric（84） Consistent with all polymers |
Chain Lo
77–128（52 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 | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric（82） Consistent with all polymers |
Chain Lo
77–128（52 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 |
| 8XU8 State 2c(S2c) of yeast 80S ribosome bound to compact eEF2 and 2 tRNAs during peptidyl transferation Deposited 2024-01-12 | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-meric（81） Consistent with all polymers |
Chain o
77–128（52 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 | Assembly 1 Protein–RNA Heteromer；Protein × 73 PDB declaration: 77-meric（77） Consistent with all polymers |
Chain Lm
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric（82） Consistent with all polymers |
Chain o
77–128（52 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 | Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric（82） Consistent with all polymers |
Chain o
77–128（52 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 | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-meric（81） Consistent with all polymers |
Chain o
77–128（52 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 | Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric（82） Consistent with all polymers |
Chain o
77–128（52 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 | Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 79-meric（79） Consistent with all polymers |
Chain Lo
77–128（52 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 | Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 80-meric（80） Consistent with all polymers |
Chain Lo
77–128（52 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 | Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 81-meric（81） Consistent with all polymers |
Chain Lo
77–128（52 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 | Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 81-meric（81） Consistent with all polymers |
Chain Lo
77–128（52 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 | Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric（82） Consistent with all polymers |
Chain Lo
77–128（52 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 | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric（80） Consistent with all polymers |
Chain Am
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric（80） Consistent with all polymers |
Chain Am
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 50-meric（50） Consistent with all polymers |
Chain Y
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 152 PDB declaration: 164-meric（164） Consistent with all polymers |
Chain Le
1–128（128 aa）
Chain Me
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 59 PDB declaration: 64-meric（64） Consistent with all polymers |
Chain Z
1–128（128 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 | Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric（78） Consistent with all polymers |
Chain Am
1–128（128 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 |
| 9YRC p97Ufd1-Npl4 complex processing poly-ubiquitinated substrate in the presence of ATP Deposited 2025-10-16 | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric（9） Consistent with protein count |
Chain I
1–76（76 aa）
|
Not recorded | ATP ADENOSINE-5'-TRIPHOSPHATE × 8 ADP ADENOSINE-5'-DIPHOSPHATE × 3 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.97 Å |