Current Protein Identity：P39516
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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 |
|---|---|---|---|---|---|---|---|
| 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 C4
11–138（128 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 c4
11–138（128 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 |
| 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 P
11–138（128 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 c4
11–138（128 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 |
| 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 c4
11–138（128 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 C4
11–138（128 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 c4
11–138（128 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 C4
11–138（128 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 C4
11–138（128 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 c4
11–138（128 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 P
11–138（128 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 c4
11–138（128 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 |
| 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 P
11–138（128 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 c4
11–138（128 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 C4
11–138（128 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 c4
11–138（128 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 |
| 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 AE
12–138（127 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 AE
12–138（127 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 AE
12–138（127 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 |
| 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 P
1–138（138 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 c4
1–138（138 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 Z
11–138（128 aa）
Chain Zb
11–138（128 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 |
| 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 Z
12–138（127 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 |
| 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 SO
12–138（127 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 |
| 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 SO
12–138（127 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 |
| 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 Z
12–138（127 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 Z
12–138（127 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 OO
12–138（127 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 AE
1–138（138 aa）
|
Not recorded | ZN ZINC ION × 7 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.20 Å |
| 6XIR Cryo-EM Structure of K63 Ubiquitinated Yeast Translocating Ribosome under Oxidative Stress Deposited 2020-06-21 | Assembly 1 Protein–RNA Heteromer；Protein × 70 PDB declaration: 76-meric（76） Consistent with all polymers |
Chain AE
1–138（138 aa）
|
Not recorded | ZN ZINC ION × 6 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 6ZVI Mbf1-ribosome complex Deposited 2020-07-24 | Assembly 1 Protein–RNA Heteromer；Protein × 34 PDB declaration: 38-meric（38） Consistent with all polymers |
Chain w
11–138（128 aa）
|
Not recorded | ZN ZINC ION × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 7A1G Structure of a crosslinked yeast ABCE1-bound 43S pre-initiation complex Deposited 2020-08-13 | Assembly 1 Protein–RNA Heteromer；Protein × 36 PDB declaration: 37-meric（37） Consistent with all polymers |
Chain Z
12–138（127 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 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 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 Z
12–138（127 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 |
| 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 SZ
12–138（127 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 SZ
11–138（128 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 |
| 7SUK Structure of Bfr2-Lcp5 Complex Observed in the Small Subunit Processome Isolated from R2TP-depleted Yeast Cells Deposited 2021-11-17 | Assembly 1 Protein–RNA Heteromer；Protein × 67 PDB declaration: 70-meric（70） Consistent with all polymers |
Chain NG
11–121（111 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.99 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 AO
12–138（127 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 AO
12–138（127 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 |
| 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 AO
12–138（127 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 DO
12–138（127 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 |
| 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 C4
12–138（127 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 Z
12–138（127 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 Z
12–138（127 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 |
| 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 P
1–138（138 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 c4
1–138（138 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 P
1–138（138 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 c4
1–138（138 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 |
| 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 P
1–138（138 aa）
Chain c4
1–138（138 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 |
| 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 P
1–138（138 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 c4
1–138（138 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 |
| 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 SZ
12–138（127 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 SO
1–138（138 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 SZ
12–138（127 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 SZ
12–138（127 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 SZ
12–138（127 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 SZ
12–138（127 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 SZ
11–138（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 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 SZ
11–138（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 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 SZ
11–138（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 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 SZ
11–138（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 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 SZ
11–138（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 2.30 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 Ro
1–138（138 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 |