|
2WW9
Cryo-EM structure of the active yeast Ssh1 complex bound to the yeast 80S ribosome
Deposited 2009-10-22
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 11
PDB declaration: pentadecameric
|
Chain L
1–127（127 aa）
|
Not recorded
|
No recorded non-water small molecule
|
ELECTRON MICROSCOPY
cryo-EM buffer
20 MM HEPES/KOH, PH 7.5 100 MM KOAC, 10 MM MG(OAC)2, 1.5 MM DTT, 0.1 % (W/V) DIGITONIN；pH 7.5；20 MM HEPES/KOH, PH 7.5 100 MM KOAC, 10 MM MG(OAC)2, 1.5 MM DTT, 0.1 % (W/V) DIGITONIN
cryo-EM vitrification conditions
Cryogen ETHANE；CRYOGEN - ETHANE, HUMIDITY - 95, INSTRUMENT- VITROBOT, METHOD- BLOT FOR 10 SECONDS BEFORE PLUNGING, USE 2 LAYER OF FILTER PAPER,
|
Resolution 8.60 Å
|
|
2WWA
Cryo-EM structure of idle yeast Ssh1 complex bound to the yeast 80S ribosome
Deposited 2009-10-22
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 11
PDB declaration: pentadecameric
|
Chain L
1–127（127 aa）
|
Not recorded
|
No recorded non-water small molecule
|
ELECTRON MICROSCOPY
cryo-EM buffer
20 MM HEPES/KOH, PH 7.5 100 MM KOAC, 10 MM MG(OAC)2, 1.5 MM DTT, 0.1 % (W/V) DIGITONIN；pH 7.5；20 MM HEPES/KOH, PH 7.5 100 MM KOAC, 10 MM MG(OAC)2, 1.5 MM DTT, 0.1 % (W/V) DIGITONIN
cryo-EM vitrification conditions
Cryogen ETHANE；CRYOGEN - ETHANE, HUMIDITY - 95, INSTRUMENT- VITROBOT, METHOD- BLOT FOR 10 SECONDS BEFORE PLUNGING, USE 2 LAYER OF FILTER PAPER,
|
Resolution 8.90 Å
|
|
3J6X
S. cerevisiae 80S ribosome bound with Taura syndrome virus (TSV) IRES, 5 degree rotation (Class II)
Deposited 2014-04-16
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 75
PDB declaration: 80-meric
|
Chain 66
1–127（127 aa）
|
Not recorded
|
No recorded non-water small molecule
|
ELECTRON MICROSCOPY
cryo-EM buffer
45 mM HEPES/KOH, 10 mM MgCl2, 100 mM KCl, 2.5 mM spermine, 2 mM BME, 0.5 U/uL RNasin；pH 7.5；45 mM HEPES/KOH, 10 mM MgCl2, 100 mM KCl, 2.5 mM spermine, 2 mM BME, 0.5 U/uL RNasin
cryo-EM vitrification conditions
Fresh glow discharge, 7 second blot；Cryogen ETHANE；Fresh glow discharge, 7 second blot before plunging into liquid ehtane (FEI VITROBOT MARK II).
|
Resolution 6.10 Å
|
|
3J6Y
S. cerevisiae 80S ribosome bound with Taura syndrome virus (TSV) IRES, 2 degree rotation (Class I)
Deposited 2014-04-16
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 75
PDB declaration: 80-meric
|
Chain 66
1–127（127 aa）
|
Not recorded
|
No recorded non-water small molecule
|
ELECTRON MICROSCOPY
cryo-EM buffer
45 mM HEPES/KOH, 10 mM MgCl2, 100 mM KCl, 2.5 mM spermine, 2 mM BME, 0.5 U/uL RNasin；pH 7.5；45 mM HEPES/KOH, 10 mM MgCl2, 100 mM KCl, 2.5 mM spermine, 2 mM BME, 0.5 U/uL RNasin
cryo-EM vitrification conditions
Fresh glow discharge, 7 second blot；Cryogen ETHANE；Fresh glow discharge, 7 second blot before plunging into liquid ehtane (FEI VITROBOT MARK II).
|
Resolution 6.10 Å
|
|
3J77
Structures of yeast 80S ribosome-tRNA complexes in the rotated and non-rotated conformations (Class II - rotated ribosome with 1 tRNA)
Deposited 2014-05-29
|
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 77
PDB declaration: 83-meric
|
Chain 76
1–127（127 aa）
|
Not recorded
|
No recorded non-water small molecule
|
ELECTRON MICROSCOPY
cryo-EM buffer
20 mM Tris-HCl, 50 mM NH4Cl, 20 mM MgCl2；pH 7.5；20 mM Tris-HCl, 50 mM NH4Cl, 20 mM MgCl2
cryo-EM vitrification conditions
Cryogen ETHANE；Plunged into liquid ethane (FEI VITROBOT MARK II)
|
Resolution 6.20 Å
|
|
3J78
Structures of yeast 80S ribosome-tRNA complexes in the rotated and non-rotated conformations (Class I - non-rotated ribosome with 2 tRNAs)
Deposited 2014-05-29
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 77
PDB declaration: 84-meric
|
Chain 76
1–127（127 aa）
|
Not recorded
|
No recorded non-water small molecule
|
ELECTRON MICROSCOPY
cryo-EM buffer
20 mM Tris-HCl, 50 mM NH4Cl, 20 mM MgCl2；pH 7.5；20 mM Tris-HCl, 50 mM NH4Cl, 20 mM MgCl2
cryo-EM vitrification conditions
Cryogen ETHANE；Plunged into liquid ethane (FEI VITROBOT MARK II)
|
Resolution 6.30 Å
|
|
3JCT
Cryo-em structure of eukaryotic pre-60S ribosomal subunits
Deposited 2016-03-09
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 54
PDB declaration: 58-meric
|
Chain Y
1–127（127 aa）
|
Not recorded
|
ZN ZINC ION × 4
GTP GUANOSINE-5'-TRIPHOSPHATE × 2
MG MAGNESIUM ION × 2
|
ELECTRON MICROSCOPY
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.08 Å
|
|
4U3M
Crystal structure of Anisomycin bound to the yeast 80S ribosome
Deposited 2014-07-22
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 75
PDB declaration: 79-meric
|
Chain N6
2–127（126 aa）
|
Not recorded
|
MG MAGNESIUM ION × 678
OHX osmium (III) hexammine × 558
ZN ZINC ION × 8
ANM ANISOMYCIN × 1
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.00 Å
R-free 0.245
|
|
4U3M
Crystal structure of Anisomycin bound to the yeast 80S ribosome
Deposited 2014-07-22
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 2
Protein–RNA
Heteromer；Protein × 79
PDB declaration: 83-meric
|
Chain n6
2–127（126 aa）
|
Not recorded
|
MG MAGNESIUM ION × 732
OHX osmium (III) hexammine × 575
ZN ZINC ION × 8
ANM ANISOMYCIN × 1
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.00 Å
R-free 0.245
|
|
4U3N
Crystal structure of CCA trinucleotide bound to the yeast 80S ribosome
Deposited 2014-07-22
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 75
PDB declaration: 80-meric
|
Chain N6
2–127（126 aa）
|
Not recorded
|
MG MAGNESIUM ION × 677
OHX osmium (III) hexammine × 558
ZN ZINC ION × 8
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.20 Å
R-free 0.237
|
|
4U3N
Crystal structure of CCA trinucleotide bound to the yeast 80S ribosome
Deposited 2014-07-22
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 2
Protein–RNA
Heteromer；Protein × 79
PDB declaration: 84-meric
|
Chain n6
2–127（126 aa）
|
Not recorded
|
MG MAGNESIUM ION × 731
OHX osmium (III) hexammine × 575
ZN ZINC ION × 8
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.20 Å
R-free 0.237
|
|
4U3U
Crystal structure of Cycloheximide bound to the yeast 80S ribosome
Deposited 2014-07-22
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 75
PDB declaration: 79-meric
|
Chain N6
2–127（126 aa）
|
Not recorded
|
MG MAGNESIUM ION × 678
OHX osmium (III) hexammine × 558
ZN ZINC ION × 8
3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 2.90 Å
R-free 0.245
|
|
4U3U
Crystal structure of Cycloheximide bound to the yeast 80S ribosome
Deposited 2014-07-22
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 2
Protein–RNA
Heteromer；Protein × 79
PDB declaration: 83-meric
|
Chain n6
2–127（126 aa）
|
Not recorded
|
MG MAGNESIUM ION × 730
OHX osmium (III) hexammine × 575
ZN ZINC ION × 8
3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 2.90 Å
R-free 0.245
|
|
4U4N
Crystal structure of Edeine bound to the yeast 80S ribosome
Deposited 2014-07-24
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 75
PDB declaration: 79-meric
|
Chain N6
2–127（126 aa）
|
Not recorded
|
MG MAGNESIUM ION × 676
OHX osmium (III) hexammine × 557
EDE EDEINE B × 1
ZN ZINC ION × 8
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.10 Å
R-free 0.252
|
|
4U4N
Crystal structure of Edeine bound to the yeast 80S ribosome
Deposited 2014-07-24
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 2
Protein–RNA
Heteromer；Protein × 79
PDB declaration: 83-meric
|
Chain n6
2–127（126 aa）
|
Not recorded
|
MG MAGNESIUM ION × 730
OHX osmium (III) hexammine × 574
EDE EDEINE B × 1
ZN ZINC ION × 8
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.10 Å
R-free 0.252
|
|
4U4O
Crystal structure of Geneticin bound to the yeast 80S ribosome
Deposited 2014-07-24
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 75
PDB declaration: 79-meric
|
Chain N6
2–127（126 aa）
|
Not recorded
|
MG MAGNESIUM ION × 678
OHX osmium (III) hexammine × 556
GET GENETICIN × 1
ZN ZINC ION × 8
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.60 Å
R-free 0.267
|
|
4U4O
Crystal structure of Geneticin bound to the yeast 80S ribosome
Deposited 2014-07-24
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 2
Protein–RNA
Heteromer；Protein × 79
PDB declaration: 83-meric
|
Chain n6
2–127（126 aa）
|
Not recorded
|
MG MAGNESIUM ION × 732
OHX osmium (III) hexammine × 575
ZN ZINC ION × 8
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.60 Å
R-free 0.267
|
|
4U4Q
Crystal structure of Homoharringtonine bound to the yeast 80S ribosome
Deposited 2014-07-24
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 75
PDB declaration: 79-meric
|
Chain N6
2–127（126 aa）
|
Not recorded
|
MG MAGNESIUM ION × 678
OHX osmium (III) hexammine × 558
ZN ZINC ION × 8
HMT (3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine × 1
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.00 Å
R-free 0.255
|
|
4U4Q
Crystal structure of Homoharringtonine bound to the yeast 80S ribosome
Deposited 2014-07-24
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 2
Protein–RNA
Heteromer；Protein × 79
PDB declaration: 83-meric
|
Chain n6
2–127（126 aa）
|
Not recorded
|
MG MAGNESIUM ION × 733
OHX osmium (III) hexammine × 575
ZN ZINC ION × 8
HMT (3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine × 1
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.00 Å
R-free 0.255
|
|
4U4R
Crystal structure of Lactimidomycin bound to the yeast 80S ribosome
Deposited 2014-07-24
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 75
PDB declaration: 79-meric
|
Chain N6
2–127（126 aa）
|
Not recorded
|
MG MAGNESIUM ION × 678
OHX osmium (III) hexammine × 558
ZN ZINC ION × 8
3H3 4-{(2R,5S,6E)-2-hydroxy-5-methyl-7-[(2R,3S,4E,6Z,10E)-3-methyl-12-oxooxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl}piperidine-2,6-dione × 1
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 2.80 Å
R-free 0.246
|
|
4U4R
Crystal structure of Lactimidomycin bound to the yeast 80S ribosome
Deposited 2014-07-24
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 2
Protein–RNA
Heteromer；Protein × 79
PDB declaration: 83-meric
|
Chain n6
2–127（126 aa）
|
Not recorded
|
MG MAGNESIUM ION × 730
OHX osmium (III) hexammine × 575
ZN ZINC ION × 8
3H3 4-{(2R,5S,6E)-2-hydroxy-5-methyl-7-[(2R,3S,4E,6Z,10E)-3-methyl-12-oxooxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl}piperidine-2,6-dione × 1
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 2.80 Å
R-free 0.246
|
|
4U4U
Crystal structure of Lycorine bound to the yeast 80S ribosome
Deposited 2014-07-24
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 75
PDB declaration: 79-MERIC
|
Chain N6
2–127（126 aa）
|
Not recorded
|
MG MAGNESIUM ION × 679
OHX osmium (III) hexammine × 557
ZN ZINC ION × 8
3KD (1S,2S,12bS,12cS)-2,4,5,7,12b,12c-hexahydro-1H-[1,3]dioxolo[4,5-j]pyrrolo[3,2,1-de]phenanthridine-1,2-diol × 1
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.00 Å
R-free 0.259
|
|
4U4U
Crystal structure of Lycorine bound to the yeast 80S ribosome
Deposited 2014-07-24
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 2
Protein–RNA
Heteromer；Protein × 79
PDB declaration: 83-MERIC
|
Chain n6
2–127（126 aa）
|
Not recorded
|
MG MAGNESIUM ION × 733
OHX osmium (III) hexammine × 576
ZN ZINC ION × 8
3KD (1S,2S,12bS,12cS)-2,4,5,7,12b,12c-hexahydro-1H-[1,3]dioxolo[4,5-j]pyrrolo[3,2,1-de]phenanthridine-1,2-diol × 1
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.00 Å
R-free 0.259
|
|
4U4Y
Crystal structure of Pactamycin bound to the yeast 80S ribosome
Deposited 2014-07-24
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 75
PDB declaration: 79-meric
|
Chain N6
2–127（126 aa）
|
Not recorded
|
MG MAGNESIUM ION × 678
OHX osmium (III) hexammine × 556
PCY Pactamycin × 1
ZN ZINC ION × 8
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.20 Å
R-free 0.245
|
|
4U4Y
Crystal structure of Pactamycin bound to the yeast 80S ribosome
Deposited 2014-07-24
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 2
Protein–RNA
Heteromer；Protein × 79
PDB declaration: 85-meric
|
Chain n6
2–127（126 aa）
|
Not recorded
|
MG MAGNESIUM ION × 732
OHX osmium (III) hexammine × 574
PCY Pactamycin × 1
ZN ZINC ION × 8
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.20 Å
R-free 0.245
|
|
4U4Z
Crystal structure of Phyllanthoside bound to the yeast 80S ribosome
Deposited 2014-07-24
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 75
PDB declaration: 80-meric
|
Chain N6
2–127（126 aa）
|
Not recorded
|
MG MAGNESIUM ION × 677
OHX osmium (III) hexammine × 558
ZN ZINC ION × 8
3K5 3-O-acetyl-2-O-(3-O-acetyl-6-deoxy-beta-D-glucopyranosyl)-6-deoxy-1-O-{[(2R,2'S,3a'R,4''S,5''R,6'S,7a'S)-5''-methyl-4''-{[(2E)-3-phenylprop-2-enoyl]oxy}decahydrodispiro[oxirane-2,3'-[1]benzofuran-2',2''-pyran]-6'-yl]carbonyl}-beta-D-glucopyranose × 1
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.10 Å
R-free 0.252
|
|
4U4Z
Crystal structure of Phyllanthoside bound to the yeast 80S ribosome
Deposited 2014-07-24
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 2
Protein–RNA
Heteromer；Protein × 79
PDB declaration: 95-meric
|
Chain n6
2–127（126 aa）
|
Not recorded
|
MG MAGNESIUM ION × 731
OHX osmium (III) hexammine × 575
ZN ZINC ION × 8
3K5 3-O-acetyl-2-O-(3-O-acetyl-6-deoxy-beta-D-glucopyranosyl)-6-deoxy-1-O-{[(2R,2'S,3a'R,4''S,5''R,6'S,7a'S)-5''-methyl-4''-{[(2E)-3-phenylprop-2-enoyl]oxy}decahydrodispiro[oxirane-2,3'-[1]benzofuran-2',2''-pyran]-6'-yl]carbonyl}-beta-D-glucopyranose × 1
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.10 Å
R-free 0.252
|
|
4U50
Crystal structure of Verrucarin bound to the yeast 80S ribosome
Deposited 2014-07-24
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 75
PDB declaration: 79-meric
|
Chain N6
2–127（126 aa）
|
Not recorded
|
MG MAGNESIUM ION × 678
OHX osmium (III) hexammine × 556
ZN ZINC ION × 8
3L2 (4S,5R,10E,12Z,16R,16aS,17S,18R,19aR,23aR)-4-hydroxy-5,16a,21-trimethyl-4,5,6,7,16,16a,22,23-octahydro-3H,18H,19aH-spiro[16,18-methano[1,6,12]trioxacyclooctadecino[3,4-d]chromene-17,2'-oxirane]-3,9,14-trione × 1
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.20 Å
R-free 0.262
|
|
4U50
Crystal structure of Verrucarin bound to the yeast 80S ribosome
Deposited 2014-07-24
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 2
Protein–RNA
Heteromer；Protein × 79
PDB declaration: 83-meric
|
Chain n6
2–127（126 aa）
|
Not recorded
|
MG MAGNESIUM ION × 732
OHX osmium (III) hexammine × 576
ZN ZINC ION × 8
3L2 (4S,5R,10E,12Z,16R,16aS,17S,18R,19aR,23aR)-4-hydroxy-5,16a,21-trimethyl-4,5,6,7,16,16a,22,23-octahydro-3H,18H,19aH-spiro[16,18-methano[1,6,12]trioxacyclooctadecino[3,4-d]chromene-17,2'-oxirane]-3,9,14-trione × 1
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.20 Å
R-free 0.262
|
|
4U51
Crystal structure of Narciclasine bound to the yeast 80S ribosome
Deposited 2014-07-24
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 75
PDB declaration: 79-meric
|
Chain N6
2–127（126 aa）
|
Not recorded
|
MG MAGNESIUM ION × 676
OHX osmium (III) hexammine × 557
ZN ZINC ION × 8
3KF (2S,3R,4S,4aR)-2,3,4,7-tetrahydroxy-3,4,4a,5-tetrahydro[1,3]dioxolo[4,5-j]phenanthridin-6(2H)-one × 1
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.20 Å
R-free 0.253
|
|
4U51
Crystal structure of Narciclasine bound to the yeast 80S ribosome
Deposited 2014-07-24
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 2
Protein–RNA
Heteromer；Protein × 79
PDB declaration: 83-meric
|
Chain n6
2–127（126 aa）
|
Not recorded
|
MG MAGNESIUM ION × 732
OHX osmium (III) hexammine × 572
ZN ZINC ION × 8
3KF (2S,3R,4S,4aR)-2,3,4,7-tetrahydroxy-3,4,4a,5-tetrahydro[1,3]dioxolo[4,5-j]phenanthridin-6(2H)-one × 1
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.20 Å
R-free 0.253
|
|
4U52
Crystal structure of Nagilactone C bound to the yeast 80S ribosome
Deposited 2014-07-24
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 75
PDB declaration: 79-meric
|
Chain N6
2–127（126 aa）
|
Not recorded
|
MG MAGNESIUM ION × 679
OHX osmium (III) hexammine × 556
ZN ZINC ION × 8
3J2 Nagilactone C × 1
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.00 Å
R-free 0.258
|
|
4U52
Crystal structure of Nagilactone C bound to the yeast 80S ribosome
Deposited 2014-07-24
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 2
Protein–RNA
Heteromer；Protein × 79
PDB declaration: 83-meric
|
Chain n6
2–127（126 aa）
|
Not recorded
|
MG MAGNESIUM ION × 734
OHX osmium (III) hexammine × 575
ZN ZINC ION × 8
3J2 Nagilactone C × 1
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.00 Å
R-free 0.258
|
|
4U53
Crystal structure of Deoxynivalenol bound to the yeast 80S ribosome
Deposited 2014-07-24
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 75
PDB declaration: 79-meric
|
Chain N6
2–127（126 aa）
|
Not recorded
|
MG MAGNESIUM ION × 676
OHX osmium (III) hexammine × 556
ZN ZINC ION × 8
3J6 (3beta,7alpha)-3,7,15-trihydroxy-12,13-epoxytrichothec-9-en-8-one × 1
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.30 Å
R-free 0.255
|
|
4U53
Crystal structure of Deoxynivalenol bound to the yeast 80S ribosome
Deposited 2014-07-24
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 2
Protein–RNA
Heteromer；Protein × 79
PDB declaration: 83-meric
|
Chain n6
2–127（126 aa）
|
Not recorded
|
MG MAGNESIUM ION × 730
OHX osmium (III) hexammine × 574
ZN ZINC ION × 8
3J6 (3beta,7alpha)-3,7,15-trihydroxy-12,13-epoxytrichothec-9-en-8-one × 1
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.30 Å
R-free 0.255
|
|
4U55
Crystal structure of Cryptopleurine bound to the yeast 80S ribosome
Deposited 2014-07-24
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 75
PDB declaration: 79-MERIC
|
Chain N6
2–127（126 aa）
|
Not recorded
|
MG MAGNESIUM ION × 678
OHX osmium (III) hexammine × 557
3K8 (14aR)-2,3,6-trimethoxy-11,12,13,14,14a,15-hexahydro-9H-dibenzo[f,h]pyrido[1,2-b]isoquinoline × 1
ZN ZINC ION × 8
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.20 Å
R-free 0.246
|
|
4U55
Crystal structure of Cryptopleurine bound to the yeast 80S ribosome
Deposited 2014-07-24
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 2
Protein–RNA
Heteromer；Protein × 79
PDB declaration: 83-MERIC
|
Chain n6
2–127（126 aa）
|
Not recorded
|
MG MAGNESIUM ION × 732
OHX osmium (III) hexammine × 574
3K8 (14aR)-2,3,6-trimethoxy-11,12,13,14,14a,15-hexahydro-9H-dibenzo[f,h]pyrido[1,2-b]isoquinoline × 1
ZN ZINC ION × 8
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.20 Å
R-free 0.246
|
|
4U56
Crystal structure of Blasticidin S bound to the yeast 80S ribosome
Deposited 2014-07-24
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 75
PDB declaration: 80-meric
|
Chain N6
2–127（126 aa）
|
Not recorded
|
MG MAGNESIUM ION × 675
OHX osmium (III) hexammine × 558
ZN ZINC ION × 8
BLS BLASTICIDIN S × 1
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.45 Å
R-free 0.260
|
|
4U56
Crystal structure of Blasticidin S bound to the yeast 80S ribosome
Deposited 2014-07-24
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 2
Protein–RNA
Heteromer；Protein × 79
PDB declaration: 85-meric
|
Chain n6
2–127（126 aa）
|
Not recorded
|
MG MAGNESIUM ION × 732
OHX osmium (III) hexammine × 574
ZN ZINC ION × 8
BLS BLASTICIDIN S × 1
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.45 Å
R-free 0.260
|
|
4U6F
Crystal structure of T-2 toxin bound to the yeast 80S ribosome
Deposited 2014-07-28
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 75
PDB declaration: 79-meric
|
Chain N6
2–127（126 aa）
|
Not recorded
|
MG MAGNESIUM ION × 678
OHX osmium (III) hexammine × 557
ZN ZINC ION × 8
ZBA 12,13-Epoxytrichothec-9-ene-3,4,8,15-tetrol-4,15-diacetate-8-isovalerate × 1
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.10 Å
R-free 0.247
|
|
4U6F
Crystal structure of T-2 toxin bound to the yeast 80S ribosome
Deposited 2014-07-28
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 2
Protein–RNA
Heteromer；Protein × 79
PDB declaration: 83-meric
|
Chain n6
2–127（126 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
|
|
4V4B
Structure of the ribosomal 80S-eEF2-sordarin complex from yeast obtained by docking atomic models for RNA and protein components into a 11.7 A cryo-EM map.
Deposited 2004-01-06
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 44
PDB declaration: 47-meric
|
Chain BU
1–126（126 aa）
|
Not recorded
|
No recorded non-water small molecule
|
ELECTRON MICROSCOPY
cryo-EM vitrification conditions
Cryogen ETHANE；Rapid-freezing in liquid ethane
|
Resolution 11.70 Å
|
|
4V6I
Localization of the small subunit ribosomal proteins into a 6.1 A cryo-EM map of Saccharomyces cerevisiae translating 80S ribosome
Deposited 2010-10-12
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 80
PDB declaration: 86-meric
|
Chain BY
1–123（123 aa）
|
Not recorded
|
No recorded non-water small molecule
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 8.80 Å
|
|
4V7F
Arx1 pre-60S particle.
Deposited 2013-12-10
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 45
PDB declaration: 48-meric
|
Chain X
1–127（127 aa）
|
Not recorded
|
No recorded non-water small molecule
|
ELECTRON MICROSCOPY
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 8.70 Å
|
|
4V7R
Yeast 80S ribosome.
Deposited 2010-07-23
|
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 69
PDB declaration: 73-meric
|
Chain BX
1–127（127 aa）
|
Not recorded
|
OHX osmium (III) hexammine × 355
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7；297 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine, pH 7, VAPOR DIFFUSION, temperature 297K
|
Resolution 4.00 Å
R-free 0.341
|
|
4V7R
Yeast 80S ribosome.
Deposited 2010-07-23
|
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 2
Protein–RNA
Heteromer；Protein × 62
PDB declaration: 66-meric
|
Chain DX
1–127（127 aa）
|
Not recorded
|
OHX osmium (III) hexammine × 360
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7；297 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine, pH 7, VAPOR DIFFUSION, temperature 297K
|
Resolution 4.00 Å
R-free 0.341
|
|
4V88
The structure of the eukaryotic ribosome at 3.0 A resolution.
Deposited 2011-10-11
|
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 75
PDB declaration: 79-meric
|
Chain BY
1–127（127 aa）
|
Not recorded
|
OHX osmium (III) hexammine × 657
MG MAGNESIUM ION × 1035
ZN ZINC ION × 8
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 3.00 Å
R-free 0.229
|
|
4V88
The structure of the eukaryotic ribosome at 3.0 A resolution.
Deposited 2011-10-11
|
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 2
Protein–RNA
Heteromer；Protein × 79
PDB declaration: 83-meric
|
Chain DY
1–127（127 aa）
|
Not recorded
|
OHX osmium (III) hexammine × 688
MG MAGNESIUM ION × 1170
ZN ZINC ION × 8
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 3.00 Å
R-free 0.229
|
|
4V8T
Cryo-EM Structure of the 60S Ribosomal Subunit in Complex with Arx1 and Rei1
Deposited 2012-08-07
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 46
PDB declaration: 50-meric
|
Chain Y
1–127（127 aa）
|
Not recorded
|
ZN ZINC ION × 4
|
ELECTRON MICROSCOPY
cryo-EM buffer
20 MM HEPES-NAOH PH 8.0, 50 MM NACL, 5 MM BETA- MERCAPTOETHANOL, 5 MM MGCL2；pH 8；20 MM HEPES-NAOH PH 8.0, 50 MM NACL, 5 MM BETA- MERCAPTOETHANOL, 5 MM MGCL2
cryo-EM vitrification conditions
Cryogen ETHANE；PLUNGE FREEZING IN LIQUID ETHANE AFTER MANUAL BLOTTING USING A MANUAL PLUNGE FREEZING DEVICE
|
Resolution 8.10 Å
|
|
4V8Y
Cryo-EM reconstruction of the 80S-eIF5B-Met-itRNAMet Eukaryotic Translation Initiation Complex
Deposited 2013-07-20
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 81
PDB declaration: 87-meric
|
Chain BY
2–127（126 aa）
|
Not recorded
|
ZN ZINC ION × 6
MG MAGNESIUM ION × 191
OHX osmium (III) hexammine × 197
GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
3MM HEPES-KOH, 6.6 MM TRIS-ACETATE PH 7.2, 3 MM NH4CL, 6.6 MM NH4- ACETATE, 48 MM K-ACETATE, 4 MM MG-ACETATE, 2.4 MM DTT；pH 7.2；3MM HEPES-KOH, 6.6 MM TRIS-ACETATE PH 7.2, 3 MM NH4CL, 6.6 MM NH4- ACETATE, 48 MM K-ACETATE, 4 MM MG-ACETATE, 2.4 MM DTT
cryo-EM vitrification conditions
Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 90, INSTRUMENT- FEI VITROBOT MARK II, METHOD- BLOT 2.5 SECONDS BEFORE PLUNGING,
|
Resolution 4.30 Å
|
|
4V8Z
Cryo-EM reconstruction of the 80S-eIF5B-Met-itRNAMet Eukaryotic Translation Initiation Complex
Deposited 2013-07-20
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Insufficient information
Heteromer；Protein × 79
PDB declaration: 85-meric
|
Chain BY
2–127（126 aa）
|
Not recorded
|
ZN ZINC ION × 6
MG MAGNESIUM ION × 226
OHX osmium (III) hexammine × 210
GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
3MM HEPES-KOH, 6.6 MM TRIS-ACETATE PH 7.2, 3 MM NH4CL, 6.6 MM NH4- ACETATE, 48 MM K-ACETATE, 4 MM MG-ACETATE, 2.4 MM DTT；pH 7.2；3MM HEPES-KOH, 6.6 MM TRIS-ACETATE PH 7.2, 3 MM NH4CL, 6.6 MM NH4- ACETATE, 48 MM K-ACETATE, 4 MM MG-ACETATE, 2.4 MM DTT
cryo-EM vitrification conditions
Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 90, INSTRUMENT- FEI VITROBOT MARK II, METHOD- BLOT 2.5 SECONDS BEFORE PLUNGING,
|
Resolution 6.60 Å
|
|
5APN
Structure of the yeast 60S ribosomal subunit in complex with Arx1, Alb1 and N-terminally tagged Rei1
Deposited 2015-09-17
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 44
PDB declaration: 47-meric
|
Chain Y
1–127（127 aa）
|
Not recorded
|
MG MAGNESIUM ION × 280
ZN ZINC ION × 6
|
ELECTRON MICROSCOPY
cryo-EM buffer
20MM；pH 8；20MM
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE；PLUNGE-FROZEN
|
Resolution 3.91 Å
|
|
5APO
Structure of the yeast 60S ribosomal subunit in complex with Arx1, Alb1 and C-terminally tagged Rei1
Deposited 2015-09-17
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 44
PDB declaration: 47-meric
|
Chain Y
1–127（127 aa）
|
Not recorded
|
MG MAGNESIUM ION × 280
ZN ZINC ION × 6
|
ELECTRON MICROSCOPY
cryo-EM buffer
20MM HEPES-KOH, 100mM NACL, 5mM MGCL2, 5mM BETA-MERCAPTOETHANOL；pH 8；20MM HEPES-KOH, 100mM NACL, 5mM MGCL2, 5mM BETA-MERCAPTOETHANOL
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE；PLUNGE-FROZEN
|
Resolution 3.41 Å
|
|
5DAT
Complex of yeast 80S ribosome with hypusine-containing eIF5A
Deposited 2015-08-20
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 81
PDB declaration: 86-MERIC
|
Chain n6
2–127（126 aa）
|
Not recorded
|
MG MAGNESIUM ION × 580
OHX osmium (III) hexammine × 601
ZN ZINC ION × 8
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
|
Resolution 3.15 Å
R-free 0.252
|
|
5DAT
Complex of yeast 80S ribosome with hypusine-containing eIF5A
Deposited 2015-08-20
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 2
Protein–RNA
Heteromer；Protein × 75
PDB declaration: 86-MERIC
|
Chain N6
2–127（126 aa）
|
Not recorded
|
MG MAGNESIUM ION × 528
OHX osmium (III) hexammine × 565
ZN ZINC ION × 8
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
|
Resolution 3.15 Å
R-free 0.252
|
|
5DC3
Complex of yeast 80S ribosome with non-modified eIF5A
Deposited 2015-08-23
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 75
PDB declaration: 81-meric
|
Chain N6
2–127（126 aa）
|
Not recorded
|
ZN ZINC ION × 8
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
|
Resolution 3.25 Å
R-free 0.301
|
|
5DC3
Complex of yeast 80S ribosome with non-modified eIF5A
Deposited 2015-08-23
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 2
Protein–RNA
Heteromer；Protein × 80
PDB declaration: 81-meric
|
Chain n6
2–127（126 aa）
|
Not recorded
|
ZN ZINC ION × 8
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
|
Resolution 3.25 Å
R-free 0.301
|
|
5DGE
Coping with proline stalling: structural basis of hypusine-induced protein synthesis by the eukaryotic ribosome
Deposited 2015-08-27
|
Different construct
Different mutation/modification
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 155
PDB declaration: 165-meric
|
Chain N6
2–127（126 aa）
Chain n6
2–127（126 aa）
|
Not recorded
|
MG MAGNESIUM ION × 1093
OHX osmium (III) hexammine × 1169
ZN ZINC ION × 16
SPS SPARSOMYCIN × 2
PRO PROLINE × 4
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
|
Resolution 3.45 Å
R-free 0.263
|
|
5DGF
Complex of yeast 80S ribosome with hypusine-containing/non-modified eIF5A and/or a peptidyl-tRNA analog
Deposited 2015-08-27
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 75
PDB declaration: TRIMERIC
|
Chain N6
2–127（126 aa）
|
Not recorded
|
ZN ZINC ION × 8
SPS SPARSOMYCIN × 1
MG MAGNESIUM ION × 4
OHX osmium (III) hexammine × 2
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
|
Resolution 3.30 Å
R-free 0.310
|
|
5DGF
Complex of yeast 80S ribosome with hypusine-containing/non-modified eIF5A and/or a peptidyl-tRNA analog
Deposited 2015-08-27
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 2
Protein–RNA
Heteromer；Protein × 80
PDB declaration: TRIMERIC
|
Chain n6
2–127（126 aa）
|
Not recorded
|
ZN ZINC ION × 8
SPS SPARSOMYCIN × 1
MG MAGNESIUM ION × 8
OHX osmium (III) hexammine × 1
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
|
Resolution 3.30 Å
R-free 0.310
|
|
5DGV
Complex of yeast 80S ribosome with hypusine-containing/non-modified eIF5A and/or a peptidyl-tRNA analog
Deposited 2015-08-28
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 79
PDB declaration: 81-MERIC
|
Chain n6
2–127（126 aa）
|
Not recorded
|
ZN ZINC ION × 8
SPS SPARSOMYCIN × 1
MG MAGNESIUM ION × 1
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
|
Resolution 3.10 Å
R-free 0.284
|
|
5DGV
Complex of yeast 80S ribosome with hypusine-containing/non-modified eIF5A and/or a peptidyl-tRNA analog
Deposited 2015-08-28
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 2
Protein–RNA
Heteromer；Protein × 75
PDB declaration: 81-MERIC
|
Chain N6
2–127（126 aa）
|
Not recorded
|
ZN ZINC ION × 8
SPS SPARSOMYCIN × 1
MG MAGNESIUM ION × 1
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
|
Resolution 3.10 Å
R-free 0.284
|
|
5FCI
Structure of the vacant uL3 W255C mutant 80S yeast ribosome
Deposited 2015-12-15
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 75
PDB declaration: 79-meric
|
Chain N6
2–127（126 aa）
|
Not recorded
|
OHX osmium (III) hexammine × 874
MG MAGNESIUM ION × 994
ZN ZINC ION × 8
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-Acetate pH 7.0, KSCN, Mg-Acetate, Glycerol, Spermidine, PEG20000
|
Resolution 3.40 Å
R-free 0.284
|
|
5FCI
Structure of the vacant uL3 W255C mutant 80S yeast ribosome
Deposited 2015-12-15
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 2
Protein–RNA
Heteromer；Protein × 79
PDB declaration: 83-meric
|
Chain n6
2–127（126 aa）
|
Not recorded
|
OHX osmium (III) hexammine × 561
MG MAGNESIUM ION × 626
ZN ZINC ION × 8
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-Acetate pH 7.0, KSCN, Mg-Acetate, Glycerol, Spermidine, PEG20000
|
Resolution 3.40 Å
R-free 0.284
|
|
5FCJ
Structure of the anisomycin-containing uL3 W255C mutant 80S yeast ribosome
Deposited 2015-12-15
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 79
PDB declaration: 82-meric
|
Chain n6
2–127（126 aa）
|
Not recorded
|
MG MAGNESIUM ION × 517
OHX osmium (III) hexammine × 534
ZN ZINC ION × 8
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277.15 K；Tris-Acetate pH7.0, KSCN, Mg-Acetate, Glycerol, Spermidine, PEG20000
|
Resolution 3.10 Å
R-free 0.291
|
|
5FCJ
Structure of the anisomycin-containing uL3 W255C mutant 80S yeast ribosome
Deposited 2015-12-15
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 2
Protein–RNA
Heteromer；Protein × 75
PDB declaration: 79-meric
|
Chain N6
2–127（126 aa）
|
Not recorded
|
MG MAGNESIUM ION × 462
OHX osmium (III) hexammine × 500
ZN ZINC ION × 8
ANM ANISOMYCIN × 1
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277.15 K；Tris-Acetate pH7.0, KSCN, Mg-Acetate, Glycerol, Spermidine, PEG20000
|
Resolution 3.10 Å
R-free 0.291
|
|
5GAK
Yeast 60S ribosomal subunit with A-site tRNA, P-site tRNA and eIF-5A
Deposited 2015-12-09
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 44
PDB declaration: 49-meric
|
Chain a
1–127（127 aa）
|
Not recorded
|
3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；Details can be retrieved from EMD-3227
|
Resolution 3.88 Å
|
|
5H4P
Structural snapshot of cytoplasmic pre-60S ribosomal particles bound with Nmd3, Lsg1, Tif6 and Reh1
Deposited 2016-11-01
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 41
PDB declaration: 44-meric
|
Chain Y
1–127（127 aa）
|
Not recorded
|
No recorded non-water small molecule
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.07 Å
|
|
5I4L
Crystal structure of Amicoumacin A bound to the yeast 80S ribosome
Deposited 2016-02-12
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 75
PDB declaration: 79-meric
|
Chain N6
2–127（126 aa）
|
Not recorded
|
OHX osmium (III) hexammine × 481
MG MAGNESIUM ION × 493
ZN ZINC ION × 8
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.10 Å
R-free 0.251
|
|
5I4L
Crystal structure of Amicoumacin A bound to the yeast 80S ribosome
Deposited 2016-02-12
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 2
Protein–RNA
Heteromer；Protein × 79
PDB declaration: 83-meric
|
Chain n6
2–127（126 aa）
|
Not recorded
|
OHX osmium (III) hexammine × 512
MG MAGNESIUM ION × 526
ZN ZINC ION × 8
UAM Amicoumacin A × 1
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.10 Å
R-free 0.251
|
|
5JCS
CRYO-EM STRUCTURE OF THE RIX1-REA1 PRE-60S PARTICLE
Deposited 2016-04-15
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 45
PDB declaration: 48-meric
|
Chain Y
1–127（127 aa）
|
Not recorded
|
No recorded non-water small molecule
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 9.50 Å
|
|
5JUO
Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure I (fully rotated 40S subunit)
Deposited 2016-05-10
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 78
PDB declaration: 83-meric
|
Chain DA
1–127（127 aa）
|
Not recorded
|
GDP GUANOSINE-5'-DIPHOSPHATE × 1
MG MAGNESIUM ION × 1
SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å
|
|
5JUP
Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure II (mid-rotated 40S subunit)
Deposited 2016-05-10
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 78
PDB declaration: 83-meric
|
Chain DA
1–127（127 aa）
|
Not recorded
|
GDP GUANOSINE-5'-DIPHOSPHATE × 1
MG MAGNESIUM ION × 1
SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å
|
|
5JUS
Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure III (mid-rotated 40S subunit)
Deposited 2016-05-10
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 78
PDB declaration: 83-meric
|
Chain DA
1–127（127 aa）
|
Not recorded
|
GDP GUANOSINE-5'-DIPHOSPHATE × 1
MG MAGNESIUM ION × 1
SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
|
Resolution 4.20 Å
|
|
5JUT
Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure IV (almost non-rotated 40S subunit)
Deposited 2016-05-10
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 78
PDB declaration: 83-meric
|
Chain DA
1–127（127 aa）
|
Not recorded
|
GDP GUANOSINE-5'-DIPHOSPHATE × 1
MG MAGNESIUM ION × 1
SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å
|
|
5JUU
Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure V (least rotated 40S subunit)
Deposited 2016-05-10
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 78
PDB declaration: 83-meric
|
Chain DA
1–127（127 aa）
|
Not recorded
|
GDP GUANOSINE-5'-DIPHOSPHATE × 1
MG MAGNESIUM ION × 1
SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å
|
|
5LYB
Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCPmn
Deposited 2016-09-26
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 75
PDB declaration: 80-meric
|
Chain N6
2–127（126 aa）
|
Not recorded
|
MG MAGNESIUM ION × 1026
OHX osmium (III) hexammine × 659
ZN ZINC ION × 8
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7；277 K；Tris-Acetate pH 7.0, KSCN, MgOAc2, glycerol, spermidine, PEG20K
|
Resolution 3.25 Å
R-free 0.249
|
|
5LYB
Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCPmn
Deposited 2016-09-26
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 2
Protein–RNA
Heteromer；Protein × 79
PDB declaration: 84-meric
|
Chain n6
2–127（126 aa）
|
Not recorded
|
MG MAGNESIUM ION × 1166
OHX osmium (III) hexammine × 686
ZN ZINC ION × 8
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7；277 K；Tris-Acetate pH 7.0, KSCN, MgOAc2, glycerol, spermidine, PEG20K
|
Resolution 3.25 Å
R-free 0.249
|
|
5M1J
Nonstop ribosomal complex bound with Dom34 and Hbs1
Deposited 2016-10-07
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 76
PDB declaration: 82-meric
|
Chain Y5
2–127（126 aa）
|
Not recorded
|
ZN ZINC ION × 8
MG MAGNESIUM ION × 1058
GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1
5CR N-acetyl-L-phenylalanine × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å
|
|
5MC6
Cryo-EM structure of a native ribosome-Ski2-Ski3-Ski8 complex from S. cerevisiae
Deposited 2016-11-09
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 80
PDB declaration: 87-meric
|
Chain AK
1–127（127 aa）
|
Not recorded
|
No recorded non-water small molecule
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å
|
|
5MEI
Crystal structure of Agelastatin A bound to the 80S ribosome
Deposited 2016-11-15
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 75
PDB declaration: 78-meric
|
Chain 9
2–127（126 aa）
|
Not recorded
|
OHX osmium (III) hexammine × 517
MG MAGNESIUM ION × 673
7MB Agelastatin A × 1
ZN ZINC ION × 8
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.50 Å
R-free 0.239
|
|
5MEI
Crystal structure of Agelastatin A bound to the 80S ribosome
Deposited 2016-11-15
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 2
Protein–RNA
Heteromer；Protein × 76
PDB declaration: 80-meric
|
Chain DA
2–127（126 aa）
|
Not recorded
|
OHX osmium (III) hexammine × 553
MG MAGNESIUM ION × 733
7MB Agelastatin A × 1
ZN ZINC ION × 8
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.50 Å
R-free 0.239
|
|
5NDG
Crystal structure of geneticin (G418) bound to the yeast 80S ribosome
Deposited 2017-03-08
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 75
PDB declaration: 79-meric
|
Chain N6
2–127（126 aa）
|
Not recorded
|
MG MAGNESIUM ION × 597
GET GENETICIN × 9
ZN ZINC ION × 9
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.70 Å
R-free 0.253
|
|
5NDG
Crystal structure of geneticin (G418) bound to the yeast 80S ribosome
Deposited 2017-03-08
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 2
Protein–RNA
Heteromer；Protein × 76
PDB declaration: 80-meric
|
Chain n6
2–127（126 aa）
|
Not recorded
|
MG MAGNESIUM ION × 624
GET GENETICIN × 12
ZN ZINC ION × 9
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.70 Å
R-free 0.253
|
|
5NDV
Crystal structure of Paromomycin bound to the yeast 80S ribosome
Deposited 2017-03-09
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 74
PDB declaration: 78-meric
|
Chain n6
2–126（125 aa）
|
Not recorded
|
PAR PAROMOMYCIN × 40
MG MAGNESIUM ION × 1006
ZN ZINC ION × 8
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.30 Å
R-free 0.250
|
|
5NDV
Crystal structure of Paromomycin bound to the yeast 80S ribosome
Deposited 2017-03-09
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 2
Protein–RNA
Heteromer；Protein × 74
PDB declaration: 78-meric
|
Chain N6
2–126（125 aa）
|
Not recorded
|
PAR PAROMOMYCIN × 47
MG MAGNESIUM ION × 1133
ZN ZINC ION × 8
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.30 Å
R-free 0.250
|
|
5NDW
Crystal structure of aminoglycoside TC007 bound to the yeast 80S ribosome
Deposited 2017-03-09
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 75
PDB declaration: 79-meric
|
Chain n6
2–127（126 aa）
|
Not recorded
|
MG MAGNESIUM ION × 671
8UZ TC007 × 10
ZN ZINC ION × 8
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.70 Å
R-free 0.235
|
|
5NDW
Crystal structure of aminoglycoside TC007 bound to the yeast 80S ribosome
Deposited 2017-03-09
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 2
Protein–RNA
Heteromer；Protein × 75
PDB declaration: 79-meric
|
Chain N6
2–127（126 aa）
|
Not recorded
|
MG MAGNESIUM ION × 694
8UZ TC007 × 15
ZN ZINC ION × 9
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.70 Å
R-free 0.235
|
|
5OBM
Crystal structure of Gentamicin bound to the yeast 80S ribosome
Deposited 2017-06-28
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 75
PDB declaration: 79-MERIC
|
Chain N6
2–127（126 aa）
|
Not recorded
|
MG MAGNESIUM ION × 855
LLL (2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDR OXYCYCLOHEXYLOXY)-5-METHYL-4-(METHYLAMINO)-TETRAHYDRO-2H-PYRAN-3,5-DIOL × 22
ZN ZINC ION × 9
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.40 Å
R-free 0.238
|
|
5OBM
Crystal structure of Gentamicin bound to the yeast 80S ribosome
Deposited 2017-06-28
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 2
Protein–RNA
Heteromer；Protein × 78
PDB declaration: 82-MERIC
|
Chain n6
2–127（126 aa）
|
Not recorded
|
MG MAGNESIUM ION × 1211
LLL (2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDR OXYCYCLOHEXYLOXY)-5-METHYL-4-(METHYLAMINO)-TETRAHYDRO-2H-PYRAN-3,5-DIOL × 47
ZN ZINC ION × 9
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.40 Å
R-free 0.238
|
|
5ON6
Crystal structure of haemanthamine bound to the 80S ribosome
Deposited 2017-08-03
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 75
PDB declaration: 78-meric
|
Chain 9
2–127（126 aa）
|
Not recorded
|
OHX osmium (III) hexammine × 515
MG MAGNESIUM ION × 703
HN8 Haemanthamine × 1
GOL GLYCEROL × 2
ZN ZINC ION × 8
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.10 Å
R-free 0.252
|
|
5ON6
Crystal structure of haemanthamine bound to the 80S ribosome
Deposited 2017-08-03
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 2
Protein–RNA
Heteromer；Protein × 77
PDB declaration: 80-meric
|
Chain DA
2–127（126 aa）
|
Not recorded
|
OHX osmium (III) hexammine × 549
MG MAGNESIUM ION × 758
HN8 Haemanthamine × 1
GOL GLYCEROL × 3
ZN ZINC ION × 8
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.10 Å
R-free 0.252
|
|
5T62
Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis: 60S-Nmd3-Tif6-Lsg1 Complex
Deposited 2016-09-01
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 44
PDB declaration: 47-meric
|
Chain l
1–127（127 aa）
|
Not recorded
|
MG MAGNESIUM ION × 160
K POTASSIUM ION × 2
GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å
|
|
5T6R
Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis: 60S-Nmd3 Complex
Deposited 2016-09-01
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Insufficient information
Heteromer；Protein × 42
PDB declaration: 45-meric
|
Chain l
1–127（127 aa）
|
Not recorded
|
MG MAGNESIUM ION × 86
K POTASSIUM ION × 3
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.20 Å
|
|
5TBW
Crystal structure of chlorolissoclimide bound to the yeast 80S ribosome
Deposited 2016-09-13
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 75
PDB declaration: 79-meric
|
Chain 9
2–127（126 aa）
|
Not recorded
|
OHX osmium (III) hexammine × 518
MG MAGNESIUM ION × 666
7AL Chlorolissoclimide × 1
ZN ZINC ION × 8
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
|
Resolution 3.00 Å
R-free 0.227
|
|
5TBW
Crystal structure of chlorolissoclimide bound to the yeast 80S ribosome
Deposited 2016-09-13
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 2
Protein–RNA
Heteromer；Protein × 76
PDB declaration: 80-meric
|
Chain DA
2–127（126 aa）
|
Not recorded
|
OHX osmium (III) hexammine × 556
MG MAGNESIUM ION × 728
7AL Chlorolissoclimide × 1
ZN ZINC ION × 8
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
|
Resolution 3.00 Å
R-free 0.227
|
|
5TGA
Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCA-Pro
Deposited 2016-09-27
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 75
PDB declaration: 80-meric
|
Chain N6
2–127（126 aa）
|
Not recorded
|
OHX osmium (III) hexammine × 659
MG MAGNESIUM ION × 1026
ZN ZINC ION × 8
PRO PROLINE × 1
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；PEG20000
|
Resolution 3.30 Å
R-free 0.265
|
|
5TGA
Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCA-Pro
Deposited 2016-09-27
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 2
Protein–RNA
Heteromer；Protein × 79
PDB declaration: 84-meric
|
Chain n6
2–127（126 aa）
|
Not recorded
|
OHX osmium (III) hexammine × 686
MG MAGNESIUM ION × 1166
ZN ZINC ION × 8
PRO PROLINE × 1
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；PEG20000
|
Resolution 3.30 Å
R-free 0.265
|
|
5TGM
Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCA-Pro
Deposited 2016-09-28
|
Different construct
Different mutation/modification
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 154
PDB declaration: 164-meric
|
Chain N6
2–127（126 aa）
Chain n6
2–127（126 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
|
|
5Z3G
Cryo-EM structure of a nucleolar pre-60S ribosome (Rpf1-TAP)
Deposited 2018-01-06
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 32
PDB declaration: 35-meric
|
Chain c
1–127（127 aa）
|
Not recorded
|
No recorded non-water small molecule
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 1-3 seconds before plunging
|
Resolution 3.65 Å
|
|
6C0F
Yeast nucleolar pre-60S ribosomal subunit (state 2)
Deposited 2017-12-29
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 40
PDB declaration: 43-meric
|
Chain Y
1–127（127 aa）
|
Not recorded
|
ZN ZINC ION × 3
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å
|
|
6CB1
Yeast nucleolar pre-60S ribosomal subunit (state 3)
Deposited 2018-02-01
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Insufficient information
Heteromer；Protein × 37
PDB declaration: 40-meric
|
Chain Y
1–127（127 aa）
|
Not recorded
|
ZN ZINC ION × 2
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.60 Å
|
|
6ELZ
State E (TAP-Flag-Ytm1 E80A) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes
Deposited 2017-09-30
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 51
PDB declaration: 54-meric
|
Chain Y
1–127（127 aa）
|
Not recorded
|
ZN ZINC ION × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å
|
|
6EM1
State C (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes
Deposited 2017-10-01
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 40
PDB declaration: 43-meric
|
Chain Y
1–127（127 aa）
|
Not recorded
|
ZN ZINC ION × 2
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å
|
|
6EM3
State A architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes
Deposited 2017-10-01
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 30
PDB declaration: 33-meric
|
Chain Y
1–127（127 aa）
|
Not recorded
|
No recorded non-water small molecule
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å
|
|
6EM4
State B architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes
Deposited 2017-10-01
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 34
PDB declaration: 37-meric
|
Chain Y
1–127（127 aa）
|
Not recorded
|
No recorded non-water small molecule
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.10 Å
|
|
6EM5
State D architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes
Deposited 2017-10-01
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 54
PDB declaration: 57-meric
|
Chain Y
1–127（127 aa）
|
Not recorded
|
No recorded non-water small molecule
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.30 Å
|
|
6FT6
Structure of the Nop53 pre-60S particle bound to the exosome nuclear cofactors
Deposited 2018-02-20
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 54
PDB declaration: 57-meric
|
Chain Y
1–127（127 aa）
|
Not recorded
|
ZN ZINC ION × 4
GTP GUANOSINE-5'-TRIPHOSPHATE × 2
MG MAGNESIUM ION × 2
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 3.90 Å
|
|
6GQ1
Cryo-EM reconstruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GMPPCP/sordarin)
Deposited 2018-06-07
|
Different construct
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 77
PDB declaration: 83-meric
|
Chain Y
2–127（126 aa）
|
Not recorded
|
ZN ZINC ION × 8
SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1
GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；blot force 4, blot waiting time 30 s
|
Resolution 4.40 Å
|
|
6GQB
Cryo-EM reconstruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GDP+AlF4/sordarin)
Deposited 2018-06-07
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 78
PDB declaration: 84-meric
|
Chain Y
2–127（126 aa）
|
Not recorded
|
ZN ZINC ION × 8
SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1
GDP GUANOSINE-5'-DIPHOSPHATE × 1
ALF TETRAFLUOROALUMINATE ION × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；blot force 4, blot waiting time 30 s
|
Resolution 3.90 Å
|
|
6GQV
Cryo-EM recosntruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GMPPCP)
Deposited 2018-06-08
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 78
PDB declaration: 84-meric
|
Chain Y
2–127（126 aa）
|
Not recorded
|
ZN ZINC ION × 8
GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；blot force 4, blot waiting time 30 s
|
Resolution 4.00 Å
|
|
6HD7
Cryo-EM structure of the ribosome-NatA complex
Deposited 2018-08-17
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 46
PDB declaration: 51-meric
|
Chain a
1–127（127 aa）
|
Not recorded
|
3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å
|
|
6HHQ
Crystal structure of compound C45 bound to the yeast 80S ribosome
Deposited 2018-08-28
|
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 75
PDB declaration: 79-meric
|
Chain 9
1–127（127 aa）
|
Not recorded
|
OHX osmium (III) hexammine × 513
MG MAGNESIUM ION × 717
G5B (3~{R})-3-[(1~{S})-2-[(1~{S},4~{a}~{R},6~{S},7~{S},8~{a}~{R})-6,7-bis(chloranyl)-5,5,8~{a}-trimethyl-2-methylidene-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1
ZN ZINC ION × 8
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.10 Å
R-free 0.264
|
|
6HHQ
Crystal structure of compound C45 bound to the yeast 80S ribosome
Deposited 2018-08-28
|
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 2
Protein–RNA
Heteromer；Protein × 76
PDB declaration: 80-meric
|
Chain DA
1–127（127 aa）
|
Not recorded
|
OHX osmium (III) hexammine × 544
MG MAGNESIUM ION × 792
G5B (3~{R})-3-[(1~{S})-2-[(1~{S},4~{a}~{R},6~{S},7~{S},8~{a}~{R})-6,7-bis(chloranyl)-5,5,8~{a}-trimethyl-2-methylidene-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1
ZN ZINC ION × 8
GOL GLYCEROL × 2
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.10 Å
R-free 0.264
|
|
6I7O
The structure of a di-ribosome (disome) as a unit for RQC and NGD quality control pathways recognition.
Deposited 2018-11-16
|
Different construct
Different mutation/modification
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 150
PDB declaration: 163-meric
|
Chain AK
2–125（124 aa）
Chain XK
2–125（124 aa）
|
Not recorded
|
ZN ZINC ION × 15
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.30 Å
|
|
6M62
Cryo-Em structure of eukaryotic pre-60S ribosome subunit from Saccharomyces cerevisiae rpf2 delta 255-344 strain, C4 state.
Deposited 2020-03-12
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 54
PDB declaration: 58-meric
|
Chain Y
1–127（127 aa）
|
Not recorded
|
ZN ZINC ION × 4
GTP GUANOSINE-5'-TRIPHOSPHATE × 2
MG MAGNESIUM ION × 2
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å
|
|
6N8J
Cryo-EM structure of late nuclear (LN) pre-60S ribosomal subunit
Deposited 2018-11-29
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 46
PDB declaration: 49-meric
|
Chain Y
1–127（127 aa）
|
Not recorded
|
GTP GUANOSINE-5'-TRIPHOSPHATE × 2
MG MAGNESIUM ION × 2
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å
|
|
6N8K
Cryo-EM structure of early cytoplasmic-immediate (ECI) pre-60S ribosomal subunit
Deposited 2018-11-29
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 45
PDB declaration: 48-meric
|
Chain Y
1–127（127 aa）
|
Not recorded
|
GTP GUANOSINE-5'-TRIPHOSPHATE × 1
MG MAGNESIUM ION × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å
|
|
6N8L
Cryo-EM structure of early cytoplasmic-late (ECL) pre-60S ribosomal subunit
Deposited 2018-11-29
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 45
PDB declaration: 48-meric
|
Chain Y
1–127（127 aa）
|
Not recorded
|
No recorded non-water small molecule
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å
|
|
6N8M
Cryo-EM structure of pre-Lsg1 (PL) pre-60S ribosomal subunit
Deposited 2018-11-29
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 44
PDB declaration: 47-meric
|
Chain l
1–127（127 aa）
|
Not recorded
|
No recorded non-water small molecule
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å
|
|
6N8N
Cryo-EM structure of Lsg1-engaged (LE) pre-60S ribosomal subunit
Deposited 2018-11-29
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 45
PDB declaration: 48-meric
|
Chain l
1–127（127 aa）
|
Not recorded
|
No recorded non-water small molecule
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å
|
|
6N8O
Cryo-EM structure of Rpl10-inserted (RI) pre-60S ribosomal subunit
Deposited 2018-11-29
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 46
PDB declaration: 49-meric
|
Chain l
1–127（127 aa）
|
Not recorded
|
No recorded non-water small molecule
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å
|
|
6OIG
Subunit joining exposes nascent pre-40S rRNA for processing and quality control
Deposited 2019-04-09
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 45
PDB declaration: 48-meric
|
Chain Y
2–127（126 aa）
|
Not recorded
|
No recorded non-water small molecule
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 6.8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å
|
|
6Q8Y
Cryo-EM structure of the mRNA translating and degrading yeast 80S ribosome-Xrn1 nuclease complex
Deposited 2018-12-16
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 75
PDB declaration: 82-meric
|
Chain AK
2–127（126 aa）
|
Not recorded
|
ZN ZINC ION × 8
MG MAGNESIUM ION × 2
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å
|
|
6QIK
Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles
Deposited 2019-01-20
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 44
PDB declaration: 47-meric
|
Chain X
1–127（127 aa）
|
Not recorded
|
ZN ZINC ION × 7
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å
|
|
6QT0
Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles
Deposited 2019-02-22
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 42
PDB declaration: 45-meric
|
Chain X
1–127（127 aa）
|
Not recorded
|
ZN ZINC ION × 5
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å
|
|
6QTZ
Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles
Deposited 2019-02-26
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 45
PDB declaration: 48-meric
|
Chain X
1–127（127 aa）
|
Not recorded
|
ZN ZINC ION × 7
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å
|
|
6R84
Yeast Vms1 (Q295L)-60S ribosomal subunit complex (pre-state with Arb1)
Deposited 2019-03-31
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 46
PDB declaration: 50-meric
|
Chain a
2–127（126 aa）
|
Not recorded
|
ZN ZINC ION × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å
|
|
6R86
Yeast Vms1-60S ribosomal subunit complex (post-state)
Deposited 2019-03-31
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 45
PDB declaration: 47-meric
|
Chain a
2–127（126 aa）
|
Not recorded
|
ZN ZINC ION × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å
|
|
6R87
Yeast Vms1 (Q295L)-60S ribosomal subunit complex (pre-state without Arb1)
Deposited 2019-03-31
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 45
PDB declaration: 49-meric
|
Chain a
2–127（126 aa）
|
Not recorded
|
ZN ZINC ION × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å
|
|
6RI5
Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles
Deposited 2019-04-23
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 45
PDB declaration: 48-meric
|
Chain X
1–127（127 aa）
|
Not recorded
|
ZN ZINC ION × 7
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å
|
|
6RZZ
Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles
Deposited 2019-06-13
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 45
PDB declaration: 48-meric
|
Chain X
1–127（127 aa）
|
Not recorded
|
ZN ZINC ION × 10
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å
|
|
6S05
Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles
Deposited 2019-06-13
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 44
PDB declaration: 47-meric
|
Chain X
1–127（127 aa）
|
Not recorded
|
ZN ZINC ION × 8
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å
|
|
6S47
Saccharomyces cerevisiae 80S ribosome bound with ABCF protein New1
Deposited 2019-06-26
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 75
PDB declaration: 79-meric
|
Chain Aa
2–127（126 aa）
|
Not recorded
|
ATP ADENOSINE-5'-TRIPHOSPHATE × 2
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 3.28 Å
|
|
6SNT
Yeast 80S ribosome stalled on SDD1 mRNA.
Deposited 2019-08-27
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 75
PDB declaration: 81-meric
|
Chain ar
1–127（127 aa）
|
Not recorded
|
MG MAGNESIUM ION × 87
ZN ZINC ION × 7
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å
|
|
6SV4
The cryo-EM structure of SDD1-stalled collided trisome.
Deposited 2019-09-17
|
Different construct
Different mutation/modification
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 225
PDB declaration: 242-meric
|
Chain AK
1–127（127 aa）
Chain XK
1–127（127 aa）
Chain zK
1–127（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 3.30 Å
|
|
6T4Q
Structure of yeast 80S ribosome stalled on the CGA-CCG inhibitory codon combination.
Deposited 2019-10-14
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 75
PDB declaration: 82-meric
|
Chain LY
2–126（125 aa）
|
Not recorded
|
MG MAGNESIUM ION × 291
ZN ZINC ION × 7
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.60 Å
|
|
6T7I
Structure of yeast 80S ribosome stalled on the CGA-CGA inhibitory codon combination.
Deposited 2019-10-22
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 74
PDB declaration: 81-meric
|
Chain LY
1–127（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 3.20 Å
|
|
6T7T
Structure of yeast 80S ribosome stalled on poly(A) tract.
Deposited 2019-10-23
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 75
PDB declaration: 82-meric
|
Chain LY
2–126（125 aa）
|
Not recorded
|
No recorded non-water small molecule
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å
|
|
6T83
Structure of yeast disome (di-ribosome) stalled on poly(A) tract.
Deposited 2019-10-24
|
Different construct
Different mutation/modification
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 149
PDB declaration: 159-meric
|
Chain J
1–127（127 aa）
Chain Yy
1–127（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 4.00 Å
|
|
6TB3
yeast 80S ribosome in complex with the Not5 subunit of the CCR4-NOT complex
Deposited 2019-10-31
|
Different construct
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 77
PDB declaration: 83-meric
|
Chain AK
2–126（125 aa）
|
Not recorded
|
MG MAGNESIUM ION × 327
ZN ZINC ION × 7
SPD SPERMIDINE × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å
|
|
6TNU
Yeast 80S ribosome in complex with eIF5A and decoding A-site and P-site tRNAs.
Deposited 2019-12-10
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 76
PDB declaration: 83-meric
|
Chain AK
2–126（125 aa）
|
Not recorded
|
ZN ZINC ION × 7
SPD SPERMIDINE × 1
3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å
|
|
6WOO
CryoEM structure of yeast 80S ribosome with Met-tRNAiMet, eIF5B, and GDP
Deposited 2020-04-25
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 78
PDB declaration: 84-meric
|
Chain Y
3–127（125 aa）
|
Not recorded
|
ZN ZINC ION × 6
GDP GUANOSINE-5'-DIPHOSPHATE × 1
U6A N-carboxy-L-threonine × 1
MET METHIONINE × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å
|
|
6XIQ
Cryo-EM Structure of K63R Ubiquitin Mutant Ribosome under Oxidative Stress
Deposited 2020-06-21
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 75
PDB declaration: 82-meric
|
Chain Y
1–127（127 aa）
|
Not recorded
|
ZN ZINC ION × 7
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.20 Å
|
|
6XIR
Cryo-EM Structure of K63 Ubiquitinated Yeast Translocating Ribosome under Oxidative Stress
Deposited 2020-06-21
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 70
PDB declaration: 76-meric
|
Chain Y
1–127（127 aa）
|
Not recorded
|
ZN ZINC ION × 6
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å
|
|
6YLG
Rix1-Rea1 pre-60S particle - 60S core, body 1 (rigid body refinement)
Deposited 2020-04-07
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 52
PDB declaration: 55-meric
|
Chain Y
1–127（127 aa）
|
Not recorded
|
ZN ZINC ION × 4
GTP GUANOSINE-5'-TRIPHOSPHATE × 2
MG MAGNESIUM ION × 2
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å
|
|
6YLH
Rix1-Rea1 pre-60S particle - full composite structure
Deposited 2020-04-07
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 57
PDB declaration: 60-meric
|
Chain Y
1–127（127 aa）
|
Not recorded
|
ZN ZINC ION × 4
GTP GUANOSINE-5'-TRIPHOSPHATE × 2
MG MAGNESIUM ION × 2
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å
|
|
6YLX
pre-60S State NE1 (TAP-Flag-Nop53)
Deposited 2020-04-07
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 44
PDB declaration: 47-meric
|
Chain Y
1–127（127 aa）
|
Not recorded
|
No recorded non-water small molecule
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å
|
|
6YLY
pre-60S State NE2 (TAP-Flag-Nop53)
Deposited 2020-04-07
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 46
PDB declaration: 49-meric
|
Chain Y
1–127（127 aa）
|
Not recorded
|
ZN ZINC ION × 3
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å
|
|
6Z6J
Cryo-EM structure of yeast Lso2 bound to 80S ribosomes under native condition
Deposited 2020-05-28
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 75
PDB declaration: 79-meric
|
Chain LY
1–127（127 aa）
|
Not recorded
|
ZN ZINC ION × 9
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å
|
|
6Z6K
Cryo-EM structure of yeast reconstituted Lso2 bound to 80S ribosomes
Deposited 2020-05-28
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 75
PDB declaration: 79-meric
|
Chain LY
1–127（127 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
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 39
PDB declaration: 42-meric
|
Chain q
1–127（127 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
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 75
PDB declaration: 82-meric
|
Chain LU
2–126（125 aa）
|
Not recorded
|
ATP ADENOSINE-5'-TRIPHOSPHATE × 2
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 6.5
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 3.30 Å
|
|
7BT6
Cryo-EM structure of pre-60S ribosome from Saccharomyces cerevisiae rpl4delta63-87 strain at 3.12 Angstroms resolution(state R1)
Deposited 2020-03-31
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 44
PDB declaration: 47-meric
|
Chain Y
1–127（127 aa）
|
Not recorded
|
GTP GUANOSINE-5'-TRIPHOSPHATE × 2
MG MAGNESIUM ION × 2
ZN ZINC ION × 3
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.12 Å
|
|
7BTB
Cryo-EM structure of pre-60S ribosome from Saccharomyces cerevisiae rpl4delta63-87 strain at 3.22 Angstroms resolution(state R2)
Deposited 2020-04-01
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 49
PDB declaration: 53-meric
|
Chain Y
1–127（127 aa）
|
Not recorded
|
GTP GUANOSINE-5'-TRIPHOSPHATE × 2
MG MAGNESIUM ION × 2
ZN ZINC ION × 3
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.22 Å
|
|
7MPI
Stm1 bound vacant 80S structure isolated from cbf5-D95A
Deposited 2021-05-04
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 75
PDB declaration: 79-meric
|
Chain AY
2–127（126 aa）
|
Not recorded
|
MG MAGNESIUM ION × 366
ZN ZINC ION × 2
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.05 Å
|
|
7MPJ
Stm1 bound vacant 80S structure isolated from wild-type
Deposited 2021-05-04
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 75
PDB declaration: 79-meric
|
Chain AY
2–127（126 aa）
|
Not recorded
|
MG MAGNESIUM ION × 745
ZN ZINC ION × 2
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.70 Å
|
|
7N8B
Cycloheximide bound vacant 80S structure isolated from cbf5-D95A
Deposited 2021-06-14
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 75
PDB declaration: 79-meric
|
Chain AY
2–127（126 aa）
|
Not recorded
|
3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1
MG MAGNESIUM ION × 374
ZN ZINC ION × 2
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.05 Å
|
|
7NAC
State E2 nucleolar 60S ribosomal biogenesis intermediate - Composite model
Deposited 2021-06-21
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 55
PDB declaration: 58-meric
|
Chain Y
1–127（127 aa）
|
Not recorded
|
ZN ZINC ION × 2
SAH S-ADENOSYL-L-HOMOCYSTEINE × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.04 Å
|
|
7NRC
Structure of the yeast Gcn1 bound to a leading stalled 80S ribosome with Rbg2, Gir2, A- and P-tRNA and eIF5A
Deposited 2021-03-03
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 79
PDB declaration: 86-meric
|
Chain La
2–126（125 aa）
|
Not recorded
|
No recorded non-water small molecule
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 3.90 Å
|
|
7NRD
Structure of the yeast Gcn1 bound to a colliding stalled 80S ribosome with MBF1, A/P-tRNA and P/E-tRNA
Deposited 2021-03-03
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 75
PDB declaration: 82-meric
|
Chain La
2–126（125 aa）
|
Not recorded
|
No recorded non-water small molecule
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 4.36 Å
|
|
7OF1
Nog1-TAP associated immature ribosomal particle population A from S. cerevisiae
Deposited 2021-05-04
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 39
PDB declaration: 42-meric
|
Chain Y
1–127（127 aa）
|
Not recorded
|
MG MAGNESIUM ION × 2
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å
|
|
7OH3
Nog1-TAP associated immature ribosomal particle population B from S. cerevisiae
Deposited 2021-05-08
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 47
PDB declaration: 50-meric
|
Chain Y
1–127（127 aa）
|
Not recorded
|
MG MAGNESIUM ION × 2
ZN ZINC ION × 3
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å
|
|
7OHP
Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL25 expression shut down, population A
Deposited 2021-05-11
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 31
PDB declaration: 34-meric
|
Chain Y
1–127（127 aa）
|
Not recorded
|
ZN ZINC ION × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å
|
|
7OHQ
Nog1-TAP associated immature ribosomal particle population C from S. cerevisiae
Deposited 2021-05-11
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 52
PDB declaration: 56-meric
|
Chain Y
1–127（127 aa）
|
Not recorded
|
MG MAGNESIUM ION × 2
ZN ZINC ION × 3
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å
|
|
7OHR
Nog1-TAP associated immature ribosomal particle population E from S. cerevisiae
Deposited 2021-05-11
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 48
PDB declaration: 51-meric
|
Chain Y
1–127（127 aa）
|
Not recorded
|
ZN ZINC ION × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.72 Å
|
|
7OHS
Nog1-TAP associated immature ribosomal particle population F from S. cerevisiae
Deposited 2021-05-11
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 37
PDB declaration: 40-meric
|
Chain Y
1–127（127 aa）
|
Not recorded
|
ZN ZINC ION × 2
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.38 Å
|
|
7OHU
Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL2 expression shut down, population B
Deposited 2021-05-11
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 25
PDB declaration: 27-meric
|
Chain Y
1–127（127 aa）
|
Not recorded
|
ZN ZINC ION × 2
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å
|
|
7OHV
Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL2 expression shut down, population C
Deposited 2021-05-11
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 43
PDB declaration: 46-meric
|
Chain Y
1–127（127 aa）
|
Not recorded
|
ZN ZINC ION × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å
|
|
7OHW
Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL25 expression shut down, population B
Deposited 2021-05-11
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 37
PDB declaration: 40-meric
|
Chain Y
1–127（127 aa）
|
Not recorded
|
ZN ZINC ION × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å
|
|
7OHX
Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL34 expression shut down, population A
Deposited 2021-05-11
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 34
PDB declaration: 37-meric
|
Chain Y
1–127（127 aa）
|
Not recorded
|
ZN ZINC ION × 2
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å
|
|
7OHY
Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL34 expression shut down, population B
Deposited 2021-05-11
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 24
PDB declaration: 26-meric
|
Chain Y
1–127（127 aa）
|
Not recorded
|
ZN ZINC ION × 2
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å
|
|
7OSM
Intermediate translocation complex of 80 S.cerevisiae ribosome with eEF2 and ligands
Deposited 2021-06-09
|
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 76
PDB declaration: 83-meric
|
Chain uL24
1–127（127 aa）
|
Not recorded
|
MG MAGNESIUM ION × 499
ZN ZINC ION × 8
GTP GUANOSINE-5'-TRIPHOSPHATE × 1
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；PEG 6000, KSCN, Tris-HAc
|
Resolution 3.00 Å
R-free 0.284
|
|
7R7A
State E1 nucleolar 60S ribosome biogenesis intermediate - Composite model
Deposited 2021-06-24
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 54
PDB declaration: 57-meric
|
Chain Y
1–127（127 aa）
|
Not recorded
|
ZN ZINC ION × 2
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.04 Å
|
|
7RR5
Structure of ribosomal complex bound with Rbg1/Tma46
Deposited 2021-08-09
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 80
PDB declaration: 87-meric
|
Chain LY
1–127（127 aa）
|
Not recorded
|
MG MAGNESIUM ION × 286
ASP ASPARTIC ACID × 1
ZN ZINC ION × 8
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.23 Å
|
|
7TOO
Yeast 80S ribosome bound with the ALS/FTD-associated dipeptide repeat protein GR20
Deposited 2022-01-24
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 44
PDB declaration: 48-meric
|
Chain AL26
1–127（127 aa）
|
Not recorded
|
ZN ZINC ION × 4
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.70 Å
|
|
7TOP
Yeast 80S ribosome bound with the ALS/FTD-associated dipeptide repeat protein PR20
Deposited 2022-01-24
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 44
PDB declaration: 48-meric
|
Chain AL26
1–127（127 aa）
|
Not recorded
|
ZN ZINC ION × 4
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.40 Å
|
|
7U0H
State NE1 nucleolar 60S ribosome biogenesis intermediate - Overall model
Deposited 2022-02-18
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 46
PDB declaration: 49-meric
|
Chain Y
1–127（127 aa）
|
Not recorded
|
MG MAGNESIUM ION × 1
ZN ZINC ION × 4
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.76 Å
|
|
7UG6
Cryo-EM structure of pre-60S ribosomal subunit, unmethylated G2922
Deposited 2022-03-24
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 49
PDB declaration: 52-meric
|
Chain Y
1–127（127 aa）
|
Not recorded
|
GDP GUANOSINE-5'-DIPHOSPHATE × 1
MG MAGNESIUM ION × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE；One blotting step of 2 seconds at force 0
|
Resolution 2.90 Å
|
|
7UOO
Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state
Deposited 2022-04-13
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 56
PDB declaration: 60-meric
|
Chain Y
1–127（127 aa）
|
Not recorded
|
MG MAGNESIUM ION × 81
B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3
ZN ZINC ION × 5
GDP GUANOSINE-5'-DIPHOSPHATE × 1
GTP GUANOSINE-5'-TRIPHOSPHATE × 1
K POTASSIUM ION × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.34 Å
|
|
7UQB
Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a SPB1-D52A strain with AlF4
Deposited 2022-04-19
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 56
PDB declaration: 60-meric
|
Chain Y
1–127（127 aa）
|
Not recorded
|
B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3
MG MAGNESIUM ION × 81
ZN ZINC ION × 5
GDP GUANOSINE-5'-DIPHOSPHATE × 2
ALF TETRAFLUOROALUMINATE ION × 1
K POTASSIUM ION × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.43 Å
|
|
7UQZ
Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a SPB1 D52A strain
Deposited 2022-04-20
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 56
PDB declaration: 60-meric
|
Chain Y
1–127（127 aa）
|
Not recorded
|
MG MAGNESIUM ION × 81
B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3
ZN ZINC ION × 5
GDP GUANOSINE-5'-DIPHOSPHATE × 2
K POTASSIUM ION × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.44 Å
|
|
7V08
Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a Spb1 D52A suppressor 3 strain
Deposited 2022-05-10
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 56
PDB declaration: 60-meric
|
Chain Y
1–127（127 aa）
|
Not recorded
|
MG MAGNESIUM ION × 81
B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3
ZN ZINC ION × 5
GDP GUANOSINE-5'-DIPHOSPHATE × 2
K POTASSIUM ION × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.36 Å
|
|
7Z34
Structure of pre-60S particle bound to DRG1(AFG2).
Deposited 2022-03-01
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 55
PDB declaration: 58-meric
|
Chain Y
1–127（127 aa）
|
Not recorded
|
AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 11
MG MAGNESIUM ION × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å
|
|
7ZPQ
Structure of the RQT-bound 80S ribosome from S. cerevisiae (C1)
Deposited 2022-04-28
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 77
PDB declaration: 82-meric
|
Chain BX
2–126（125 aa）
|
Not recorded
|
MG MAGNESIUM ION × 86
ZN ZINC ION × 9
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.47 Å
|
|
7ZRS
Structure of the RQT-bound 80S ribosome from S. cerevisiae (C2) - composite map
Deposited 2022-05-05
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 77
PDB declaration: 82-meric
|
Chain BX
2–126（125 aa）
|
Not recorded
|
MG MAGNESIUM ION × 4
ZN ZINC ION × 9
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.80 Å
|
|
7ZS5
Structure of 60S ribosomal subunit from S. cerevisiae with eIF6 and tRNA
Deposited 2022-05-06
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 42
PDB declaration: 45-meric
|
Chain BZ
1–127（127 aa）
|
Not recorded
|
MG MAGNESIUM ION × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å
|
|
7ZUW
Structure of RQT (C1) bound to the stalled ribosome in a disome unit from S. cerevisiae
Deposited 2022-05-13
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 77
PDB declaration: 82-meric
|
Chain BX
2–126（125 aa）
|
Not recorded
|
MG MAGNESIUM ION × 86
ZN ZINC ION × 9
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.30 Å
|
|
7ZUX
Collided ribosome in a disome unit from S. cerevisiae
Deposited 2022-05-13
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 74
PDB declaration: 80-meric
|
Chain EX
2–126（125 aa）
|
Not recorded
|
MG MAGNESIUM ION × 86
ZN ZINC ION × 7
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.50 Å
|
|
7ZW0
FAP-80S Complex - Rotated state
Deposited 2022-05-17
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 79
PDB declaration: 86-meric
|
Chain Lb
1–127（127 aa）
|
Not recorded
|
MG MAGNESIUM ION × 324
SPD SPERMIDINE × 1
ZN ZINC ION × 34
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.40 Å
|
|
8AAF
Yeast RQC complex in state G
Deposited 2022-07-01
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 49
PDB declaration: 54-meric
|
Chain L
1–127（127 aa）
|
Not recorded
|
MG MAGNESIUM ION × 13
ZN ZINC ION × 7
SPD SPERMIDINE × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 6.8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.50 Å
|
|
8AGT
Yeast RQC complex in state F
Deposited 2022-07-20
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 49
PDB declaration: 54-meric
|
Chain L
1–127（127 aa）
|
Not recorded
|
MG MAGNESIUM ION × 13
ZN ZINC ION × 7
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 6.8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.60 Å
|
|
8AGU
Yeast RQC complex in state E
Deposited 2022-07-20
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 49
PDB declaration: 53-meric
|
Chain L
1–127（127 aa）
|
Not recorded
|
MG MAGNESIUM ION × 13
ZN ZINC ION × 7
SPD SPERMIDINE × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 6.8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.70 Å
|
|
8AGV
Yeast RQC complex in state H
Deposited 2022-07-20
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 49
PDB declaration: 54-meric
|
Chain L
1–127（127 aa）
|
Not recorded
|
MG MAGNESIUM ION × 13
ZN ZINC ION × 7
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 6.8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.60 Å
|
|
8AGW
Yeast RQC complex in state D
Deposited 2022-07-20
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 48
PDB declaration: 53-meric
|
Chain L
1–127（127 aa）
|
Not recorded
|
MG MAGNESIUM ION × 13
ZN ZINC ION × 7
SPD SPERMIDINE × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 6.8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.60 Å
|
|
8AGX
Yeast RQC complex in state with the RING domain of Ltn1 in the IN position
Deposited 2022-07-20
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 48
PDB declaration: 52-meric
|
Chain L
1–127（127 aa）
|
Not recorded
|
MG MAGNESIUM ION × 13
ZN ZINC ION × 7
SPD SPERMIDINE × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 6.8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.40 Å
|
|
8AGZ
Yeast RQC complex in state with the RING domain of Ltn1 in the OUT position
Deposited 2022-07-20
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 49
PDB declaration: 54-meric
|
Chain L
1–127（127 aa）
|
Not recorded
|
MG MAGNESIUM ION × 13
ZN ZINC ION × 7
SPD SPERMIDINE × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 6.8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.60 Å
|
|
8BIP
Structure of a yeast 80S ribosome-bound N-Acetyltransferase B complex
Deposited 2022-11-02
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 44
PDB declaration: 47-meric
|
Chain LY
2–126（125 aa）
|
Not recorded
|
MG MAGNESIUM ION × 206
ZN ZINC ION × 5
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å
|
|
8BJQ
Structure of a yeast 80S ribosome-bound N-Acetyltransferase B complex
Deposited 2022-11-05
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 45
PDB declaration: 48-meric
|
Chain LY
2–126（125 aa）
|
Not recorded
|
MG MAGNESIUM ION × 206
ZN ZINC ION × 5
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å
|
|
8BN3
Yeast 80S, ES7s delta, eIF5A, Stm1 containing
Deposited 2022-11-12
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 77
PDB declaration: 81-meric
|
Chain N6
2–127（126 aa）
|
Not recorded
|
MG MAGNESIUM ION × 220
K POTASSIUM ION × 72
3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1
SPD SPERMIDINE × 3
ZN ZINC ION × 7
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 2.40 Å
|
|
8BQD
Yeast 80S ribosome in complex with Map1 (conformation 1)
Deposited 2022-11-21
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 76
PDB declaration: 80-meric
|
Chain AK
2–126（125 aa）
|
Not recorded
|
ZN ZINC ION × 7
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å
|
|
8BQX
Yeast 80S ribosome in complex with Map1 (conformation 2)
Deposited 2022-11-21
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 76
PDB declaration: 80-meric
|
Chain AK
2–126（125 aa）
|
Not recorded
|
ZN ZINC ION × 7
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å
|
|
8CCS
80S S. cerevisiae ribosome with ligands in hybrid-1 pre-translocation (PRE-H1) complex
Deposited 2023-01-27
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 76
PDB declaration: 83-meric
|
Chain K
1–127（127 aa）
|
Not recorded
|
ZN ZINC ION × 8
MG MAGNESIUM ION × 281
K POTASSIUM ION × 22
SPD SPERMIDINE × 4
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 1.97 Å
|
|
8CDL
80S S. cerevisiae ribosome with ligands in hybrid-2 pre-translocation (PRE-H2) complex
Deposited 2023-01-31
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 76
PDB declaration: 83-meric
|
Chain K
1–127（127 aa）
|
Not recorded
|
ZN ZINC ION × 8
MG MAGNESIUM ION × 258
K POTASSIUM ION × 21
SPD SPERMIDINE × 4
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.72 Å
|
|
8CDR
Translocation intermediate 2 (TI-2) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin
Deposited 2023-01-31
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 77
PDB declaration: 84-meric
|
Chain K
1–127（127 aa）
|
Not recorded
|
ZN ZINC ION × 8
MG MAGNESIUM ION × 267
SPD SPERMIDINE × 4
K POTASSIUM ION × 21
GDP GUANOSINE-5'-DIPHOSPHATE × 1
SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.04 Å
|
|
8CEH
Translocation intermediate 4 (TI-4) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin
Deposited 2023-02-01
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 77
PDB declaration: 84-meric
|
Chain K
1–127（127 aa）
|
Not recorded
|
ZN ZINC ION × 8
MG MAGNESIUM ION × 262
K POTASSIUM ION × 21
SPD SPERMIDINE × 3
GDP GUANOSINE-5'-DIPHOSPHATE × 1
PO4 PHOSPHATE ION × 1
SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.05 Å
|
|
8CF5
Translocation intermediate 1 (TI-1) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin
Deposited 2023-02-02
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 77
PDB declaration: 84-meric
|
Chain K
1–127（127 aa）
|
Not recorded
|
ZN ZINC ION × 8
MG MAGNESIUM ION × 241
K POTASSIUM ION × 21
SPD SPERMIDINE × 11
GTP GUANOSINE-5'-TRIPHOSPHATE × 1
SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.71 Å
|
|
8CG8
Translocation intermediate 3 (TI-3) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin
Deposited 2023-02-03
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 77
PDB declaration: 84-meric
|
Chain K
1–127（127 aa）
|
Not recorded
|
ZN ZINC ION × 8
MG MAGNESIUM ION × 241
SPD SPERMIDINE × 8
K POTASSIUM ION × 19
GTP GUANOSINE-5'-TRIPHOSPHATE × 1
SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.57 Å
|
|
8CGN
Non-rotated 80S S. cerevisiae ribosome with ligands
Deposited 2023-02-06
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 75
PDB declaration: 82-meric
|
Chain K
1–127（127 aa）
|
Not recorded
|
ZN ZINC ION × 8
MG MAGNESIUM ION × 263
K POTASSIUM ION × 19
SPD SPERMIDINE × 4
MET METHIONINE × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.28 Å
|
|
8CIV
Translocation intermediate 5 (TI-5) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin
Deposited 2023-02-10
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 77
PDB declaration: 84-meric
|
Chain K
1–127（127 aa）
|
Not recorded
|
ZN ZINC ION × 8
MG MAGNESIUM ION × 251
K POTASSIUM ION × 21
SPD SPERMIDINE × 3
SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1
GDP GUANOSINE-5'-DIPHOSPHATE × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.47 Å
|
|
8CKU
Translocation intermediate 1 (TI-1*) of 80S S. cerevisiae ribosome with ligands and eEF2 in the absence of sordarin
Deposited 2023-02-16
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 76
PDB declaration: 83-meric
|
Chain K
1–127（127 aa）
|
Not recorded
|
ZN ZINC ION × 8
MG MAGNESIUM ION × 205
K POTASSIUM ION × 16
SPD SPERMIDINE × 3
GTP GUANOSINE-5'-TRIPHOSPHATE × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.11 Å
|
|
8CMJ
Translocation intermediate 4 (TI-4*) of 80S S. cerevisiae ribosome with eEF2 in the absence of sordarin
Deposited 2023-02-20
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 76
PDB declaration: 80-meric
|
Chain K
1–127（127 aa）
|
Not recorded
|
ZN ZINC ION × 8
MG MAGNESIUM ION × 153
K POTASSIUM ION × 10
GTP GUANOSINE-5'-TRIPHOSPHATE × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.79 Å
|
|
8EUB
Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2 and GDP, Structure I
Deposited 2022-10-18
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 77
PDB declaration: 82-meric
|
Chain AY
1–127（127 aa）
|
Not recorded
|
MG MAGNESIUM ION × 255
ZN ZINC ION × 1
GDP GUANOSINE-5'-DIPHOSPHATE × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.52 Å
|
|
8EVP
Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), Structure I
Deposited 2022-10-20
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 75
PDB declaration: 80-meric
|
Chain AY
1–127（127 aa）
|
Not recorded
|
MG MAGNESIUM ION × 256
ZN ZINC ION × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.38 Å
|
|
8EVQ
Hypopseudouridylated Ribosome bound with TSV IRES, eEF2, GDP, and sordarin, Structure I
Deposited 2022-10-20
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 77
PDB declaration: 82-meric
|
Chain AY
1–127（127 aa）
|
Not recorded
|
MG MAGNESIUM ION × 241
ZN ZINC ION × 1
GDP GUANOSINE-5'-DIPHOSPHATE × 1
SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.72 Å
|
|
8EVR
Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure II
Deposited 2022-10-20
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 77
PDB declaration: 82-meric
|
Chain AY
1–127（127 aa）
|
Not recorded
|
MG MAGNESIUM ION × 217
ZN ZINC ION × 1
GDP GUANOSINE-5'-DIPHOSPHATE × 1
W9C (1S,3S,3aR,4S,4aR,7R,7aR,8aS)-8a-{[(6-deoxy-4-O-methyl-alpha-D-altropyranosyl)oxy]methyl}-4-formyl-7-methyl-3-(propan-2-yl)decahydro-1,4-methano-s-indacene-3a(1H)-carboxylate × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.87 Å
|
|
8EVS
Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2 and GDP, Structure II
Deposited 2022-10-20
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 77
PDB declaration: 82-meric
|
Chain AY
1–127（127 aa）
|
Not recorded
|
MG MAGNESIUM ION × 254
ZN ZINC ION × 1
GDP GUANOSINE-5'-DIPHOSPHATE × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.62 Å
|
|
8EVT
Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES) refined against a composite map
Deposited 2022-10-20
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 75
PDB declaration: 80-meric
|
Chain AY
1–127（127 aa）
|
Not recorded
|
MG MAGNESIUM ION × 272
ZN ZINC ION × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.20 Å
|
|
8EWB
Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2 and GDP, Structure III
Deposited 2022-10-22
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 77
PDB declaration: 82-meric
|
Chain AY
1–127（127 aa）
|
Not recorded
|
MG MAGNESIUM ION × 242
ZN ZINC ION × 1
GDP GUANOSINE-5'-DIPHOSPHATE × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.87 Å
|
|
8EWC
Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), Structure II
Deposited 2022-10-22
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 75
PDB declaration: 80-meric
|
Chain AY
1–127（127 aa）
|
Not recorded
|
MG MAGNESIUM ION × 247
ZN ZINC ION × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.45 Å
|
|
8HFR
NPC-trapped pre-60S particle
Deposited 2022-11-12
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 58
PDB declaration: 61-meric
|
Chain YU
1–127（127 aa）
|
Not recorded
|
MG MAGNESIUM ION × 237
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.64 Å
|
|
8K2D
Cryo-EM structure of the yeast 80S ribosome with tigecycline, eEF2, Stm1 and eIF5A
Deposited 2023-07-12
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 80
PDB declaration: 84-meric
|
Chain LY
1–127（127 aa）
|
Not recorded
|
ZN ZINC ION × 9
T1C TIGECYCLINE × 6
MG MAGNESIUM ION × 4
GDP GUANOSINE-5'-DIPHOSPHATE × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å
|
|
8K82
Cryo-EM structure of the yeast 80S ribosome with tigecycline, Not5 and P-site tRNA
Deposited 2023-07-28
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 79
PDB declaration: 85-meric
|
Chain LY
1–127（127 aa）
|
Not recorded
|
MG MAGNESIUM ION × 316
T1C TIGECYCLINE × 6
SPD SPERMIDINE × 1
ZN ZINC ION × 9
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å
|
|
8P4V
80S yeast ribosome in complex with HaterumaimideQ
Deposited 2023-05-23
|
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 75
PDB declaration: 79-meric
|
Chain 9
1–127（127 aa）
|
Not recorded
|
OHX osmium (III) hexammine × 461
MG MAGNESIUM ION × 711
K POTASSIUM ION × 2
SPD SPERMIDINE × 1
X1K (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},8~{a}~{S})-5,5,8~{a}-trimethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1
ZN ZINC ION × 8
OS OSMIUM ION × 1
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
|
Resolution 3.16 Å
R-free 0.251
|
|
8P4V
80S yeast ribosome in complex with HaterumaimideQ
Deposited 2023-05-23
|
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 2
Protein–RNA
Heteromer；Protein × 76
PDB declaration: 80-meric
|
Chain DA
1–127（127 aa）
|
Not recorded
|
OHX osmium (III) hexammine × 492
MG MAGNESIUM ION × 766
K POTASSIUM ION × 5
SPD SPERMIDINE × 1
X1K (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},8~{a}~{S})-5,5,8~{a}-trimethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1
ZN ZINC ION × 7
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
|
Resolution 3.16 Å
R-free 0.251
|
|
8P85
80S yeast ribosome in complex with Fluorolissoclimide
Deposited 2023-08-31
|
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 74
PDB declaration: 78-meric
|
Chain 9
1–127（127 aa）
|
Not recorded
|
OHX osmium (III) hexammine × 484
MG MAGNESIUM ION × 717
K POTASSIUM ION × 2
SPD SPERMIDINE × 1
VDU fluorolissoclimide × 1
ZN ZINC ION × 8
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
|
Resolution 2.90 Å
R-free 0.223
|
|
8P85
80S yeast ribosome in complex with Fluorolissoclimide
Deposited 2023-08-31
|
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 2
Protein–RNA
Heteromer；Protein × 75
PDB declaration: 79-meric
|
Chain DA
1–127（127 aa）
|
Not recorded
|
OHX osmium (III) hexammine × 519
MG MAGNESIUM ION × 785
K POTASSIUM ION × 2
SPD SPERMIDINE × 1
VDU fluorolissoclimide × 1
ZN ZINC ION × 9
5XU (2~{S})-2-azanylpropanal × 5
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
|
Resolution 2.90 Å
R-free 0.223
|
|
8P8M
Yeast 60S ribosomal subunit, RPL39 deletion
Deposited 2023-06-01
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 40
PDB declaration: 43-meric
|
Chain QY
1–127（127 aa）
|
Not recorded
|
MG MAGNESIUM ION × 156
SPM SPERMINE × 1
SPD SPERMIDINE × 1
ZN ZINC ION × 5
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 2.66 Å
|
|
8P8N
Mouse RPL39 integrated into the yeast 60S ribosomal subunit
Deposited 2023-06-02
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 40
PDB declaration: 43-meric
|
Chain QY
1–127（127 aa）
|
Not recorded
|
MG MAGNESIUM ION × 152
CL CHLORIDE ION × 20
SPD SPERMIDINE × 1
SPM SPERMINE × 1
ZN ZINC ION × 5
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 2.15 Å
|
|
8P8U
Yeast 60S ribosomal subunit
Deposited 2023-06-02
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 40
PDB declaration: 43-meric
|
Chain QY
1–127（127 aa）
|
Not recorded
|
MG MAGNESIUM ION × 129
CL CHLORIDE ION × 24
SPM SPERMINE × 1
SPD SPERMIDINE × 1
ZN ZINC ION × 5
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 2.23 Å
|
|
8P9A
80S yeast ribosome in complex with Methyllissoclimide
Deposited 2023-06-05
|
Different construct
Different mutation/modification
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 150
PDB declaration: 158-meric
|
Chain 9
1–127（127 aa）
Chain DA
1–127（127 aa）
|
Not recorded
|
OHX osmium (III) hexammine × 930
MG MAGNESIUM ION × 1464
SPD SPERMIDINE × 2
XBI (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},7~{S},8~{a}~{S})-5,5,7,8~{a}-tetramethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 2
ZN ZINC ION × 18
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
|
Resolution 2.90 Å
|
|
8PFR
Mouse RPL39L integrated into the yeast 60S ribosomal subunit
Deposited 2023-06-16
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 40
PDB declaration: 43-meric
|
Chain QY
1–127（127 aa）
|
Not recorded
|
MG MAGNESIUM ION × 170
CL CHLORIDE ION × 24
SPM SPERMINE × 1
SPD SPERMIDINE × 1
ZN ZINC ION × 5
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6；50mM Hepes pH 7.6, 200 mM KCl, 10 mM
MgCl2, 5 mM EDTA, 2 mM DTT
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE；30s pre-blot incubation
|
Resolution 2.15 Å
|
|
8PNN
80S yeast ribosome in complex with Bromolissoclimide
Deposited 2023-06-30
|
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 74
PDB declaration: 78-meric
|
Chain 9
1–127（127 aa）
|
Not recorded
|
OHX osmium (III) hexammine × 456
MG MAGNESIUM ION × 707
ZN ZINC ION × 8
K POTASSIUM ION × 1
ZWB (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},7~{S},8~{a}~{S})-7-bromanyl-5,5,8~{a}-trimethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1
SPD SPERMIDINE × 1
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
|
Resolution 2.90 Å
R-free 0.230
|
|
8PNN
80S yeast ribosome in complex with Bromolissoclimide
Deposited 2023-06-30
|
Different oligomeric state
Different ligand/ion
Different experimental conditions
Different structure-quality metrics
|
Assembly 2
Protein–RNA
Heteromer；Protein × 74
PDB declaration: 78-meric
|
Chain DA
1–127（127 aa）
|
Not recorded
|
OHX osmium (III) hexammine × 479
MG MAGNESIUM ION × 783
ZN ZINC ION × 7
K POTASSIUM ION × 3
ZWB (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},7~{S},8~{a}~{S})-7-bromanyl-5,5,8~{a}-trimethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1
SPD SPERMIDINE × 3
|
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
|
Resolution 2.90 Å
R-free 0.230
|
|
8T2X
Hypomethylated yeast 80S bound with cycloheximide, P-site tRNA, A-site tRNA, messenger RNA and eIF5A, PRE
Deposited 2023-06-07
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 76
PDB declaration: 83-meric
|
Chain AY
1–127（127 aa）
|
Not recorded
|
MG MAGNESIUM ION × 181
K POTASSIUM ION × 23
SPD SPERMIDINE × 1
3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1
ZN ZINC ION × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.46 Å
|
|
8T2Y
Hypomethylated yeast 80S bound with cycloheximide, P-site tRNA, and A-site tRNA, messenger RNA, PRE
Deposited 2023-06-07
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 74
PDB declaration: 81-meric
|
Chain AY
1–127（127 aa）
|
Not recorded
|
MG MAGNESIUM ION × 197
SPD SPERMIDINE × 1
3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1
ZN ZINC ION × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.20 Å
|
|
8T2Z
Hypomethylated yeast 80S bound with cycloheximide, P-site tRNA, and A-site tRNA, messenger RNA, POST
Deposited 2023-06-07
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 74
PDB declaration: 81-meric
|
Chain AY
1–127（127 aa）
|
Not recorded
|
SPD SPERMIDINE × 1
3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1
ZN ZINC ION × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.40 Å
|
|
8T30
Hypomethylated yeast 80S bound with cycloheximide, unmodified U2921, mid rotated
Deposited 2023-06-07
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 74
PDB declaration: 78-meric
|
Chain AY
1–127（127 aa）
|
Not recorded
|
SPD SPERMIDINE × 1
3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1
ZN ZINC ION × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.88 Å
|
|
8T3A
Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, sordarin, and hibernating factor Los2
Deposited 2023-06-07
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 77
PDB declaration: 82-meric
|
Chain AY
1–127（127 aa）
|
Not recorded
|
ZN ZINC ION × 1
GDP GUANOSINE-5'-DIPHOSPHATE × 1
MG MAGNESIUM ION × 1
SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.86 Å
|
|
8T3B
Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure I
Deposited 2023-06-07
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 76
PDB declaration: 81-meric
|
Chain AY
1–127（127 aa）
|
Not recorded
|
ZN ZINC ION × 1
GDP GUANOSINE-5'-DIPHOSPHATE × 1
MG MAGNESIUM ION × 1
SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.08 Å
|
|
8T3C
Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure II
Deposited 2023-06-07
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 76
PDB declaration: 81-meric
|
Chain AY
1–127（127 aa）
|
Not recorded
|
ZN ZINC ION × 1
GDP GUANOSINE-5'-DIPHOSPHATE × 1
MG MAGNESIUM ION × 1
SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.86 Å
|
|
8T3D
Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure III
Deposited 2023-06-07
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 76
PDB declaration: 81-meric
|
Chain AY
1–127（127 aa）
|
Not recorded
|
ZN ZINC ION × 1
GDP GUANOSINE-5'-DIPHOSPHATE × 1
MG MAGNESIUM ION × 1
SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.95 Å
|
|
8T3E
Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure IV
Deposited 2023-06-07
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 76
PDB declaration: 81-meric
|
Chain AY
1–127（127 aa）
|
Not recorded
|
ZN ZINC ION × 1
GDP GUANOSINE-5'-DIPHOSPHATE × 1
MG MAGNESIUM ION × 1
SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.04 Å
|
|
8T3F
Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure V
Deposited 2023-06-07
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 76
PDB declaration: 81-meric
|
Chain AY
1–127（127 aa）
|
Not recorded
|
ZN ZINC ION × 1
GDP GUANOSINE-5'-DIPHOSPHATE × 1
MG MAGNESIUM ION × 1
SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.09 Å
|
|
8UT0
Eukaryotic 80S ribosome with Reh1, eIF5A and A/P site tRNA
Deposited 2023-10-30
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 77
PDB declaration: 84-meric
|
Chain La
2–126（125 aa）
|
Not recorded
|
3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.22 Å
|
|
8UTI
Eukaryotic 80S ribosome with Reh1 and A/P site tRNA
Deposited 2023-10-31
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 75
PDB declaration: 82-meric
|
Chain La
2–126（125 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
|
|
8V83
60S ribosome biogenesis intermediate (Dbp10 pre-catalytic structure - Overall map)
Deposited 2023-12-04
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 45
PDB declaration: 48-meric
|
Chain Y
1–127（127 aa）
|
Not recorded
|
ZN ZINC ION × 2
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.53 Å
|
|
8V84
60S ribosome biogenesis intermediate (Dbp10 catalytic structure - Overall map)
Deposited 2023-12-04
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 46
PDB declaration: 49-meric
|
Chain Y
1–127（127 aa）
|
Not recorded
|
GDP GUANOSINE-5'-DIPHOSPHATE × 1
MG MAGNESIUM ION × 1
ZN ZINC ION × 2
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.70 Å
|
|
8V87
60S ribosome biogenesis intermediate (Dbp10 post-catalytic structure - Overall map)
Deposited 2023-12-04
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 53
PDB declaration: 56-meric
|
Chain Y
1–127（127 aa）
|
Not recorded
|
ADP ADENOSINE-5'-DIPHOSPHATE × 1
MG MAGNESIUM ION × 2
GDP GUANOSINE-5'-DIPHOSPHATE × 1
K POTASSIUM ION × 1
ZN ZINC ION × 2
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.66 Å
|
|
8XU8
State 2c(S2c) of yeast 80S ribosome bound to compact eEF2 and 2 tRNAs during peptidyl transferation
Deposited 2024-01-12
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 75
PDB declaration: 81-meric
|
Chain a
2–126（125 aa）
|
Not recorded
|
No recorded non-water small molecule
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 4.5；YPD
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å
|
|
8Y0U
dormant ribosome with STM1
Deposited 2024-01-23
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 73
PDB declaration: 77-meric
|
Chain LY
1–127（127 aa）
|
Not recorded
|
MG MAGNESIUM ION × 281
ZN ZINC ION × 7
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；50mM HEPES, pH7.5, 100mM KOAc, 5mM Mg(OAc)2, 1mM DTT
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.59 Å
|
|
8YLD
State 4a (S4a) of yeast 80S ribosome bound to 2 tRNAs and open eEF3 and eEF2 during translocation
Deposited 2024-03-06
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 76
PDB declaration: 82-meric
|
Chain a
2–126（125 aa）
|
Not recorded
|
No recorded non-water small molecule
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 4.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å
|
|
8YLR
State 6 (S6) of yeast 80S ribosome bound to 2 tRNAs and eEF2 and eEF3 during tranlocation
Deposited 2024-03-06
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 76
PDB declaration: 82-meric
|
Chain a
2–126（125 aa）
|
Not recorded
|
No recorded non-water small molecule
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 4.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å
|
|
8Z70
State 1 (S1) of yeast 80S ribosome bound to 2 tRNAs during mRNA decoding
Deposited 2024-04-19
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 75
PDB declaration: 81-meric
|
Chain a
2–126（125 aa）
|
Not recorded
|
No recorded non-water small molecule
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 4.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å
|
|
8Z71
State 1a (S1a) of yeast 80S ribosome bound to open eEF3 and 2 tRNAs and eEF1A during mRNA decoding
Deposited 2024-04-19
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 76
PDB declaration: 82-meric
|
Chain a
2–126（125 aa）
|
Not recorded
|
No recorded non-water small molecule
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 4.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å
|
|
8ZGR
80S ribosome with A/A tRNA and mRNA of WNV
Deposited 2024-05-09
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 74
PDB declaration: 79-meric
|
Chain La
2–126（125 aa）
|
Not recorded
|
No recorded non-water small molecule
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.70 Å
|
|
8ZGY
80S ribosome with P/E tRNA and mRNA of WNV
Deposited 2024-05-10
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 74
PDB declaration: 80-meric
|
Chain La
2–126（125 aa）
|
Not recorded
|
No recorded non-water small molecule
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å
|
|
8ZH3
80S ribosome with A/P-P/E tRNA and mRNA of WNV
Deposited 2024-05-10
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 74
PDB declaration: 81-meric
|
Chain La
2–126（125 aa）
|
Not recorded
|
No recorded non-water small molecule
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.70 Å
|
|
8ZHB
80S ribosome with A/A P/E tRNA and mRNA of WNV
Deposited 2024-05-10
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 74
PDB declaration: 81-meric
|
Chain La
2–126（125 aa）
|
Not recorded
|
No recorded non-water small molecule
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.60 Å
|
|
8ZHC
pre-frameshift complex of yeast 80S ribosome with eRF1 and mRNA of WNV
Deposited 2024-05-10
|
Different construct
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 76
PDB declaration: 82-meric
|
Chain La
2–126（125 aa）
|
Not recorded
|
No recorded non-water small molecule
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.30 Å
|
|
9DOV
Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES) and hygromycin B
Deposited 2024-09-19
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 75
PDB declaration: 80-meric
|
Chain AY
1–127（127 aa）
|
Not recorded
|
MG MAGNESIUM ION × 257
HYG HYGROMYCIN B × 1
ZN ZINC ION × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.49 Å
|
|
9DP7
Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES) and hygromycin B, Class II
Deposited 2024-09-20
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 75
PDB declaration: 80-meric
|
Chain AY
1–127（127 aa）
|
Not recorded
|
MG MAGNESIUM ION × 247
HYG HYGROMYCIN B × 1
ZN ZINC ION × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.38 Å
|
|
9F58
Gcn2 dimer bound to the 60S ribosomal subunit
Deposited 2024-04-28
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 47
PDB declaration: 50-meric
|
Chain J
1–127（127 aa）
|
Not recorded
|
ZN ZINC ION × 5
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 3.10 Å
|
|
9F9S
Yeast SDD1 Disome with Mbf1
Deposited 2024-05-08
|
Different construct
Different mutation/modification
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 152
PDB declaration: 164-meric
|
Chain Ls
1–127（127 aa）
Chain Ms
1–127（127 aa）
|
Not recorded
|
MG MAGNESIUM ION × 295
ZN ZINC ION × 13
K POTASSIUM ION × 16
SPD SPERMIDINE × 3
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å
|
|
9OFV
Consensus reconstruction of the eukaryotic Ribosome-associated Quality Control complex
Deposited 2025-04-30
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 59
PDB declaration: 64-meric
|
Chain L
1–127（127 aa）
|
Not recorded
|
ATP ADENOSINE-5'-TRIPHOSPHATE × 9
ADP ADENOSINE-5'-DIPHOSPHATE × 1
ZN ZINC ION × 7
MG MAGNESIUM ION × 12
SPD SPERMIDINE × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.16 Å
|
|
9PN5
Composite map of hypomethylated 80S ribosome treated with hygromycin B
Deposited 2025-07-19
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 74
PDB declaration: 78-meric
|
Chain AY
1–127（127 aa）
|
Not recorded
|
MG MAGNESIUM ION × 174
K POTASSIUM ION × 27
ZN ZINC ION × 1
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 1.75 Å
|
|
9R9O
Yeast 80S with nascent chain in complex with Ssb1-ADP in the S1 state
Deposited 2025-05-20
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 73
PDB declaration: 79-meric
|
Chain LY
1–127（127 aa）
|
Not recorded
|
No recorded non-water small molecule
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å
|
|
9R9P
Yeast 80S with nascent chain in complex with Ssb1-ADP in the S2 state
Deposited 2025-05-20
|
Different oligomeric state
Different ligand/ion
Different experimental method
Different experimental conditions
Different structure-quality metrics
|
Assembly 1
Protein–RNA
Heteromer；Protein × 73
PDB declaration: 79-meric
|
Chain LY
1–127（127 aa）
|
Not recorded
|
No recorded non-water small molecule
|
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å
|
