← Back to search

Protein Structures and Oligomeric States

Enter a protein name, UniProt accession or PDB ID. Name searches ask you to confirm the protein identity before related structures are queried.

Current Protein Identity：P53927 New Search
33PDB entries
38Biological assembly
40chain/assembly records
Main Difference Dimensions in This Set
Different construct Different mutation/modification Different assembly state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics

Difference tags compare only the current result set; every original PDB and assembly record remains separate.

Related-Structure Differences

Each row represents one biological assembly in one PDB entry; multiple monomers of the same protein are listed separately.

PDB Entry Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Experimental Method Experimental Conditions Structure Quality
3JCT Cryo-em structure of eukaryotic pre-60S ribosomal subunits Deposited 2016-03-09 Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 58-meric（58） Consistent with all polymers
Chain o 1–220（220 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
5T9P Structural analysis reveals the flexible C-terminus of Nop15 undergoes rearrangement to recognize a pre-ribosomal RNA folding intermediate Deposited 2016-09-09 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain B 81–191（111 aa） Fragment：residues 81-191
Not recorded SO4 SULFATE ION × 5 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.25；295 K；18% (w/v) PEG 4000, 0.2 M ammonium sulfate, pH 5.25 and 9% (v/v) Jeffamine 600
Resolution 2.00 Å R-free 0.236
5T9P Structural analysis reveals the flexible C-terminus of Nop15 undergoes rearrangement to recognize a pre-ribosomal RNA folding intermediate Deposited 2016-09-09 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain C 81–191（111 aa） Fragment：residues 81-191
Not recorded SO4 SULFATE ION × 4 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.25；295 K；18% (w/v) PEG 4000, 0.2 M ammonium sulfate, pH 5.25 and 9% (v/v) Jeffamine 600
Resolution 2.00 Å R-free 0.236
5T9P Structural analysis reveals the flexible C-terminus of Nop15 undergoes rearrangement to recognize a pre-ribosomal RNA folding intermediate Deposited 2016-09-09 Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 81–191（111 aa） Fragment：residues 81-191
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.25；295 K；18% (w/v) PEG 4000, 0.2 M ammonium sulfate, pH 5.25 and 9% (v/v) Jeffamine 600
Resolution 2.00 Å R-free 0.236
5T9P Structural analysis reveals the flexible C-terminus of Nop15 undergoes rearrangement to recognize a pre-ribosomal RNA folding intermediate Deposited 2016-09-09 Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain D 81–191（111 aa） Fragment：residues 81-191
Not recorded SO4 SULFATE ION × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.25；295 K；18% (w/v) PEG 4000, 0.2 M ammonium sulfate, pH 5.25 and 9% (v/v) Jeffamine 600
Resolution 2.00 Å R-free 0.236
5T9P Structural analysis reveals the flexible C-terminus of Nop15 undergoes rearrangement to recognize a pre-ribosomal RNA folding intermediate Deposited 2016-09-09 Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain A 81–191（111 aa） Fragment：residues 81-191
Chain B 81–191（111 aa） Fragment：residues 81-191
Not recorded SO4 SULFATE ION × 6 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.25；295 K；18% (w/v) PEG 4000, 0.2 M ammonium sulfate, pH 5.25 and 9% (v/v) Jeffamine 600
Resolution 2.00 Å R-free 0.236
5T9P Structural analysis reveals the flexible C-terminus of Nop15 undergoes rearrangement to recognize a pre-ribosomal RNA folding intermediate Deposited 2016-09-09 Assembly 6 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain C 81–191（111 aa） Fragment：residues 81-191
Chain D 81–191（111 aa） Fragment：residues 81-191
Not recorded SO4 SULFATE ION × 5 CL CHLORIDE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.25；295 K；18% (w/v) PEG 4000, 0.2 M ammonium sulfate, pH 5.25 and 9% (v/v) Jeffamine 600
Resolution 2.00 Å R-free 0.236
5Z3G Cryo-EM structure of a nucleolar pre-60S ribosome (Rpf1-TAP) Deposited 2018-01-06 Assembly 1 Protein–RNA Heteromer；Protein × 32 PDB declaration: 35-meric（35） Consistent with all polymers
Chain E 1–220（220 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 Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric（43） Consistent with all polymers
Chain o 1–220（220 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 Assembly 1 Insufficient information Heteromer；Protein × 37 PDB declaration: 40-meric（40） Consistent with all polymers
Chain o 1–220（220 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 Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 54-meric（54） Consistent with all polymers
Chain o 1–220（220 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 Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric（43） Consistent with all polymers
Chain o 1–220（220 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 Assembly 1 Protein–RNA Heteromer；Protein × 30 PDB declaration: 33-meric（33） Consistent with all polymers
Chain o 1–220（220 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 Assembly 1 Protein–RNA Heteromer；Protein × 34 PDB declaration: 37-meric（37） Consistent with all polymers
Chain o 1–220（220 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 Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric（57） Consistent with all polymers
Chain o 1–220（220 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
6M62 Cryo-Em structure of eukaryotic pre-60S ribosome subunit from Saccharomyces cerevisiae rpf2 delta 255-344 strain, C4 state. Deposited 2020-03-12 Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 58-meric（58） Consistent with all polymers
Chain o 1–220（220 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
6YLX pre-60S State NE1 (TAP-Flag-Nop53) Deposited 2020-04-07 Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric（47） Consistent with all polymers
Chain o 1–220（220 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 Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric（49） Consistent with all polymers
Chain o 1–220（220 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
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 Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 53-meric（53） Consistent with all polymers
Chain o 1–220（220 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
7NAC State E2 nucleolar 60S ribosomal biogenesis intermediate - Composite model Deposited 2021-06-21 Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 58-meric（58） Consistent with all polymers
Chain o 1–220（220 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
7OHP Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL25 expression shut down, population A Deposited 2021-05-11 Assembly 1 Protein–RNA Heteromer；Protein × 31 PDB declaration: 34-meric（34） Consistent with all polymers
Chain o 1–220（220 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 Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 56-meric（56） Consistent with all polymers
Chain o 1–220（220 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 Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 51-meric（51） Consistent with all polymers
Chain o 1–220（220 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 Assembly 1 Protein–RNA Heteromer；Protein × 37 PDB declaration: 40-meric（40） Consistent with all polymers
Chain o 1–220（220 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.38 Å
7OHV Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL2 expression shut down, population C Deposited 2021-05-11 Assembly 1 Protein–RNA Heteromer；Protein × 43 PDB declaration: 46-meric（46） Consistent with all polymers
Chain o 1–220（220 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 Assembly 1 Protein–RNA Heteromer；Protein × 37 PDB declaration: 40-meric（40） Consistent with all polymers
Chain o 1–220（220 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 Assembly 1 Protein–RNA Heteromer；Protein × 34 PDB declaration: 37-meric（37） Consistent with all polymers
Chain o 1–220（220 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7R6Q State E2 nucleolar 60S ribosome biogenesis intermediate - Foot region model Deposited 2021-06-23 Assembly 1 Protein–RNA Heteromer；Protein × 16 PDB declaration: nonadecameric（19） Consistent with all polymers
Chain o 1–220（220 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.98 Å
7R7A State E1 nucleolar 60S ribosome biogenesis intermediate - Composite model Deposited 2021-06-24 Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric（57） Consistent with all polymers
Chain o 1–220（220 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
7U0H State NE1 nucleolar 60S ribosome biogenesis intermediate - Overall model Deposited 2022-02-18 Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric（49） Consistent with all polymers
Chain o 1–220（220 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
7UOO Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state Deposited 2022-04-13 Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric（60） Consistent with all polymers
Chain o 1–220（220 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 Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric（60） Consistent with all polymers
Chain o 1–220（220 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 Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric（60） Consistent with all polymers
Chain o 1–220（220 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 Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric（60） Consistent with all polymers
Chain o 1–220（220 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
8E5T Yeast co-transcriptional Noc1-Noc2 RNP assembly checkpoint intermediate Deposited 2022-08-22 Assembly 1 Protein–RNA Heteromer；Protein × 25 PDB declaration: 28-meric（28） Consistent with all polymers
Chain o 1–220（220 aa）
Not recorded MG MAGNESIUM ION × 33 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
8V83 60S ribosome biogenesis intermediate (Dbp10 pre-catalytic structure - Overall map) Deposited 2023-12-04 Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric（48） Consistent with all polymers
Chain o 1–220（220 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 Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric（49） Consistent with all polymers
Chain o 1–220（220 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 Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 56-meric（56） Consistent with all polymers
Chain o 1–220（220 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

This page presents structural evidence recorded in PDB/mmCIF.“No recorded non-water small molecule” does not prove that the experimental sample was ligand-free; experimental conditions belong to the PDB experiment, while ligands and copy counts are shown for each biological assembly.