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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：Q04660 New Search
21PDB entries
21Biological assembly
21chain/assembly records
Main Difference Dimensions in This Set
Different construct 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
4U7A The carboxy-terminal domain of Erb1 is a seven-bladed beta-propeller that binds RNA. Deposited 2014-07-30 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: Monomeric（1） Consistent with protein count
Chain A 1–807（807 aa）
Not recorded EDO 1,2-ETHANEDIOL × 2 GOL GLYCEROL × 1 EOH ETHANOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；10% PEG 8000, 8% ethylene glycol, 0.1M Hepes pH 7.5, 3% ethanol
Resolution 1.60 Å R-free 0.174
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 s 372–807（436 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 m 1–807（807 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 m 1–807（807 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 B 1–807（807 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 H 1–807（807 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 m 1–807（807 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
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 m 1–807（807 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 m 1–807（807 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 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 m 1–807（807 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 m 1–807（807 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 m 1–807（807 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 m 1–807（807 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 m 1–807（807 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7R6K State E2 nucleolar 60S ribosomal intermediate - Model for Noc2/Noc3 region Deposited 2021-06-22 Assembly 1 Protein–RNA Heteromer；Protein × 15 PDB declaration: hexadecameric（16） Consistent with all polymers
Chain m 1–807（807 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.17 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 m 1–807（807 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 m 1–807（807 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 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 s 1–807（807 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 m 1–807（807 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 m 1–807（807 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 m 1–807（807 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.