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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：Q12250 New Search
30PDB entries
31Biological assembly
31chain/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
3J47 Formation of an intricate helical bundle dictates the assembly of the 26S proteasome lid Deposited 2013-06-27 Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric（8） Consistent with protein count
Chain P 409–442（34 aa） Fragment：C-terminal helix (UNP residues 409-442)
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.1
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.40 Å
3JCK Structure of the yeast 26S proteasome lid sub-complex Deposited 2015-12-20 Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric（9） Consistent with protein count
Chain B 1–445（445 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer 50 mM HEPES, 100 mM NaCl, 100 mM KCl, 1 mM TCEP；pH 7.5；50 mM HEPES, 100 mM NaCl, 100 mM KCl, 1 mM TCEP
cryo-EM vitrification conditions 4 uL sample was applied to the grid, blotted for 2 seconds, and plunged into liquid ethane.；85 K；Cryogen ETHANE；4 uL sample was applied to the grid, blotted for 2 seconds at 4 degrees C, and plunged into liquid ethane using a manual plunger.
Resolution 3.50 Å
3JCO Structure of yeast 26S proteasome in M1 state derived from Titan dataset Deposited 2016-01-06 Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric（47） Consistent with protein count
Chain P 1–445（445 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 50mM Tris pH 7.5, 100mM NaCl, 5mM MgCl2, 2mM ATP；pH 7.5；50mM Tris pH 7.5, 100mM NaCl, 5mM MgCl2, 2mM ATP
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
3JCP Structure of yeast 26S proteasome in M2 state derived from Titan dataset Deposited 2016-01-06 Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric（47） Consistent with protein count
Chain P 1–445（445 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 50mM Tris pH 7.5, 100mM NaCl, 5mM MgCl2, 2mM ATP；pH 7.5；50mM Tris pH 7.5, 100mM NaCl, 5mM MgCl2, 2mM ATP
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
4CR2 Deep classification of a large cryo-EM dataset defines the conformational landscape of the 26S proteasome Deposited 2014-02-25 Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric（33） Consistent with protein count
Chain P 1–445（445 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.1
cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, INSTRUMENT- HOMEMADE PLUNGER,
Resolution 7.70 Å
4CR3 Deep classification of a large cryo-EM dataset defines the conformational landscape of the 26S proteasome Deposited 2014-02-25 Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric（33） Consistent with protein count
Chain P 1–445（445 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.1
cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, INSTRUMENT- HOMEMADE PLUNGER,
Resolution 9.30 Å
4CR4 Deep classification of a large cryo-EM dataset defines the conformational landscape of the 26S proteasome Deposited 2014-02-25 Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric（33） Consistent with protein count
Chain P 1–445（445 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.1
cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, INSTRUMENT- HOMEMADE PLUNGER,
Resolution 8.80 Å
5A5B Structure of the 26S proteasome-Ubp6 complex Deposited 2015-06-17 Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric（35） Consistent with protein count
Chain P 1–445（445 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, INSTRUMENT- HOMEMADE PLUNGER,
Resolution 9.50 Å
5MPB 26S proteasome in presence of AMP-PNP (s3) Deposited 2016-12-16 Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric（47） Consistent with protein count
Chain P 1–445（445 aa）
Not recorded ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 5 MG MAGNESIUM ION × 6 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 7.80 Å
5MPC 26S proteasome in presence of BeFx (s4) Deposited 2016-12-16 Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric（48） Consistent with protein count
Chain P 1–445（445 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 6 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 7.70 Å
5MPD 26S proteasome in presence of ATP (s1) Deposited 2016-12-16 Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric（13） Consistent with protein count
Chain P 1–445（445 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.10 Å
5MPE 26S proteasome in presence of ATP (s2) Deposited 2016-12-16 Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric（13） Consistent with protein count
Chain P 1–445（445 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.50 Å
5MPE 26S proteasome in presence of ATP (s2) Deposited 2016-12-16 Assembly 2 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric（12） Consistent with protein count
Chain P 1–445（445 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.50 Å
5WVI The resting state of yeast proteasome Deposited 2016-12-25 Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric（47） Consistent with protein count
Chain P 1–445（445 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.30 Å
5WVK Yeast proteasome-ADP-AlFx Deposited 2016-12-25 Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric（47） Consistent with protein count
Chain P 1–445（445 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
5ZMR Solution Structure of the N-terminal Domain of the Yeast Rpn5 Deposited 2018-04-05 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 1–136（136 aa） Fragment：N terminal domain, residues 1-136
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 50 mM sodium phosphate buffer, 50 mM Na2SO4；Pressure ambient
NMR sample composition 0.3 mM [U-95% 13C; U-95% 15N] 26S proteasome regulatory subunit Rpn5, 10 % v/v [U-99% 2H] D2O, 0.1 mg/mL DSS, 1 mM DTT, 50 mM sodium phosphate, 50 mM sodium sulfate, 2 % v/v trifluoroethanol, 5 % w/v sucrose, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
6FVT 26S proteasome, s1 state Deposited 2018-03-05 Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric（47） Consistent with protein count
Chain P 1–440（440 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 5 MG MAGNESIUM ION × 6 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.10 Å
6FVU 26S proteasome, s2 state Deposited 2018-03-05 Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric（47） Consistent with protein count
Chain P 1–440（440 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 5 MG MAGNESIUM ION × 6 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.50 Å
6FVV 26S proteasome, s3 state Deposited 2018-03-05 Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric（47） Consistent with protein count
Chain P 1–440（440 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 6 ATP ADENOSINE-5'-TRIPHOSPHATE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 5.40 Å
6FVW 26S proteasome, s4 state Deposited 2018-03-05 Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric（47） Consistent with protein count
Chain P 1–440（440 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 6 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.50 Å
6FVX 26S proteasome, s5 state Deposited 2018-03-05 Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric（47） Consistent with protein count
Chain P 1–440（440 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 5 MG MAGNESIUM ION × 6 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.90 Å
6FVY 26S proteasome, s6 state Deposited 2018-03-05 Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric（47） Consistent with protein count
Chain P 1–440（440 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 6 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 6.10 Å
6J2C Yeast proteasome in translocation competent state (C3-a) Deposited 2019-01-01 Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric（47） Consistent with protein count
Chain P 1–445（445 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.00 Å
6J2N yeast proteasome in substrate-processing state (C3-b) Deposited 2019-01-02 Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric（47） Consistent with protein count
Chain P 1–445（445 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.50 Å
6J2Q Yeast proteasome in Ub-accepted state (C1-b) Deposited 2019-01-02 Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric（47） Consistent with protein count
Chain P 1–445（445 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
6J2X Yeast proteasome in resting state (C1-a) Deposited 2019-01-03 Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric（47） Consistent with protein count
Chain P 1–445（445 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
6J30 yeast proteasome in Ub-engaged state (C2) Deposited 2019-01-03 Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric（47） Consistent with protein count
Chain P 1–445（445 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
7QO3 Structure of the 26S proteasome-Ubp6 complex in the si state (Core Particle and Lid) Deposited 2021-12-23 Assembly 1 Protein heterocomplex Heteromer；Protein × 41 PDB declaration: 41-meric（41） Consistent with protein count
Chain P 1–445（445 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.10 Å
7QO5 26S proteasome Rpt1-RK -Ubp6-UbVS complex in the si state Deposited 2021-12-23 Assembly 1 Protein heterocomplex Heteromer；Protein × 49 PDB declaration: 49-meric（49） Consistent with protein count
Chain P 1–445（445 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 5 MG MAGNESIUM ION × 6 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.00 Å
9CGC Yeast 26S proteasome non-substrate-engaged (S1 state) Deposited 2024-06-28 Assembly 1 Protein heterocomplex Heteromer；Protein × 39 PDB declaration: 39-meric（39） Consistent with protein count
Chain P 1–445（445 aa）
Not recorded MG MAGNESIUM ION × 5 ATP ADENOSINE-5'-TRIPHOSPHATE × 5 ZN ZINC ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；30 mM HEPES pH7.4, 25 mM NaCl, 25 mM KCl, 3% (v/v) glycerol, 5 mM MgCl2 2 mM ATP and 0.5 mM TCEP, 0.02% NP-40.
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.61 Å
9IWR 26S proteasome trimer Deposited 2024-07-25 Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric（47） Consistent with protein count
Chain P 1–445（445 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8；YPD buffer
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 9.10 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.