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5mpd

26S proteasome in presence of ATP (s1)

Method: ELECTRON MICROSCOPY Dmax: 253.2 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

26S proteasome regulatory subunit RPN10

OrganismNot specified

UniProt P38886

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 13 PDB declaration: tridecameric（13） Consistent with protein copy count Chain W； UniProt 1–268 Not recorded Ubiquitin carboxyl-terminal hydrolase RPN11 × 1 （P43588） 26S proteasome regulatory subunit RPN12 × 1 （P32496） 26S proteasome regulatory subunit RPN13 × 1 （O13563） 26S proteasome complex subunit SEM1 × 1 （O94742） 26S proteasome regulatory subunit RPN1 × 1 （P38764） 26S proteasome regulatory subunit RPN2 × 1 （P32565） 26S proteasome regulatory subunit RPN3 × 1 （P40016） 26S proteasome regulatory subunit RPN5 × 1 （Q12250） 26S proteasome regulatory subunit RPN6 × 1 （Q12377） 26S proteasome regulatory subunit RPN7 × 1 （Q06103） 26S proteasome regulatory subunit RPN8 × 1 （Q08723） 26S proteasome regulatory subunit RPN9 × 1 （Q04062） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE-PROPANE Resolution 4.10 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 5MPD Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3JCO Structure of yeast 26S proteasome in M1 state derived from Titan dataset Deposited 2016-01-06 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain W 1–268（268 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain W 1–268（268 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain W 1–268（268 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain W 1–268（268 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain W 1–268（268 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain W 1–268（268 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
5LN1 STRUCTURE OF UBIQUITYLATED-RPN10 FROM YEAST; Deposited 2016-08-02 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–191（191 aa） Fragment：UNP RESIDUES 1-191
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION, RECRYSTALLIZATION；pH 6.5；292 K；12% (W/V) PEG 20000, 0.1M MES PH 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 292K
Resolution 3.14 Å R-free 0.248
5MPB 26S proteasome in presence of AMP-PNP (s3) Deposited 2016-12-16 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain W 1–268（268 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 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric
Chain W 1–268（268 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
5MPE 26S proteasome in presence of ATP (s2) Deposited 2016-12-16 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain W 1–268（268 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 Different oligomeric state Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain W 1–268（268 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain W 1–268（268 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain W 1–268（268 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
6FVT 26S proteasome, s1 state Deposited 2018-03-05 Different construct Different oligomeric state Different ligand/ion Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain W 1–197（197 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 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain W 1–197（197 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 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain W 1–197（197 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 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain W 1–197（197 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 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain W 1–197（197 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 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain W 1–197（197 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain W 1–268（268 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain W 1–268（268 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain W 1–268（268 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain W 1–268（268 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain W 1–268（268 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 41 PDB declaration: 41-meric
Chain W 1–268（268 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 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 49 PDB declaration: 49-meric
Chain W 1–268（268 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 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 39 PDB declaration: 39-meric
Chain W 1–268（268 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain W 1–268（268 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

27 other PDB entries and 28 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RPN10_YEAST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain W； PDBConstruct 1–268； UniProt 1–268

Ubiquitin carboxyl-terminal hydrolase RPN11

OrganismNot specified

UniProt P43588

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 13 PDB declaration: tridecameric（13） Consistent with protein copy count Chain V； UniProt 1–306 Not recorded 26S proteasome regulatory subunit RPN10 × 1 （P38886） 26S proteasome regulatory subunit RPN12 × 1 （P32496） 26S proteasome regulatory subunit RPN13 × 1 （O13563） 26S proteasome complex subunit SEM1 × 1 （O94742） 26S proteasome regulatory subunit RPN1 × 1 （P38764） 26S proteasome regulatory subunit RPN2 × 1 （P32565） 26S proteasome regulatory subunit RPN3 × 1 （P40016） 26S proteasome regulatory subunit RPN5 × 1 （Q12250） 26S proteasome regulatory subunit RPN6 × 1 （Q12377） 26S proteasome regulatory subunit RPN7 × 1 （Q06103） 26S proteasome regulatory subunit RPN8 × 1 （Q08723） 26S proteasome regulatory subunit RPN9 × 1 （Q04062） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE-PROPANE Resolution 4.10 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 5MPD Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3J47 Formation of an intricate helical bundle dictates the assembly of the 26S proteasome lid Deposited 2013-06-27 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain V 230–298（69 aa） Fragment：last three C-terminal helices (UNP residues 230-298)
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 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain G 1–306（306 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain V 1–306（306 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain V 1–306（306 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain V 1–306（306 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain V 1–306（306 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain V 1–306（306 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
4O8X Zinc-bound Rpn11 in complex with Rpn8 Deposited 2013-12-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2–239（238 aa） Fragment：UNP residues 2-239
Not recorded EDO 1,2-ETHANEDIOL × 31 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；15% PEG8000, 12% ethylene glycol and 100 mM HEPES (pH 7.5), VAPOR DIFFUSION, HANGING DROP
Resolution 1.99 Å R-free 0.195
4O8Y Zinc-free Rpn11 in complex with Rpn8 Deposited 2013-12-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2–239（238 aa）
Not recorded EDO 1,2-ETHANEDIOL × 21 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；15% PEG8000, 30% ethylene glycol, and 100 mM HEPES (pH7.5), VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.95 Å R-free 0.209
4OCL Crystal Structure of the Rpn8-Rpn11 MPN domain heterodimer, crystal form Ia Deposited 2014-01-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–220（220 aa） Fragment：UNP residues 1-220
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROPS；pH 6；291 K；50 mM MES, pH 6.0, 200 mM calcium acetate, 22% PEG3350, VAPOR DIFFUSION, SITTING DROPS, temperature 291K
Resolution 2.40 Å R-free 0.252
4OCL Crystal Structure of the Rpn8-Rpn11 MPN domain heterodimer, crystal form Ia Deposited 2014-01-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 1–220（220 aa） Fragment：UNP residues 1-220
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROPS；pH 6；291 K；50 mM MES, pH 6.0, 200 mM calcium acetate, 22% PEG3350, VAPOR DIFFUSION, SITTING DROPS, temperature 291K
Resolution 2.40 Å R-free 0.252
4OCM Crystal Structure of the Rpn8-Rpn11 MPN domain heterodimer, crystal form Ib Deposited 2014-01-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–220（220 aa） Fragment：UNP residues 1-220
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROPS；pH 6；291 K；50 mM MES, pH 6.0, 200 mM calcium acetate, 22% PEG3350, VAPOR DIFFUSION, HANGING DROPS, temperature 291K
Resolution 1.99 Å R-free 0.262
4OCM Crystal Structure of the Rpn8-Rpn11 MPN domain heterodimer, crystal form Ib Deposited 2014-01-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 1–220（220 aa） Fragment：UNP residues 1-220
Not recorded ZN ZINC ION × 1 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROPS；pH 6；291 K；50 mM MES, pH 6.0, 200 mM calcium acetate, 22% PEG3350, VAPOR DIFFUSION, HANGING DROPS, temperature 291K
Resolution 1.99 Å R-free 0.262
4OCN Crystal Structure of the Rpn8-Rpn11 MPN domain heterodimer, crystal form II Deposited 2014-01-09 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–220（220 aa） Fragment：UNP residues 1-220
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROPS；pH 6；291 K；50 mM MES, pH 6.0, 100 mM magnesium chloride, 21% PEG3350, VAPOR DIFFUSION, HANGING DROPS, temperature 291K
Resolution 2.25 Å R-free 0.281
4OCN Crystal Structure of the Rpn8-Rpn11 MPN domain heterodimer, crystal form II Deposited 2014-01-09 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 1–220（220 aa） Fragment：UNP residues 1-220
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROPS；pH 6；291 K；50 mM MES, pH 6.0, 100 mM magnesium chloride, 21% PEG3350, VAPOR DIFFUSION, HANGING DROPS, temperature 291K
Resolution 2.25 Å R-free 0.281
4OWP Crystal structure of rpn11 in a heterodimer complex with rpn8, representing the active portion of the proteasome lid. Deposited 2014-02-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2–229（228 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；10% PEG 5000, 5% Tacsimate, 0.1 M Hepes pH 7.0
Resolution 2.35 Å R-free 0.242
5A5B Structure of the 26S proteasome-Ubp6 complex Deposited 2015-06-17 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain V 1–306（306 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 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain V 1–306（306 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 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric
Chain V 1–306（306 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
5MPE 26S proteasome in presence of ATP (s2) Deposited 2016-12-16 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain V 1–306（306 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 Different oligomeric state Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain V 1–306（306 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
5U4P Protein-protein complex between 26S proteasome regulatory subunit RPN8, RPN11, and Ubiquitin S31 Deposited 2016-12-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 2–219（218 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.8；291 K；1.5 M ammonium tartrate
Resolution 2.50 Å R-free 0.234
5U4P Protein-protein complex between 26S proteasome regulatory subunit RPN8, RPN11, and Ubiquitin S31 Deposited 2016-12-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 2–219（218 aa）
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.8；291 K；1.5 M ammonium tartrate
Resolution 2.50 Å R-free 0.234
5W83 Rpn8/Rpn11 dimer complex Deposited 2017-06-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–222（222 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；291 K；1.5 M ammonium tartrate pH 6.8
Resolution 1.55 Å R-free 0.234
5WVI The resting state of yeast proteasome Deposited 2016-12-25 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain V 1–306（306 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain V 1–306（306 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
6EF3 Yeast 26S proteasome bound to ubiquitinated substrate (4D motor state) Deposited 2018-08-15 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 24 PDB declaration: 24-meric
Chain r 1–306（306 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；specimens were manually blotted with Whatman #1 filter paper
Resolution 4.17 Å
6FVT 26S proteasome, s1 state Deposited 2018-03-05 Different construct Different oligomeric state Different ligand/ion Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain V 18–306（289 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 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain V 18–306（289 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 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain V 18–306（289 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 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain V 18–306（289 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 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain V 18–306（289 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 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain V 18–306（289 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain V 1–306（306 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain V 1–306（306 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain V 1–306（306 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain V 1–306（306 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain V 1–306（306 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 41 PDB declaration: 41-meric
Chain V 1–306（306 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 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 49 PDB declaration: 49-meric
Chain V 1–306（306 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 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 39 PDB declaration: 39-meric
Chain V 1–306（306 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain V 1–306（306 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

37 other PDB entries and 42 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RPN11_YEAST
Isoform —
PDB entities 2
Chains and sequence ranges Author chain V； PDBConstruct 1–306； UniProt 1–306

26S proteasome regulatory subunit RPN12

OrganismNot specified

UniProt P32496

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 13 PDB declaration: tridecameric（13） Consistent with protein copy count Chain T； UniProt 1–274 Not recorded 26S proteasome regulatory subunit RPN10 × 1 （P38886） Ubiquitin carboxyl-terminal hydrolase RPN11 × 1 （P43588） 26S proteasome regulatory subunit RPN13 × 1 （O13563） 26S proteasome complex subunit SEM1 × 1 （O94742） 26S proteasome regulatory subunit RPN1 × 1 （P38764） 26S proteasome regulatory subunit RPN2 × 1 （P32565） 26S proteasome regulatory subunit RPN3 × 1 （P40016） 26S proteasome regulatory subunit RPN5 × 1 （Q12250） 26S proteasome regulatory subunit RPN6 × 1 （Q12377） 26S proteasome regulatory subunit RPN7 × 1 （Q06103） 26S proteasome regulatory subunit RPN8 × 1 （Q08723） 26S proteasome regulatory subunit RPN9 × 1 （Q04062） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE-PROPANE Resolution 4.10 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 5MPD Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3J47 Formation of an intricate helical bundle dictates the assembly of the 26S proteasome lid Deposited 2013-06-27 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain T 256–272（17 aa） Fragment：C-terminal helix (UNP residues 256-272)
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 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain H 1–274（274 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain T 1–274（274 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain T 1–274（274 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain T 1–274（274 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain T 1–274（274 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain T 1–274（274 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain T 1–274（274 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 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain T 1–274（274 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 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric
Chain T 1–274（274 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
5MPE 26S proteasome in presence of ATP (s2) Deposited 2016-12-16 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain T 1–274（274 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 Different oligomeric state Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain T 1–274（274 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain T 1–274（274 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain T 1–274（274 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
6FVT 26S proteasome, s1 state Deposited 2018-03-05 Different construct Different oligomeric state Different ligand/ion Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain T 7–272（266 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 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain T 7–272（266 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 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain T 7–272（266 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 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain T 7–272（266 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 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain T 7–272（266 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 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain T 7–272（266 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain T 1–274（274 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain T 1–274（274 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain T 1–274（274 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain T 1–274（274 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain T 1–274（274 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 41 PDB declaration: 41-meric
Chain T 1–274（274 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 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 49 PDB declaration: 49-meric
Chain T 1–274（274 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 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 39 PDB declaration: 39-meric
Chain T 1–274（274 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain T 1–274（274 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

28 other PDB entries and 29 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RPN12_YEAST
Isoform —
PDB entities 3
Chains and sequence ranges Author chain T； PDBConstruct 1–274； UniProt 1–274

26S proteasome regulatory subunit RPN13

OrganismNot specified

UniProt O13563

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 13 PDB declaration: tridecameric（13） Consistent with protein copy count Chain X； UniProt 1–156 Not recorded 26S proteasome regulatory subunit RPN10 × 1 （P38886） Ubiquitin carboxyl-terminal hydrolase RPN11 × 1 （P43588） 26S proteasome regulatory subunit RPN12 × 1 （P32496） 26S proteasome complex subunit SEM1 × 1 （O94742） 26S proteasome regulatory subunit RPN1 × 1 （P38764） 26S proteasome regulatory subunit RPN2 × 1 （P32565） 26S proteasome regulatory subunit RPN3 × 1 （P40016） 26S proteasome regulatory subunit RPN5 × 1 （Q12250） 26S proteasome regulatory subunit RPN6 × 1 （Q12377） 26S proteasome regulatory subunit RPN7 × 1 （Q06103） 26S proteasome regulatory subunit RPN8 × 1 （Q08723） 26S proteasome regulatory subunit RPN9 × 1 （Q04062） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE-PROPANE Resolution 4.10 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 5MPD Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2Z4D NMR Structures of Yeast Proteasome Component Rpn13 Deposited 2007-06-15 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 6–101（96 aa） Fragment：residues 6-101
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 20mM phosphate, 50mM NaCl；Pressure ambient
NMR sample composition 0.4mM Rpn13 U-15N, 13C; U-70% 2H; 20mM phosphate buffer; 50mM NaCl; 4mM DTT; 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition 0.5mM Rpn13 U-15N; U-50% 2H; 20mM phosphate buffer; 50mM NaCl; 4mM DTT; 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition 0.5mM Rpn13 U-13C; 20mM phosphate buffer; 50mM NaCl; 4mM DTT; 100% D2O | 100% D2O
Resolution not provided
3JCO Structure of yeast 26S proteasome in M1 state derived from Titan dataset Deposited 2016-01-06 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain X 1–156（156 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain X 1–156（156 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain X 1–156（156 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain X 1–156（156 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain X 1–156（156 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain X 1–156（156 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 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain X 1–156（156 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 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric
Chain X 1–156（156 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
5MPE 26S proteasome in presence of ATP (s2) Deposited 2016-12-16 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain X 1–156（156 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain X 1–156（156 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain X 1–156（156 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
6FVT 26S proteasome, s1 state Deposited 2018-03-05 Different construct Different oligomeric state Different ligand/ion Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain X 5–131（127 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 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain X 5–131（127 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 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain X 5–131（127 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 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain X 5–131（127 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 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain X 5–131（127 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 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain X 5–131（127 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain X 1–156（156 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain X 1–156（156 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain X 1–156（156 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain X 1–156（156 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain X 1–156（156 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 41 PDB declaration: 41-meric
Chain X 1–156（156 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 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 49 PDB declaration: 49-meric
Chain X 1–156（156 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
9IWR 26S proteasome trimer Deposited 2024-07-25 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain X 1–156（156 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

26 other PDB entries and 26 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RPN13_YEAST
Isoform —
PDB entities 4
Chains and sequence ranges Author chain X； PDBConstruct 1–156； UniProt 1–156

26S proteasome complex subunit SEM1

OrganismNot specified

UniProt O94742

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 13 PDB declaration: tridecameric（13） Consistent with protein copy count Chain Y； UniProt 1–89 Not recorded 26S proteasome regulatory subunit RPN10 × 1 （P38886） Ubiquitin carboxyl-terminal hydrolase RPN11 × 1 （P43588） 26S proteasome regulatory subunit RPN12 × 1 （P32496） 26S proteasome regulatory subunit RPN13 × 1 （O13563） 26S proteasome regulatory subunit RPN1 × 1 （P38764） 26S proteasome regulatory subunit RPN2 × 1 （P32565） 26S proteasome regulatory subunit RPN3 × 1 （P40016） 26S proteasome regulatory subunit RPN5 × 1 （Q12250） 26S proteasome regulatory subunit RPN6 × 1 （Q12377） 26S proteasome regulatory subunit RPN7 × 1 （Q06103） 26S proteasome regulatory subunit RPN8 × 1 （Q08723） 26S proteasome regulatory subunit RPN9 × 1 （Q04062） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE-PROPANE Resolution 4.10 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 5MPD Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3JCK Structure of the yeast 26S proteasome lid sub-complex Deposited 2015-12-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain I 1–89（89 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain Y 1–89（89 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain Y 1–89（89 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
3T5V Sac3:Thp1:Sem1 complex Deposited 2011-07-28 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–89（89 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；292 K；see publication, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 2.90 Å R-free 0.231
3T5V Sac3:Thp1:Sem1 complex Deposited 2011-07-28 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 1–89（89 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；292 K；see publication, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 2.90 Å R-free 0.231
4CR2 Deep classification of a large cryo-EM dataset defines the conformational landscape of the 26S proteasome Deposited 2014-02-25 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain Y 1–89（89 aa） Fragment：SEM1
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 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain Y 1–89（89 aa） Fragment：SEM1
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 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain Y 1–89（89 aa） Fragment：SEM1
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
4TRQ Crystal structure of Sac3/Thp1/Sem1 Deposited 2014-06-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: Hexameric
Chain C 30–89（60 aa）
Chain F 30–89（60 aa）
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；0.5M Li2SO4, 10% PEG-8.000
Resolution 3.10 Å R-free 0.238
5A5B Structure of the 26S proteasome-Ubp6 complex Deposited 2015-06-17 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain Y 1–89（89 aa） Fragment：SEM1
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
5G5P Structure of the Saccharomyces cerevisiae TREX-2 complex Deposited 2016-05-26 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 1–89（89 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 20 MM HEPES, 300 MM NACL, 5 MM DTT；pH 8；20 mM HEPES, 300 mM NaCl, 5 mM DTT
cryo-EM vitrification conditions 85 K；Cryogen ETHANE；LIQUID ETHANE
Resolution 5.30 Å
5L3T Structure of the Saccharomyces cerevisiae TREX-2 complex Deposited 2016-05-24 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 1–89（89 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Precipitant: 20% PEG 3350, 0.2 M Mg formate; protein 16.5 mg/ml in 0.3 M NaCl, 50 mM HEPES, pH 8, 5 mM DTT.
Resolution 4.93 Å R-free 0.370
5MPB 26S proteasome in presence of AMP-PNP (s3) Deposited 2016-12-16 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain Y 1–89（89 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 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric
Chain Y 1–89（89 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
5MPE 26S proteasome in presence of ATP (s2) Deposited 2016-12-16 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain Y 1–89（89 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 Different oligomeric state Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain Y 1–89（89 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
5UBP TREX2 M-region Deposited 2016-12-21 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–89（89 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；20 % PEG3350, 0.17 M MgFormate
Resolution 2.30 Å R-free 0.217
5WVI The resting state of yeast proteasome Deposited 2016-12-25 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain Y 1–89（89 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain Y 1–89（89 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
6FVT 26S proteasome, s1 state Deposited 2018-03-05 Different oligomeric state Different ligand/ion Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain Y 1–89（89 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 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain Y 1–89（89 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 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain Y 1–89（89 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 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain Y 1–89（89 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 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain Y 1–89（89 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 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain Y 1–89（89 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain Y 1–89（89 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain Y 1–89（89 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain Y 1–89（89 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 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain Y 1–89（89 aa） Fragment：SEM1
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 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain Y 1–89（89 aa） Fragment：SEM1
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
7EWF Selenomethionine-substituted structure of S. cerevisiae Csn12 in complex with Thp3 and Sem1 Deposited 2021-05-25 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–89（89 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；12% PEG3350, 100 mM Sodium malonate buffer (pH 5.0) and 3% Methanol
Resolution 2.85 Å R-free 0.257
7EWM Native crystal structure of S. cerevisiae Csn12 in complex with Thp3 and Sem1 Deposited 2021-05-25 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–89（89 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；12% PEG3350, 100 mM Sodium malonate buffer (pH 5.0) and 3% Methanol
Resolution 2.90 Å R-free 0.251
7QO3 Structure of the 26S proteasome-Ubp6 complex in the si state (Core Particle and Lid) Deposited 2021-12-23 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 41 PDB declaration: 41-meric
Chain Y 1–89（89 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 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 49 PDB declaration: 49-meric
Chain Y 1–89（89 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
7QO6 26S proteasome Rpt1-RK -Ubp6-UbVS complex in the s2 state Deposited 2021-12-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 49 PDB declaration: 49-meric
Chain Y 1–89（89 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 6.30 Å
8U8C Crystal structure of the TREX-2 complex in complex with the N-terminal motif of Sub2 Deposited 2023-09-17 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–89（89 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M MES, pH 6.5, and 20% PEG3350
Resolution 2.40 Å R-free 0.231
9IWR 26S proteasome trimer Deposited 2024-07-25 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain Y 1–89（89 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

35 other PDB entries and 37 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SEM1_YEAST
Isoform —
PDB entities 5
Chains and sequence ranges Author chain Y； PDBConstruct 1–89； UniProt 1–89

26S proteasome regulatory subunit RPN1

OrganismNot specified

UniProt P38764

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 13 PDB declaration: tridecameric（13） Consistent with protein copy count Chain Z； UniProt 1–993 Not recorded 26S proteasome regulatory subunit RPN10 × 1 （P38886） Ubiquitin carboxyl-terminal hydrolase RPN11 × 1 （P43588） 26S proteasome regulatory subunit RPN12 × 1 （P32496） 26S proteasome regulatory subunit RPN13 × 1 （O13563） 26S proteasome complex subunit SEM1 × 1 （O94742） 26S proteasome regulatory subunit RPN2 × 1 （P32565） 26S proteasome regulatory subunit RPN3 × 1 （P40016） 26S proteasome regulatory subunit RPN5 × 1 （Q12250） 26S proteasome regulatory subunit RPN6 × 1 （Q12377） 26S proteasome regulatory subunit RPN7 × 1 （Q06103） 26S proteasome regulatory subunit RPN8 × 1 （Q08723） 26S proteasome regulatory subunit RPN9 × 1 （Q04062） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE-PROPANE Resolution 4.10 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 5MPD Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2N3T Solution structure of the Rpn1 substrate receptor site toroid 1 (T1) Deposited 2015-06-10 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 482–612（131 aa） Fragment：UNP residues 482-612
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.7；298 K；Ionic strength (raw mmCIF value) 50；Pressure ambient
NMR sample composition 0.7 mM [U-100% 13C; U-100% 15N; U-80% 2H] protein, 50 mM HEPES, 50 mM sodium chloride, 2 mM DTT, 1 mM EDTA, 0.1 % sodium azide, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 0.7 mM [U-100% 15N] protein, 50 mM HEPES, 50 mM sodium chloride, 2 mM DTT, 1 mM EDTA, 0.1 % sodium azide, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 0.7 mM [U-100% 13C] protein, 50 mM HEPES, 50 mM sodium chloride, 2 mM DTT, 1 mM EDTA, 0.1 % sodium azide, 100% D2O | 100% D2O
Resolution not provided
2N3U Solution structure of the Rpn1 T1 site engaging two monoubiquitin molecules Deposited 2015-06-10 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 482–612（131 aa） Fragment：UNP residues 482-612
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.7；298 K；Ionic strength (raw mmCIF value) 50；Pressure ambient
NMR sample composition 0.6 mM [U-100% 15N] protein_1, 0.6 mM protein_2, 50 mM HEPES, 50 mM sodium chloride, 2 mM DTT, 1 mM EDTA, 0.1 % sodium azide, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 0.5 mM protein_1, 0.5 mM [U-100% 15N] protein_2, 50 mM HEPES, 50 mM sodium chloride, 2 mM DTT, 1 mM EDTA, 0.1 % sodium azide, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 0.6 mM [U-13C] protein_1, 0.6 mM protein_2, 50 mM HEPES, 50 mM sodium chloride, 2 mM DTT, 1 mM EDTA, 0.1 % sodium azide, 100% D2O | 100% D2O
NMR sample composition 0.6 mM protein_1, 0.6 mM [U-13C] protein_2, 50 mM HEPES, 50 mM sodium chloride, 2 mM DTT, 1 mM EDTA, 0.1 % sodium azide, 100% D2O | 100% D2O
Resolution not provided
2N3V Solution structure of the Rpn1 T1 site with K48-linked diubiquitin in the extended binding mode Deposited 2015-06-10 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 482–612（131 aa） Fragment：UNP residues 482-612
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.7；298 K；Ionic strength (raw mmCIF value) 50；Pressure AMBIENT
NMR sample composition 0.3 MM [U-100% 15N] PROTEIN_1, 0.04-1.2 MM PROTEIN_2, 50 MM HEPES, 50 MM SODIUM CHLORIDE, 1 MM EDTA, 2 MM DTT, 0.1 % SODIUM AZIDE, 95% H2O/5% D2O
NMR sample composition 0.08-0.3 MM PROTEIN_1, 0.3 MM [U-100% 15N] PROTEIN_2, 50 MM HEPES, 50 MM SODIUM CHLORIDE, 1 MM EDTA, 2 MM DTT, 0.1 % SODIUM AZIDE, 95% H2O/ 5% D2O
NMR sample composition 0.06-0.5 MM PROTEIN_1, 0.5 MM [U-13C] PROTEIN_2, 50 MM HEPES, 50 MM SODIUM CHLORIDE, 1 MM EDTA, 2 MM DTT, 0.1 % SODIUM AZIDE, 100% D2O
NMR sample composition 0.6 MM [U-13C] PROTEIN_1, 0.6 MM PROTEIN_2, 50 MM HEPES, 50 MM SODIUM CHLORIDE, 1 MM EDTA, 2 MM DTT, 0.1 % SODIUM AZIDE, 100% D2O
NMR sample composition 0.5 MM PROTEIN_ 1, 0.5 MM [U-13C] PROTEIN_2, 50 MM HEPES, 50 MM SODIUM CHLORIDE, 1 MM EDTA, 2 MM DTT, 0.1 % SODIUM AZIDE, 100% D2O
NMR sample composition 0.6 MM [U-13C] PROTEIN_1, 0.12-0.6 MM PROTEIN_2, 50 MM HEPES, 50 MM SODIUM CHLORIDE, 1 MM EDTA, 2 MM DTT, 0.1 % SODIUM AZIDE, 100% D2O
Resolution not provided
2N3W Solution structure of the Rpn1 T1 site with K48-linked diubiquitin in the contracted binding mode Deposited 2015-06-10 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 482–612（131 aa） Fragment：UNP residues 482-612
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.7；298 K；Ionic strength (raw mmCIF value) 50；Pressure ambient
NMR sample composition 0.3 mM [U-100% 15N] protein_1, 0.04-1.2 mM protein_2, 50 mM HEPES, 50 mM sodium chloride, 2 mM DTT, 1 mM EDTA, 0.1 % sodium azide, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 0.08-0.3 mM protein_1, 0.3 mM [U-100% 15N] protein_2, 50 mM HEPES, 50 mM sodium chloride, 2 mM DTT, 1 mM EDTA, 0.1 % sodium azide, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 0.06-0.5 mM protein_1, 0.5 mM [U-13C] protein_2, 50 mM HEPES, 50 mM sodium chloride, 2 mM DTT, 1 mM EDTA, 0.1 % sodium azide, 100% D2O | 100% D2O
NMR sample composition 0.6 mM [U-13C] protein_1, 0.6 mM protein_2, 50 mM HEPES, 50 mM sodium chloride, 2 mM DTT, 1 mM EDTA, 0.1 % sodium azide, 100% D2O | 100% D2O
NMR sample composition 0.5 mM protein_1, 0.5 mM [U-13C] protein_2, 50 mM HEPES, 50 mM sodium chloride, 2 mM DTT, 1 mM EDTA, 0.1 % sodium azide, 100% D2O | 100% D2O
NMR sample composition 0.6 mM [U-13C] protein_1, 0.12-0.6 mM protein_2, 50 mM HEPES, 50 mM sodium chloride, 2 mM DTT, 1 mM EDTA, 0.1 % sodium azide, 100% D2O | 100% D2O
Resolution not provided
2NBW Solution structure of the Rpn1 T1 site with the Rad23 UBL domain Deposited 2016-03-14 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 482–612（131 aa） Fragment：residues 482-612
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.7；298 K；Ionic strength (raw mmCIF value) 50；Pressure ambient
NMR sample composition 0.3 mM [U-100% 15N] protein_1, 0.04-1.2 mM protein_2, 50 mM HEPES, 50 mM sodium chloride, 1 mM EDTA, 2 mM DTT, 0.1 % sodium azide, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 0.04-0.6 mM protein_1, 0.3 mM [U-100% 15N] protein_2, 50 mM HEPES, 50 mM sodium chloride, 1 mM EDTA, 2 mM DTT, 0.1 % sodium azide, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 0.6 mM [U-13C] protein_1, 0.6 mM protein_2, 50 mM HEPES, 50 mM sodium chloride, 1 mM EDTA, 2 mM DTT, 0.1 % sodium azide, 100% D2O | 100% D2O
NMR sample composition 0.6 mM protein_1, 0.6 mM [U-13C] protein_2, 50 mM HEPES, 50 mM sodium chloride, 1 mM EDTA, 2 mM DTT, 0.1 % sodium azide, 100% D2O | 100% D2O
Resolution not provided
3JCO Structure of yeast 26S proteasome in M1 state derived from Titan dataset Deposited 2016-01-06 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain Z 1–993（993 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain Z 1–993（993 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain Z 1–993（993 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain Z 1–993（993 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain Z 1–993（993 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain Z 1–993（993 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 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain Z 1–993（993 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 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric
Chain Z 1–993（993 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
5MPE 26S proteasome in presence of ATP (s2) Deposited 2016-12-16 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain Z 1–993（993 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 Different oligomeric state Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain Z 1–993（993 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain Z 1–993（993 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain Z 1–993（993 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
6FVT 26S proteasome, s1 state Deposited 2018-03-05 Different construct Different oligomeric state Different ligand/ion Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain Z 1–970（970 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 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain Z 1–970（970 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 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain Z 1–970（970 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 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain Z 1–970（970 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 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain Z 1–970（970 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 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain Z 1–970（970 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain Z 1–993（993 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain Z 1–993（993 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain Z 1–993（993 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain Z 1–993（993 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain Z 1–993（993 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 41 PDB declaration: 41-meric
Chain Z 1–993（993 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
7QO4 26S proteasome WT-Ubp6-UbVS complex in the si state (ATPases, Rpn1, Ubp6, and UbVS) Deposited 2021-12-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain Z 1–993（993 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 7.00 Å
7QO5 26S proteasome Rpt1-RK -Ubp6-UbVS complex in the si state Deposited 2021-12-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 49 PDB declaration: 49-meric
Chain Z 1–993（993 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
7QO6 26S proteasome Rpt1-RK -Ubp6-UbVS complex in the s2 state Deposited 2021-12-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 49 PDB declaration: 49-meric
Chain Z 1–993（993 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 6.30 Å
9CGC Yeast 26S proteasome non-substrate-engaged (S1 state) Deposited 2024-06-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 39 PDB declaration: 39-meric
Chain o 1–993（993 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain Z 1–993（993 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

33 other PDB entries and 34 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RPN1_YEAST
Isoform —
PDB entities 6
Chains and sequence ranges Author chain Z； PDBConstruct 1–993； UniProt 1–993

26S proteasome regulatory subunit RPN2

OrganismNot specified

UniProt P32565

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 13 PDB declaration: tridecameric（13） Consistent with protein copy count Chain N； UniProt 1–945 Not recorded 26S proteasome regulatory subunit RPN10 × 1 （P38886） Ubiquitin carboxyl-terminal hydrolase RPN11 × 1 （P43588） 26S proteasome regulatory subunit RPN12 × 1 （P32496） 26S proteasome regulatory subunit RPN13 × 1 （O13563） 26S proteasome complex subunit SEM1 × 1 （O94742） 26S proteasome regulatory subunit RPN1 × 1 （P38764） 26S proteasome regulatory subunit RPN3 × 1 （P40016） 26S proteasome regulatory subunit RPN5 × 1 （Q12250） 26S proteasome regulatory subunit RPN6 × 1 （Q12377） 26S proteasome regulatory subunit RPN7 × 1 （Q06103） 26S proteasome regulatory subunit RPN8 × 1 （Q08723） 26S proteasome regulatory subunit RPN9 × 1 （Q04062） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE-PROPANE Resolution 4.10 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 5MPD Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3JCO Structure of yeast 26S proteasome in M1 state derived from Titan dataset Deposited 2016-01-06 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain N 1–945（945 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain N 1–945（945 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
4ADY Crystal structure of 26S proteasome subunit Rpn2 Deposited 2012-01-04 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–945（944 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；CRYSTALS WERE GROWN BY VAPOUR DIFFUSION IN HANGING DROPS AT 18 C. PROTEIN AT A CONCENTRATION OF 18 MG/ML WAS MIXED WITH AN EQUAL VOLUME OF RESERVOIR SOLUTION CONTAINING 100 MM BIS-TRIS PROPANE PH 7.0, 200 MM POTASSIUM SODIUM TARTRATE AND 16-18% (W/V) PEG 3350.
Resolution 2.70 Å R-free 0.240
4ADY Crystal structure of 26S proteasome subunit Rpn2 Deposited 2012-01-04 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 2–945（944 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；CRYSTALS WERE GROWN BY VAPOUR DIFFUSION IN HANGING DROPS AT 18 C. PROTEIN AT A CONCENTRATION OF 18 MG/ML WAS MIXED WITH AN EQUAL VOLUME OF RESERVOIR SOLUTION CONTAINING 100 MM BIS-TRIS PROPANE PH 7.0, 200 MM POTASSIUM SODIUM TARTRATE AND 16-18% (W/V) PEG 3350.
Resolution 2.70 Å R-free 0.240
4CR2 Deep classification of a large cryo-EM dataset defines the conformational landscape of the 26S proteasome Deposited 2014-02-25 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain N 1–945（945 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain N 1–945（945 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain N 1–945（945 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain N 1–945（945 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 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain N 1–945（945 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 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric
Chain N 1–945（945 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
5MPE 26S proteasome in presence of ATP (s2) Deposited 2016-12-16 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain N 1–945（945 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 Different oligomeric state Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain N 1–945（945 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain N 1–945（945 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain N 1–945（945 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
6FVT 26S proteasome, s1 state Deposited 2018-03-05 Different construct Different oligomeric state Different ligand/ion Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain N 4–925（922 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 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain N 4–925（922 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 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain N 4–925（922 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 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain N 4–925（922 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 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain N 4–925（922 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 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain N 4–925（922 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain N 1–945（945 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain N 1–945（945 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain N 1–945（945 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain N 1–945（945 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain N 1–945（945 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 41 PDB declaration: 41-meric
Chain N 1–945（945 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 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 49 PDB declaration: 49-meric
Chain N 1–945（945 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
7QO6 26S proteasome Rpt1-RK -Ubp6-UbVS complex in the s2 state Deposited 2021-12-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 49 PDB declaration: 49-meric
Chain N 1–945（945 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 6.30 Å
9CGC Yeast 26S proteasome non-substrate-engaged (S1 state) Deposited 2024-06-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 39 PDB declaration: 39-meric
Chain N 1–945（945 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain N 1–945（945 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

28 other PDB entries and 30 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RPN2_YEAST
Isoform —
PDB entities 7
Chains and sequence ranges Author chain N； PDBConstruct 1–945； UniProt 1–945

26S proteasome regulatory subunit RPN3

OrganismNot specified

UniProt P40016

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 13 PDB declaration: tridecameric（13） Consistent with protein copy count Chain S； UniProt 1–523 Not recorded 26S proteasome regulatory subunit RPN10 × 1 （P38886） Ubiquitin carboxyl-terminal hydrolase RPN11 × 1 （P43588） 26S proteasome regulatory subunit RPN12 × 1 （P32496） 26S proteasome regulatory subunit RPN13 × 1 （O13563） 26S proteasome complex subunit SEM1 × 1 （O94742） 26S proteasome regulatory subunit RPN1 × 1 （P38764） 26S proteasome regulatory subunit RPN2 × 1 （P32565） 26S proteasome regulatory subunit RPN5 × 1 （Q12250） 26S proteasome regulatory subunit RPN6 × 1 （Q12377） 26S proteasome regulatory subunit RPN7 × 1 （Q06103） 26S proteasome regulatory subunit RPN8 × 1 （Q08723） 26S proteasome regulatory subunit RPN9 × 1 （Q04062） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE-PROPANE Resolution 4.10 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 5MPD Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3J47 Formation of an intricate helical bundle dictates the assembly of the 26S proteasome lid Deposited 2013-06-27 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain S 455–478（24 aa） Fragment：C-terminal helix (UNP residues 455-478)
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 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain A 131–523（393 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain S 1–523（523 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain S 1–523（523 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain S 1–523（523 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain S 1–523（523 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain S 1–523（523 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain S 1–523（523 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 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain S 1–523（523 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 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric
Chain S 1–523（523 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
5MPE 26S proteasome in presence of ATP (s2) Deposited 2016-12-16 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain S 1–523（523 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 Different oligomeric state Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain S 1–523（523 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain S 1–523（523 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain S 1–523（523 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
6FVT 26S proteasome, s1 state Deposited 2018-03-05 Different construct Different oligomeric state Different ligand/ion Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain S 18–492（475 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 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain S 18–492（475 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 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain S 18–492（475 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 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain S 18–492（475 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 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain S 18–492（475 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 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain S 18–492（475 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain S 1–523（523 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain S 1–523（523 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain S 1–523（523 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain S 1–523（523 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain S 1–523（523 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 41 PDB declaration: 41-meric
Chain S 1–523（523 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 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 49 PDB declaration: 49-meric
Chain S 1–523（523 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 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 39 PDB declaration: 39-meric
Chain S 1–523（523 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain S 1–523（523 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

28 other PDB entries and 29 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RPN3_YEAST
Isoform —
PDB entities 8
Chains and sequence ranges Author chain S； PDBConstruct 1–523； UniProt 1–523

26S proteasome regulatory subunit RPN5

OrganismNot specified

UniProt Q12250

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 13 PDB declaration: tridecameric（13） Consistent with protein copy count Chain P； UniProt 1–445 Not recorded 26S proteasome regulatory subunit RPN10 × 1 （P38886） Ubiquitin carboxyl-terminal hydrolase RPN11 × 1 （P43588） 26S proteasome regulatory subunit RPN12 × 1 （P32496） 26S proteasome regulatory subunit RPN13 × 1 （O13563） 26S proteasome complex subunit SEM1 × 1 （O94742） 26S proteasome regulatory subunit RPN1 × 1 （P38764） 26S proteasome regulatory subunit RPN2 × 1 （P32565） 26S proteasome regulatory subunit RPN3 × 1 （P40016） 26S proteasome regulatory subunit RPN6 × 1 （Q12377） 26S proteasome regulatory subunit RPN7 × 1 （Q06103） 26S proteasome regulatory subunit RPN8 × 1 （Q08723） 26S proteasome regulatory subunit RPN9 × 1 （Q04062） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE-PROPANE Resolution 4.10 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 5MPD Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3J47 Formation of an intricate helical bundle dictates the assembly of the 26S proteasome lid Deposited 2013-06-27 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
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 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
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 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
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 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric
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
5MPE 26S proteasome in presence of ATP (s2) Deposited 2016-12-16 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
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 Different oligomeric state Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
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 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
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 Different construct Different oligomeric state Different ligand/ion Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
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 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
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 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
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 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
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 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
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 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 41 PDB declaration: 41-meric
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 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 49 PDB declaration: 49-meric
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 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 39 PDB declaration: 39-meric
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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
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

29 other PDB entries and 30 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RPN5_YEAST
Isoform —
PDB entities 9
Chains and sequence ranges Author chain P； PDBConstruct 1–445； UniProt 1–445

26S proteasome regulatory subunit RPN6

OrganismNot specified

UniProt Q12377

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 13 PDB declaration: tridecameric（13） Consistent with protein copy count Chain Q； UniProt 1–434 Not recorded 26S proteasome regulatory subunit RPN10 × 1 （P38886） Ubiquitin carboxyl-terminal hydrolase RPN11 × 1 （P43588） 26S proteasome regulatory subunit RPN12 × 1 （P32496） 26S proteasome regulatory subunit RPN13 × 1 （O13563） 26S proteasome complex subunit SEM1 × 1 （O94742） 26S proteasome regulatory subunit RPN1 × 1 （P38764） 26S proteasome regulatory subunit RPN2 × 1 （P32565） 26S proteasome regulatory subunit RPN3 × 1 （P40016） 26S proteasome regulatory subunit RPN5 × 1 （Q12250） 26S proteasome regulatory subunit RPN7 × 1 （Q06103） 26S proteasome regulatory subunit RPN8 × 1 （Q08723） 26S proteasome regulatory subunit RPN9 × 1 （Q04062） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE-PROPANE Resolution 4.10 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 5MPD Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3J47 Formation of an intricate helical bundle dictates the assembly of the 26S proteasome lid Deposited 2013-06-27 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain Q 407–431（25 aa） Fragment：C-terminal helix (UNP residues 407-431)
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 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain C 1–434（434 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain Q 1–434（434 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain Q 1–434（434 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain Q 1–434（434 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain Q 1–434（434 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain Q 1–434（434 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain Q 1–434（434 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 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain Q 1–434（434 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 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric
Chain Q 1–434（434 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
5MPE 26S proteasome in presence of ATP (s2) Deposited 2016-12-16 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain Q 1–434（434 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 Different oligomeric state Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain Q 1–434（434 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain Q 1–434（434 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain Q 1–434（434 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
6FVT 26S proteasome, s1 state Deposited 2018-03-05 Different oligomeric state Different ligand/ion Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain Q 1–434（434 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 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain Q 1–434（434 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 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain Q 1–434（434 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 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain Q 1–434（434 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 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain Q 1–434（434 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 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain Q 1–434（434 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain Q 1–434（434 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain Q 1–434（434 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain Q 1–434（434 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain Q 1–434（434 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain Q 1–434（434 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 41 PDB declaration: 41-meric
Chain Q 1–434（434 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 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 49 PDB declaration: 49-meric
Chain Q 1–434（434 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 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 39 PDB declaration: 39-meric
Chain Q 1–434（434 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain Q 1–434（434 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

28 other PDB entries and 29 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RPN6_YEAST
Isoform —
PDB entities 10
Chains and sequence ranges Author chain Q； PDBConstruct 1–434； UniProt 1–434

26S proteasome regulatory subunit RPN7

OrganismNot specified

UniProt Q06103

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 13 PDB declaration: tridecameric（13） Consistent with protein copy count Chain R； UniProt 1–429 Not recorded 26S proteasome regulatory subunit RPN10 × 1 （P38886） Ubiquitin carboxyl-terminal hydrolase RPN11 × 1 （P43588） 26S proteasome regulatory subunit RPN12 × 1 （P32496） 26S proteasome regulatory subunit RPN13 × 1 （O13563） 26S proteasome complex subunit SEM1 × 1 （O94742） 26S proteasome regulatory subunit RPN1 × 1 （P38764） 26S proteasome regulatory subunit RPN2 × 1 （P32565） 26S proteasome regulatory subunit RPN3 × 1 （P40016） 26S proteasome regulatory subunit RPN5 × 1 （Q12250） 26S proteasome regulatory subunit RPN6 × 1 （Q12377） 26S proteasome regulatory subunit RPN8 × 1 （Q08723） 26S proteasome regulatory subunit RPN9 × 1 （Q04062） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE-PROPANE Resolution 4.10 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 5MPD Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3J47 Formation of an intricate helical bundle dictates the assembly of the 26S proteasome lid Deposited 2013-06-27 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain R 397–422（26 aa） Fragment：C-terminal helix (UNP residues 397-422)
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 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain D 1–429（429 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain R 1–429（429 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain R 1–429（429 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain R 1–429（429 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain R 1–429（429 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain R 1–429（429 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain R 1–429（429 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 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain R 1–429（429 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 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric
Chain R 1–429（429 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
5MPE 26S proteasome in presence of ATP (s2) Deposited 2016-12-16 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain R 1–429（429 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 Different oligomeric state Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain R 1–429（429 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain R 1–429（429 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain R 1–429（429 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
6FVT 26S proteasome, s1 state Deposited 2018-03-05 Different construct Different oligomeric state Different ligand/ion Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain R 20–424（405 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 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain R 20–424（405 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 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain R 20–424（405 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 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain R 20–424（405 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 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain R 20–424（405 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 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain R 20–424（405 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain R 1–429（429 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain R 1–429（429 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain R 1–429（429 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain R 1–429（429 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain R 1–429（429 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 41 PDB declaration: 41-meric
Chain R 1–429（429 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 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 49 PDB declaration: 49-meric
Chain R 1–429（429 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 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 39 PDB declaration: 39-meric
Chain R 1–429（429 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain R 1–429（429 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

28 other PDB entries and 29 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RPN7_YEAST
Isoform —
PDB entities 11
Chains and sequence ranges Author chain R； PDBConstruct 1–429； UniProt 1–429

26S proteasome regulatory subunit RPN8

OrganismNot specified

UniProt Q08723

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 13 PDB declaration: tridecameric（13） Consistent with protein copy count Chain U； UniProt 1–338 Not recorded 26S proteasome regulatory subunit RPN10 × 1 （P38886） Ubiquitin carboxyl-terminal hydrolase RPN11 × 1 （P43588） 26S proteasome regulatory subunit RPN12 × 1 （P32496） 26S proteasome regulatory subunit RPN13 × 1 （O13563） 26S proteasome complex subunit SEM1 × 1 （O94742） 26S proteasome regulatory subunit RPN1 × 1 （P38764） 26S proteasome regulatory subunit RPN2 × 1 （P32565） 26S proteasome regulatory subunit RPN3 × 1 （P40016） 26S proteasome regulatory subunit RPN5 × 1 （Q12250） 26S proteasome regulatory subunit RPN6 × 1 （Q12377） 26S proteasome regulatory subunit RPN7 × 1 （Q06103） 26S proteasome regulatory subunit RPN9 × 1 （Q04062） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE-PROPANE Resolution 4.10 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 5MPD Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3J47 Formation of an intricate helical bundle dictates the assembly of the 26S proteasome lid Deposited 2013-06-27 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain U 188–308（121 aa） Fragment：last three C-terminal helices (UNP residues 188-308)
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 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain E 1–338（338 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain U 1–338（338 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain U 1–338（338 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain U 1–338（338 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain U 1–338（338 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain U 1–338（338 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
4O8X Zinc-bound Rpn11 in complex with Rpn8 Deposited 2013-12-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 2–178（177 aa） Fragment：UNP residues 2-178
Not recorded EDO 1,2-ETHANEDIOL × 31 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；15% PEG8000, 12% ethylene glycol and 100 mM HEPES (pH 7.5), VAPOR DIFFUSION, HANGING DROP
Resolution 1.99 Å R-free 0.195
4O8Y Zinc-free Rpn11 in complex with Rpn8 Deposited 2013-12-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 2–178（177 aa）
Not recorded EDO 1,2-ETHANEDIOL × 21 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；15% PEG8000, 30% ethylene glycol, and 100 mM HEPES (pH7.5), VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.95 Å R-free 0.209
4OCL Crystal Structure of the Rpn8-Rpn11 MPN domain heterodimer, crystal form Ia Deposited 2014-01-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–176（176 aa） Fragment：UNP residues 1-176
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROPS；pH 6；291 K；50 mM MES, pH 6.0, 200 mM calcium acetate, 22% PEG3350, VAPOR DIFFUSION, SITTING DROPS, temperature 291K
Resolution 2.40 Å R-free 0.252
4OCL Crystal Structure of the Rpn8-Rpn11 MPN domain heterodimer, crystal form Ia Deposited 2014-01-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–176（176 aa） Fragment：UNP residues 1-176
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROPS；pH 6；291 K；50 mM MES, pH 6.0, 200 mM calcium acetate, 22% PEG3350, VAPOR DIFFUSION, SITTING DROPS, temperature 291K
Resolution 2.40 Å R-free 0.252
4OCM Crystal Structure of the Rpn8-Rpn11 MPN domain heterodimer, crystal form Ib Deposited 2014-01-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–176（176 aa） Fragment：UNP residues 1-176
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROPS；pH 6；291 K；50 mM MES, pH 6.0, 200 mM calcium acetate, 22% PEG3350, VAPOR DIFFUSION, HANGING DROPS, temperature 291K
Resolution 1.99 Å R-free 0.262
4OCM Crystal Structure of the Rpn8-Rpn11 MPN domain heterodimer, crystal form Ib Deposited 2014-01-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–176（176 aa） Fragment：UNP residues 1-176
Not recorded ZN ZINC ION × 1 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROPS；pH 6；291 K；50 mM MES, pH 6.0, 200 mM calcium acetate, 22% PEG3350, VAPOR DIFFUSION, HANGING DROPS, temperature 291K
Resolution 1.99 Å R-free 0.262
4OCN Crystal Structure of the Rpn8-Rpn11 MPN domain heterodimer, crystal form II Deposited 2014-01-09 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–176（176 aa） Fragment：UNP residues 1-176
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROPS；pH 6；291 K；50 mM MES, pH 6.0, 100 mM magnesium chloride, 21% PEG3350, VAPOR DIFFUSION, HANGING DROPS, temperature 291K
Resolution 2.25 Å R-free 0.281
4OCN Crystal Structure of the Rpn8-Rpn11 MPN domain heterodimer, crystal form II Deposited 2014-01-09 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–176（176 aa） Fragment：UNP residues 1-176
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROPS；pH 6；291 K；50 mM MES, pH 6.0, 100 mM magnesium chloride, 21% PEG3350, VAPOR DIFFUSION, HANGING DROPS, temperature 291K
Resolution 2.25 Å R-free 0.281
4OWP Crystal structure of rpn11 in a heterodimer complex with rpn8, representing the active portion of the proteasome lid. Deposited 2014-02-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–186（186 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；10% PEG 5000, 5% Tacsimate, 0.1 M Hepes pH 7.0
Resolution 2.35 Å R-free 0.242
5A5B Structure of the 26S proteasome-Ubp6 complex Deposited 2015-06-17 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain U 1–338（338 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 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain U 1–338（338 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 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric
Chain U 1–338（338 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
5MPE 26S proteasome in presence of ATP (s2) Deposited 2016-12-16 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain U 1–338（338 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 Different oligomeric state Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain U 1–338（338 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
5U4P Protein-protein complex between 26S proteasome regulatory subunit RPN8, RPN11, and Ubiquitin S31 Deposited 2016-12-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–177（177 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.8；291 K；1.5 M ammonium tartrate
Resolution 2.50 Å R-free 0.234
5U4P Protein-protein complex between 26S proteasome regulatory subunit RPN8, RPN11, and Ubiquitin S31 Deposited 2016-12-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–177（177 aa）
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.8；291 K；1.5 M ammonium tartrate
Resolution 2.50 Å R-free 0.234
5W83 Rpn8/Rpn11 dimer complex Deposited 2017-06-21 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–338（338 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；291 K；1.5 M ammonium tartrate pH 6.8
Resolution 1.55 Å R-free 0.234
5WVI The resting state of yeast proteasome Deposited 2016-12-25 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain U 1–338（338 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain U 1–338（338 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
6FVT 26S proteasome, s1 state Deposited 2018-03-05 Different construct Different oligomeric state Different ligand/ion Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain U 1–304（304 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 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain U 1–304（304 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 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain U 1–304（304 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 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain U 1–304（304 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 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain U 1–304（304 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 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain U 1–304（304 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain U 1–338（338 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain U 1–338（338 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain U 1–338（338 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain U 1–338（338 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain U 1–338（338 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 41 PDB declaration: 41-meric
Chain U 1–338（338 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 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 49 PDB declaration: 49-meric
Chain U 1–338（338 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
7QO6 26S proteasome Rpt1-RK -Ubp6-UbVS complex in the s2 state Deposited 2021-12-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 49 PDB declaration: 49-meric
Chain U 1–338（338 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 6.30 Å
9CGC Yeast 26S proteasome non-substrate-engaged (S1 state) Deposited 2024-06-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 39 PDB declaration: 39-meric
Chain U 1–338（338 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain U 1–338（338 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

37 other PDB entries and 42 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RPN8_YEAST
Isoform —
PDB entities 12
Chains and sequence ranges Author chain U； PDBConstruct 1–338； UniProt 1–338

26S proteasome regulatory subunit RPN9

OrganismNot specified

UniProt Q04062

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 13 PDB declaration: tridecameric（13） Consistent with protein copy count Chain O； UniProt 1–393 Not recorded 26S proteasome regulatory subunit RPN10 × 1 （P38886） Ubiquitin carboxyl-terminal hydrolase RPN11 × 1 （P43588） 26S proteasome regulatory subunit RPN12 × 1 （P32496） 26S proteasome regulatory subunit RPN13 × 1 （O13563） 26S proteasome complex subunit SEM1 × 1 （O94742） 26S proteasome regulatory subunit RPN1 × 1 （P38764） 26S proteasome regulatory subunit RPN2 × 1 （P32565） 26S proteasome regulatory subunit RPN3 × 1 （P40016） 26S proteasome regulatory subunit RPN5 × 1 （Q12250） 26S proteasome regulatory subunit RPN6 × 1 （Q12377） 26S proteasome regulatory subunit RPN7 × 1 （Q06103） 26S proteasome regulatory subunit RPN8 × 1 （Q08723） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE-PROPANE Resolution 4.10 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 5MPD Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2MQW Solution structure of a proteasome related subunit N terminal domain Deposited 2014-06-30 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–160（160 aa） Fragment：N terminal domain, UNP RESIDUES 1-160
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 210；Pressure AMBIENT
NMR sample composition 0.5 mM [U-100% 13C; U-100% 15N] Protein-1, 50 mM sodium phosphate-2, 100 mM sodium chloride-3, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.5 mM [U-100% 15N] Protein-4, 50 mM sodium phosphate-5, 100 mM sodium chloride-6, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2MR3 A subunit of 26S proteasome lid complex Deposited 2014-06-30 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–393（393 aa） Fragment：UNP RESIDUES 1-393
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；303 K；Ionic strength (raw mmCIF value) 0.21；Pressure ambient
NMR sample composition 0.5 mM [U-100% 13C; U-100% 15N] Protein-1, 100 mM sodium chloride-2, 50 mM sodium phosphate-3, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.5 mM [U-13C; U-15N; U-2H] Protein-4, 100 mM sodium chloride-5, 50 mM sodium phosphate-6, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2MRI Solution structure of a proteasome related subunit C terminal domain Deposited 2014-07-06 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 181–356（176 aa） Fragment：UNP RESIDUES 181-356
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.5；298 K；Ionic strength (raw mmCIF value) 0.07；Pressure ambient
NMR sample composition 0.5mM [U-100% 13C, U-100% 15N] Protein-1, 20mM TRIS-2, 50mM sodium chloride-3, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
3J47 Formation of an intricate helical bundle dictates the assembly of the 26S proteasome lid Deposited 2013-06-27 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain O 360–387（28 aa） Fragment：C-terminal helix (UNP residues 360-387)
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 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain F 1–393（393 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain O 1–393（393 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain O 1–393（393 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain O 1–393（393 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain O 1–393（393 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain O 1–393（393 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain O 1–393（393 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 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain O 1–393（393 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 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric
Chain O 1–393（393 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
5MPE 26S proteasome in presence of ATP (s2) Deposited 2016-12-16 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain O 1–393（393 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 Different oligomeric state Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain O 1–393（393 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain O 1–393（393 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain O 1–393（393 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
6FVT 26S proteasome, s1 state Deposited 2018-03-05 Different construct Different oligomeric state Different ligand/ion Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain O 6–393（388 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 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain O 6–393（388 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 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain O 6–393（388 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 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain O 6–393（388 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 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain O 6–393（388 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 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain O 6–393（388 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain O 1–393（393 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain O 1–393（393 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain O 1–393（393 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain O 1–393（393 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain O 1–393（393 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 41 PDB declaration: 41-meric
Chain O 1–393（393 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 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 49 PDB declaration: 49-meric
Chain O 1–393（393 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
7QO6 26S proteasome Rpt1-RK -Ubp6-UbVS complex in the s2 state Deposited 2021-12-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 49 PDB declaration: 49-meric
Chain O 1–393（393 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 6.30 Å
9CGC Yeast 26S proteasome non-substrate-engaged (S1 state) Deposited 2024-06-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 39 PDB declaration: 39-meric
Chain O 1–393（393 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain O 1–393（393 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

32 other PDB entries and 33 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RPN9_YEAST
Isoform —
PDB entities 13
Chains and sequence ranges Author chain O； PDBConstruct 1–393； UniProt 1–393

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 5mpd

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5mpd
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5mpd
Deposition date deposition_date2016-12-16
Structure title title26S proteasome in presence of ATP (s1)
Keywords keywordsMacromolecular complex, 26S proteasome, Protease, hydrolase; HYDROLASE
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier73.85 Å
Radius of gyration Rg (electron density) rg_electron73.63 Å
Forward intensity I(0) i04551390000.00
Molecular weight molecular_weight582110.0 kDa
Excluded volume excluded_volume733170 ų
Envelope volume envelope_volume1331300 ų
Hydration-shell volume shell_volume152970 ų
Envelope diameter envelope_diameter237.3 Å
Shell Rg shell_rg74.17 Å
Envelope Rg envelope_rg69.41 Å
Shape Rg shape_rg73.64 Å
Total Rg total_rg73.62 Å
Total atoms total_atoms40974
Residues n_residues5142
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax253.2 Å
Rg (real space) rg_real73.97 Å
Rg uncertainty (real space) rg_real_error2.09 Å
I(0) (real space) i0_real4.5540e+09
I(0) uncertainty (real space) i0_real_error1.0320e+08
Rg (reciprocal space) rg_reciprocal74.48 Å
I(0) (reciprocal space) i0_reciprocal4559000000.0000
Solution quality estimate total_estimate0.8837
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary96.5 Å
Skewness Skewness skewness0.090
Kurtosis Kurtosis kurtosis-0.527
Angular range angular_range— – 0.1050 Å−1
Current regularization parameter α current_alpha0.0808
Highest regularization parameter α highest_alpha206600000.0000
Real-space data points n_real_points22
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.865; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.968; Smooth: 0.921
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (13)

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8. Citations (1)

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9. Files and Curves (10)