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3j47

Formation of an intricate helical bundle dictates the assembly of the 26S proteasome lid

Method: ELECTRON MICROSCOPY Dmax: 95.8 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

26S proteasome regulatory subunit 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 × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain V； UniProt 230–298 Fragment：last three C-terminal helices (UNP residues 230-298) 26S proteasome regulatory subunit RPN8 × 1 （Q08723） 26S proteasome regulatory subunit RPN9 × 1 （Q04062） 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 RPN3 × 1 （P40016） 26S proteasome regulatory subunit RPN12 × 1 （P32496） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.1 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 7.40 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 3J47 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 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 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 construct 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 construct 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 construct 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 construct 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 construct 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 construct 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 construct Different oligomeric state Different ligand/ion 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 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 construct Different oligomeric state Different ligand/ion Different experimental conditions 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
5MPD 26S proteasome in presence of ATP (s1) Deposited 2016-12-16 Different construct Different oligomeric state Different experimental conditions 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 4.10 Å
5MPE 26S proteasome in presence of ATP (s2) Deposited 2016-12-16 Different construct Different oligomeric state Different experimental conditions 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 construct Different oligomeric state Different experimental conditions 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 construct 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 construct 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 construct 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 Different experimental conditions 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 4.10 Å
6FVU 26S proteasome, s2 state Deposited 2018-03-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions 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 experimental conditions 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 experimental conditions 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 experimental conditions 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 experimental conditions 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 construct 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 construct 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 construct 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 construct 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 construct 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 construct 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 construct 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 construct 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 construct 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 1
Chains and sequence ranges Author chain V； PDBConstruct 1–69； UniProt 230–298

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 × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain U； UniProt 188–308 Fragment：last three C-terminal helices (UNP residues 188-308) 26S proteasome regulatory subunit RPN11 × 1 （P43588） 26S proteasome regulatory subunit RPN9 × 1 （Q04062） 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 RPN3 × 1 （P40016） 26S proteasome regulatory subunit RPN12 × 1 （P32496） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.1 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 7.40 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 3J47 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 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 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 construct 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 construct 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 construct 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 construct 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 construct 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 construct 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 construct Different oligomeric state Different ligand/ion 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 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 construct Different oligomeric state Different ligand/ion Different experimental conditions 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
5MPD 26S proteasome in presence of ATP (s1) Deposited 2016-12-16 Different construct Different oligomeric state Different experimental conditions 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 4.10 Å
5MPE 26S proteasome in presence of ATP (s2) Deposited 2016-12-16 Different construct Different oligomeric state Different experimental conditions 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 construct Different oligomeric state Different experimental conditions 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 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 1–338（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 construct 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 construct 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 Different experimental conditions 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 4.10 Å
6FVU 26S proteasome, s2 state Deposited 2018-03-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions 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 experimental conditions 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 experimental conditions 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 experimental conditions 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 experimental conditions 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 construct 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 construct 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 construct 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 construct 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 construct 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 construct 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 construct 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 construct 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 construct 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 construct 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 2
Chains and sequence ranges Author chain U； PDBConstruct 1–121； UniProt 188–308

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 × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain O； UniProt 360–387 Fragment：C-terminal helix (UNP residues 360-387) 26S proteasome regulatory subunit RPN11 × 1 （P43588） 26S proteasome regulatory subunit RPN8 × 1 （Q08723） 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 RPN3 × 1 （P40016） 26S proteasome regulatory subunit RPN12 × 1 （P32496） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.1 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 7.40 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 3J47 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
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 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 construct 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 construct 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 construct 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 construct 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 construct 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 construct 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 construct Different oligomeric state Different ligand/ion 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 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 construct Different oligomeric state Different ligand/ion Different experimental conditions 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
5MPD 26S proteasome in presence of ATP (s1) Deposited 2016-12-16 Different construct Different oligomeric state Different experimental conditions 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 4.10 Å
5MPE 26S proteasome in presence of ATP (s2) Deposited 2016-12-16 Different construct Different oligomeric state Different experimental conditions 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 construct Different oligomeric state Different experimental conditions 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 construct 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 construct 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 Different experimental conditions 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 4.10 Å
6FVU 26S proteasome, s2 state Deposited 2018-03-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions 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 experimental conditions 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 experimental conditions 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 experimental conditions 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 experimental conditions 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 construct 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 construct 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 construct 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 construct 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 construct 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 construct 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 construct 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 construct 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 construct 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 construct 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 3
Chains and sequence ranges Author chain O； PDBConstruct 1–28； UniProt 360–387

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 × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain P； UniProt 409–442 Fragment：C-terminal helix (UNP residues 409-442) 26S proteasome regulatory subunit RPN11 × 1 （P43588） 26S proteasome regulatory subunit RPN8 × 1 （Q08723） 26S proteasome regulatory subunit RPN9 × 1 （Q04062） 26S proteasome regulatory subunit RPN6 × 1 （Q12377） 26S proteasome regulatory subunit RPN7 × 1 （Q06103） 26S proteasome regulatory subunit RPN3 × 1 （P40016） 26S proteasome regulatory subunit RPN12 × 1 （P32496） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.1 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 7.40 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 3J47 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 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 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 construct 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 construct 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 construct 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 construct 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 construct 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 construct 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 construct Different oligomeric state Different ligand/ion 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 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 construct Different oligomeric state Different ligand/ion Different experimental conditions 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
5MPD 26S proteasome in presence of ATP (s1) Deposited 2016-12-16 Different construct Different oligomeric state Different experimental conditions 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 4.10 Å
5MPE 26S proteasome in presence of ATP (s2) Deposited 2016-12-16 Different construct Different oligomeric state Different experimental conditions 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 construct Different oligomeric state Different experimental conditions 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 construct 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 construct 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 Different experimental conditions 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 4.10 Å
6FVU 26S proteasome, s2 state Deposited 2018-03-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions 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 experimental conditions 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 experimental conditions 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 experimental conditions 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 experimental conditions 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 construct 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 construct 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 construct 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 construct 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 construct 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 construct 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 construct 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 construct 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 construct 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 4
Chains and sequence ranges Author chain P； PDBConstruct 1–34； UniProt 409–442

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 × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain Q； UniProt 407–431 Fragment：C-terminal helix (UNP residues 407-431) 26S proteasome regulatory subunit RPN11 × 1 （P43588） 26S proteasome regulatory subunit RPN8 × 1 （Q08723） 26S proteasome regulatory subunit RPN9 × 1 （Q04062） 26S proteasome regulatory subunit RPN5 × 1 （Q12250） 26S proteasome regulatory subunit RPN7 × 1 （Q06103） 26S proteasome regulatory subunit RPN3 × 1 （P40016） 26S proteasome regulatory subunit RPN12 × 1 （P32496） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.1 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 7.40 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 3J47 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 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 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 construct 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 construct 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 construct 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 construct 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 construct 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 construct 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 construct Different oligomeric state Different ligand/ion 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 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 construct Different oligomeric state Different ligand/ion Different experimental conditions 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
5MPD 26S proteasome in presence of ATP (s1) Deposited 2016-12-16 Different construct Different oligomeric state Different experimental conditions 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 4.10 Å
5MPE 26S proteasome in presence of ATP (s2) Deposited 2016-12-16 Different construct Different oligomeric state Different experimental conditions 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 construct Different oligomeric state Different experimental conditions 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 construct 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 construct 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 construct Different oligomeric state Different ligand/ion 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 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 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 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 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 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 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 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 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 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 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 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 construct 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 construct 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 construct 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 construct 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 construct 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 construct 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 construct 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 construct 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 construct 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 5
Chains and sequence ranges Author chain Q； PDBConstruct 1–25； UniProt 407–431

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 × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain R； UniProt 397–422 Fragment：C-terminal helix (UNP residues 397-422) 26S proteasome regulatory subunit RPN11 × 1 （P43588） 26S proteasome regulatory subunit RPN8 × 1 （Q08723） 26S proteasome regulatory subunit RPN9 × 1 （Q04062） 26S proteasome regulatory subunit RPN5 × 1 （Q12250） 26S proteasome regulatory subunit RPN6 × 1 （Q12377） 26S proteasome regulatory subunit RPN3 × 1 （P40016） 26S proteasome regulatory subunit RPN12 × 1 （P32496） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.1 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 7.40 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 3J47 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 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 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 construct 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 construct 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 construct 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 construct 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 construct 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 construct 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 construct Different oligomeric state Different ligand/ion 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 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 construct Different oligomeric state Different ligand/ion Different experimental conditions 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
5MPD 26S proteasome in presence of ATP (s1) Deposited 2016-12-16 Different construct Different oligomeric state Different experimental conditions 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 4.10 Å
5MPE 26S proteasome in presence of ATP (s2) Deposited 2016-12-16 Different construct Different oligomeric state Different experimental conditions 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 construct Different oligomeric state Different experimental conditions 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 construct 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 construct 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 Different experimental conditions 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 4.10 Å
6FVU 26S proteasome, s2 state Deposited 2018-03-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions 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 experimental conditions 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 experimental conditions 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 experimental conditions 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 experimental conditions 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 construct 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 construct 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 construct 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 construct 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 construct 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 construct 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 construct 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 construct 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 construct 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 6
Chains and sequence ranges Author chain R； PDBConstruct 1–26； UniProt 397–422

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 × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain S； UniProt 455–478 Fragment：C-terminal helix (UNP residues 455-478) 26S proteasome regulatory subunit RPN11 × 1 （P43588） 26S proteasome regulatory subunit RPN8 × 1 （Q08723） 26S proteasome regulatory subunit RPN9 × 1 （Q04062） 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 RPN12 × 1 （P32496） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.1 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 7.40 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 3J47 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 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 construct 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 construct 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 construct 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 construct 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 construct 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 construct 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 construct Different oligomeric state Different ligand/ion 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 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 construct Different oligomeric state Different ligand/ion Different experimental conditions 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
5MPD 26S proteasome in presence of ATP (s1) Deposited 2016-12-16 Different construct Different oligomeric state Different experimental conditions 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 4.10 Å
5MPE 26S proteasome in presence of ATP (s2) Deposited 2016-12-16 Different construct Different oligomeric state Different experimental conditions 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 construct Different oligomeric state Different experimental conditions 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 construct 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 construct 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 Different experimental conditions 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 4.10 Å
6FVU 26S proteasome, s2 state Deposited 2018-03-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions 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 experimental conditions 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 experimental conditions 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 experimental conditions 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 experimental conditions 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 construct 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 construct 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 construct 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 construct 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 construct 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 construct 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 construct 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 construct 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 construct 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 7
Chains and sequence ranges Author chain S； PDBConstruct 1–24； UniProt 455–478

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 × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain T； UniProt 256–272 Fragment：C-terminal helix (UNP residues 256-272) 26S proteasome regulatory subunit RPN11 × 1 （P43588） 26S proteasome regulatory subunit RPN8 × 1 （Q08723） 26S proteasome regulatory subunit RPN9 × 1 （Q04062） 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 RPN3 × 1 （P40016） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.1 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 7.40 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 3J47 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 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 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 construct 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 construct 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 construct 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 construct 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 construct 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 construct 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 construct Different oligomeric state Different ligand/ion 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 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 construct Different oligomeric state Different ligand/ion Different experimental conditions 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
5MPD 26S proteasome in presence of ATP (s1) Deposited 2016-12-16 Different construct Different oligomeric state Different experimental conditions 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 4.10 Å
5MPE 26S proteasome in presence of ATP (s2) Deposited 2016-12-16 Different construct Different oligomeric state Different experimental conditions 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 construct Different oligomeric state Different experimental conditions 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 construct 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 construct 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 Different experimental conditions 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 4.10 Å
6FVU 26S proteasome, s2 state Deposited 2018-03-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions 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 experimental conditions 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 experimental conditions 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 experimental conditions 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 experimental conditions 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 construct 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 construct 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 construct 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 construct 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 construct 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 construct 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 construct 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 construct 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 construct 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 8
Chains and sequence ranges Author chain T； PDBConstruct 1–17； UniProt 256–272

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 3j47

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3j47
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3j47
Deposition date deposition_date2013-06-27
Structure title titleFormation of an intricate helical bundle dictates the assembly of the 26S proteasome lid
Keywords keywordsalpha helix bundle, hybrid method, flexible fitting, PROTEIN BINDING; PROTEIN BINDING
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier24.66 Å
Radius of gyration Rg (electron density) rg_electron24.61 Å
Forward intensity I(0) i021210300.00
Molecular weight molecular_weight35525.0 kDa
Excluded volume excluded_volume44769 ų
Envelope volume envelope_volume55038 ų
Hydration-shell volume shell_volume20524 ų
Envelope diameter envelope_diameter96.9 Å
Shell Rg shell_rg29.04 Å
Envelope Rg envelope_rg25.17 Å
Shape Rg shape_rg24.60 Å
Total Rg total_rg25.20 Å
Total atoms total_atoms2498
Residues n_residues308
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 dmax95.8 Å
Rg (real space) rg_real25.03 Å
Rg uncertainty (real space) rg_real_error0.92 Å
I(0) (real space) i0_real2.1210e+07
I(0) uncertainty (real space) i0_real_error3.2960e+05
Rg (reciprocal space) rg_reciprocal24.94 Å
I(0) (reciprocal space) i0_reciprocal21210000.0000
Solution quality estimate total_estimate0.7252
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary22.8 Å
Skewness Skewness skewness0.662
Kurtosis Kurtosis kurtosis-0.018
Angular range angular_range— – 0.3200 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5792000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.402; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.238; Smooth: 0.978
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

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8. Citations (2)

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9. Files and Curves (10)