4ocm

Crystal Structure of the Rpn8-Rpn11 MPN domain heterodimer, crystal form Ib

Method: X-RAY DIFFRACTION D_max: 128.9 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

26S proteasome regulatory subunit RPN8

Saccharomyces cerevisiae

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 1–176	Fragment：UNP residues 1-176	26S proteasome regulatory subunit RPN11 × 1 （P43588） Nb1 × 1 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
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain D； UniProt 1–176	Fragment：UNP residues 1-176	26S proteasome regulatory subunit RPN11 × 1 （P43588） Nb1 × 1 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

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 4OCM	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3J47 Formation of an intricate helical bundle dictates the assembly of the 26S proteasome lid Deposited 2013-06-27	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain U 188–308（121 aa） Fragment：last three C-terminal helices (UNP residues 188-308)	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.1 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.40 Å
3JCK Structure of the yeast 26S proteasome lid sub-complex Deposited 2015-12-20	Different construct Different oligomeric state Different experimental method 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 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 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 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 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
4OCN Crystal Structure of the Rpn8-Rpn11 MPN domain heterodimer, crystal form II Deposited 2014-01-09	Different ligand/ion 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 ligand/ion 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 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 ligand/ion Different experimental method 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 method 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 method 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 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 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 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 method 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 method 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 method 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 method 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 method 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 method 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 method 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 method 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 method 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 ligand/ion Different experimental method 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 41 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RPN8_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–178； UniProt 1–176 Author chain D； PDBConstruct 3–178； UniProt 1–176

26S proteasome regulatory subunit RPN11

Saccharomyces cerevisiae

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain B； UniProt 1–220	Fragment：UNP residues 1-220	26S proteasome regulatory subunit RPN8 × 1 （Q08723） Nb1 × 1 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
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain E； UniProt 1–220	Fragment：UNP residues 1-220	26S proteasome regulatory subunit RPN8 × 1 （Q08723） Nb1 × 1 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 4OCM	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3J47 Formation of an intricate helical bundle dictates the assembly of the 26S proteasome lid Deposited 2013-06-27	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain V 230–298（69 aa） Fragment：last three C-terminal helices (UNP residues 230-298)	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.1 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.40 Å
3JCK Structure of the yeast 26S proteasome lid sub-complex Deposited 2015-12-20	Different construct Different oligomeric state Different experimental method 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 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 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 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 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
4OCN Crystal Structure of the Rpn8-Rpn11 MPN domain heterodimer, crystal form II Deposited 2014-01-09	Different ligand/ion 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 ligand/ion 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 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 ligand/ion Different experimental method 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 method 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 method 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 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 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 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 method 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 method 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 ligand/ion Different experimental method 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 41 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RPN11_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–220； UniProt 1–220 Author chain E； PDBConstruct 1–220； UniProt 1–220

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4ocm
Deposition date deposition_date	2014-01-09
Structure title title	Crystal Structure of the Rpn8-Rpn11 MPN domain heterodimer, crystal form Ib
Keywords keywords	26S proteasome, isopeptidase activity, regulatory particle, lid, ubiquitin, HYDROLASE, PROTEIN BINDING; HYDROLASE, PROTEIN BINDING
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	38.48 Å
Radius of gyration Rg (electron density) rg_electron	38.38 Å
Forward intensity I(0) i0	163599000.00
Molecular weight molecular_weight	103890.0 kDa
Excluded volume excluded_volume	129960 Å³
Envelope volume envelope_volume	177520 Å³
Hydration-shell volume shell_volume	38716 Å³
Envelope diameter envelope_diameter	133.0 Å
Shell Rg shell_rg	44.06 Å
Envelope Rg envelope_rg	37.79 Å
Shape Rg shape_rg	38.40 Å
Total Rg total_rg	38.69 Å
Total atoms total_atoms	7302
Residues n_residues	941
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	128.9 Å
Rg (real space) rg_real	38.65 Å
Rg uncertainty (real space) rg_real_error	1.19 Å
I(0) (real space) i0_real	1.6360e+08
I(0) uncertainty (real space) i0_real_error	2.9280e+06
Rg (reciprocal space) rg_reciprocal	38.55 Å
I(0) (reciprocal space) i0_reciprocal	163600000.0000
Solution quality estimate total_estimate	0.8740
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	37.7 Å
Skewness Skewness skewness	0.323
Kurtosis Kurtosis kurtosis	-0.618
Angular range angular_range	— – 0.2050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	15570000.0000
Real-space data points n_real_points	42
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.880; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.880; Smooth: 0.837

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	26S proteasome regulatory subunit RPN8
Molecular weight formula_weight	20838.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D
Atom count atom_count	7521

GHMSLQHEKVTIAPLVLLSALDHYERTQTKENKRCVGVILGDANSSTIRVTNSFALPFEEDEKNSDVWFLDHNYIENMNEMCKKINAKEKLIGWYHSGPKLRASDLKINELFKKYTQNNPLLLIVDVKQQGVGLPTDAYVAIEQVKDDGTSTEKTFLHLPCTIEAEEAEEIGVEHLLRGSGGSGGSG

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;Baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	26S proteasome regulatory subunit RPN11
Molecular weight formula_weight	24566.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,E

MERLQRLMMNSKVGSADTGRDDTKETVYISSIALLKMLKHGRAGVPMEVMGLMLGEFVDDYTVNVVDVFAMPQSGTGVSVEAVDDVFQAKMMDMLKQTGRDQMVVGWYHSHPGFGCWLSSVDVNTQKSFEQLNSRAVAVVVDPIQSVKGKVVIDAFRLIDTGALINNLEPRQTTSNTGLLNKANIQALIHGLNRHYYSLNIDYHKTAKETKMLMNLHKEQ

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;Baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Nb1
Molecular weight formula_weight	14854.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,F

MQVQLQESGGGLVPAGGSLRLSCVDSGRTFSSTVMAWFRQAPGKEREFVATIRWSGGNTYYADSVKGRFTISRDNARNTVYLQMNSLKPEDTAVYYCAGGTYYGTLSYKYDFWGRGTQVTVSSHHHHHHEPEA

来源 Source

来源生物 organism	Lama glama
通用名 common_name	llama
NCBI Class编号 ncbi_taxonomy_id	9844
宿主生物 host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	196

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7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (10 domains)

Domain ID domain_id	d4ocma_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.97 — Cytidine deaminase-like
Superfamily Superfamily superfamily	c.97.3 — JAB1/MPN domain
Family Family family	c.97.3.1 — JAB1/MPN domain

Domain ID domain_id	d4ocmb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.97 — Cytidine deaminase-like
Superfamily Superfamily superfamily	c.97.3 — JAB1/MPN domain
Family Family family	c.97.3.1 — JAB1/MPN domain

Domain ID domain_id	d4ocmc1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d4ocmc2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4ocmc3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4ocmd_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.97 — Cytidine deaminase-like
Superfamily Superfamily superfamily	c.97.3 — JAB1/MPN domain
Family Family family	c.97.3.1 — JAB1/MPN domain

Domain ID domain_id	d4ocme_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.97 — Cytidine deaminase-like
Superfamily Superfamily superfamily	c.97.3 — JAB1/MPN domain
Family Family family	c.97.3.1 — JAB1/MPN domain

Domain ID domain_id	d4ocmf1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d4ocmf2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4ocmf3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (6 domains)

Domain ID domain_id	4ocmA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	140 — Cytidine Deaminase; domain 2
Homologous superfamily homologous superfamily	10 — Cytidine Deaminase, domain 2

Domain ID domain_id	4ocmB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	140 — Cytidine Deaminase; domain 2
Homologous superfamily homologous superfamily	10 — Cytidine Deaminase, domain 2

Domain ID domain_id	4ocmC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4ocmD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	140 — Cytidine Deaminase; domain 2
Homologous superfamily homologous superfamily	10 — Cytidine Deaminase, domain 2

Domain ID domain_id	4ocmE00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	140 — Cytidine Deaminase; domain 2
Homologous superfamily homologous superfamily	10 — Cytidine Deaminase, domain 2

Domain ID domain_id	4ocmF00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (1)

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Unit-cell length a length_a	63.401 Å
Unit-cell length b length_b	44.970 Å
Unit-cell length c length_c	200.043 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	98.40 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 2 1
Space-group number int_tables_number	3
Crystal system crystal_system	—

Resolution resolution	1.990 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2181
R_work r_work	0.2158
R_free r_free	0.2623

fit	/app/data/saxs_computation/oc/4ocm/4ocm.fit
pddf	/app/data/pr_computation/oc/4ocm/4ocm.pr.out
profile	/app/data/saxs_computation/oc/4ocm/4ocm.dat

Crystal Structure of the Rpn8-Rpn11 MPN domain heterodimer, crystal form Ib

1. Protein Identity and Related Structures Protein Identity & Related Structures

26S proteasome regulatory subunit RPN8

State in the Current Structure

Other States of the Same Protein in the Database

26S proteasome regulatory subunit RPN11

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (10 domains)

CATH v4.4 (6 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)