7ewm

Native crystal structure of S. cerevisiae Csn12 in complex with Thp3 and Sem1

Method: X-RAY DIFFRACTION D_max: 112.2 Å Quality: GOOD

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

Protein THP3

Saccharomyces cerevisiae S288C

UniProt Q12049

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 186–470	Not recorded	Cop9 signalosome complex subunit 12 × 1 （P47130） 26S proteasome complex subunit SEM1 × 1 （O94742）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；289 K；12% PEG3350, 100 mM Sodium malonate buffer (pH 5.0) and 3% Methanol	Resolution 2.90 Å R-free 0.251

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 7EWM	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7EWF Selenomethionine-substituted structure of S. cerevisiae Csn12 in complex with Thp3 and Sem1 Deposited 2021-05-25	Different mutation/modification Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 186–470（285 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；12% PEG3350, 100 mM Sodium malonate buffer (pH 5.0) and 3% Methanol	Resolution 2.85 Å R-free 0.257

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	THP3_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–289； UniProt 186–470

Cop9 signalosome complex subunit 12

Saccharomyces cerevisiae S288C

UniProt P47130

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 1–423	Not recorded	Protein THP3 × 1 （Q12049） 26S proteasome complex subunit SEM1 × 1 （O94742）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；289 K；12% PEG3350, 100 mM Sodium malonate buffer (pH 5.0) and 3% Methanol	Resolution 2.90 Å R-free 0.251

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 7EWM	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7EWF Selenomethionine-substituted structure of S. cerevisiae Csn12 in complex with Thp3 and Sem1 Deposited 2021-05-25	Different mutation/modification Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–423（423 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；12% PEG3350, 100 mM Sodium malonate buffer (pH 5.0) and 3% Methanol	Resolution 2.85 Å R-free 0.257

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CSN12_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–423； UniProt 1–423

26S proteasome complex subunit SEM1

Saccharomyces cerevisiae S288C

UniProt O94742

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain C； UniProt 1–89	Not recorded	Protein THP3 × 1 （Q12049） Cop9 signalosome complex subunit 12 × 1 （P47130）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；289 K；12% PEG3350, 100 mM Sodium malonate buffer (pH 5.0) and 3% Methanol	Resolution 2.90 Å R-free 0.251

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 7EWM	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3JCK Structure of the yeast 26S proteasome lid sub-complex Deposited 2015-12-20	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain I 1–89（89 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer 50 mM HEPES, 100 mM NaCl, 100 mM KCl, 1 mM TCEP；pH 7.5；50 mM HEPES, 100 mM NaCl, 100 mM KCl, 1 mM TCEP cryo-EM vitrification conditions 4 uL sample was applied to the grid, blotted for 2 seconds, and plunged into liquid ethane.；85 K；Cryogen ETHANE；4 uL sample was applied to the grid, blotted for 2 seconds at 4 degrees C, and plunged into liquid ethane using a manual plunger.	Resolution 3.50 Å
3JCO Structure of yeast 26S proteasome in M1 state derived from Titan dataset Deposited 2016-01-06	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric	Chain Y 1–89（89 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 50mM Tris pH 7.5, 100mM NaCl, 5mM MgCl2, 2mM ATP；pH 7.5；50mM Tris pH 7.5, 100mM NaCl, 5mM MgCl2, 2mM ATP cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.80 Å
3JCP Structure of yeast 26S proteasome in M2 state derived from Titan dataset Deposited 2016-01-06	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric	Chain Y 1–89（89 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 50mM Tris pH 7.5, 100mM NaCl, 5mM MgCl2, 2mM ATP；pH 7.5；50mM Tris pH 7.5, 100mM NaCl, 5mM MgCl2, 2mM ATP cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.60 Å
3T5V Sac3:Thp1:Sem1 complex Deposited 2011-07-28	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–89（89 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；292 K；see publication, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.90 Å R-free 0.231
3T5V Sac3:Thp1:Sem1 complex Deposited 2011-07-28	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 1–89（89 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；292 K；see publication, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.90 Å R-free 0.231
4CR2 Deep classification of a large cryo-EM dataset defines the conformational landscape of the 26S proteasome Deposited 2014-02-25	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric	Chain Y 1–89（89 aa） Fragment：SEM1	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.1 cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, INSTRUMENT- HOMEMADE PLUNGER,	Resolution 7.70 Å
4CR3 Deep classification of a large cryo-EM dataset defines the conformational landscape of the 26S proteasome Deposited 2014-02-25	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric	Chain Y 1–89（89 aa） Fragment：SEM1	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.1 cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, INSTRUMENT- HOMEMADE PLUNGER,	Resolution 9.30 Å
4CR4 Deep classification of a large cryo-EM dataset defines the conformational landscape of the 26S proteasome Deposited 2014-02-25	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric	Chain Y 1–89（89 aa） Fragment：SEM1	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.1 cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, INSTRUMENT- HOMEMADE PLUNGER,	Resolution 8.80 Å
4TRQ Crystal structure of Sac3/Thp1/Sem1 Deposited 2014-06-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: Hexameric	Chain C 30–89（60 aa） Chain F 30–89（60 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；0.5M Li2SO4, 10% PEG-8.000	Resolution 3.10 Å R-free 0.238
5A5B Structure of the 26S proteasome-Ubp6 complex Deposited 2015-06-17	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric	Chain Y 1–89（89 aa） Fragment：SEM1	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, INSTRUMENT- HOMEMADE PLUNGER,	Resolution 9.50 Å
5G5P Structure of the Saccharomyces cerevisiae TREX-2 complex Deposited 2016-05-26	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 1–89（89 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 20 MM HEPES, 300 MM NACL, 5 MM DTT；pH 8；20 mM HEPES, 300 mM NaCl, 5 mM DTT cryo-EM vitrification conditions 85 K；Cryogen ETHANE；LIQUID ETHANE	Resolution 5.30 Å
5L3T Structure of the Saccharomyces cerevisiae TREX-2 complex Deposited 2016-05-24	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 1–89（89 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Precipitant: 20% PEG 3350, 0.2 M Mg formate; protein 16.5 mg/ml in 0.3 M NaCl, 50 mM HEPES, pH 8, 5 mM DTT.	Resolution 4.93 Å R-free 0.370
5MPB 26S proteasome in presence of AMP-PNP (s3) Deposited 2016-12-16	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric	Chain Y 1–89（89 aa）	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 5 MG MAGNESIUM ION × 6 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 7.80 Å
5MPC 26S proteasome in presence of BeFx (s4) Deposited 2016-12-16	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric	Chain Y 1–89（89 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 6 ADP ADENOSINE-5'-DIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 7.70 Å
5MPD 26S proteasome in presence of ATP (s1) Deposited 2016-12-16	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric	Chain Y 1–89（89 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 4.10 Å
5MPE 26S proteasome in presence of ATP (s2) Deposited 2016-12-16	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric	Chain Y 1–89（89 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 4.50 Å
5MPE 26S proteasome in presence of ATP (s2) Deposited 2016-12-16	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain Y 1–89（89 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 4.50 Å
5UBP TREX2 M-region Deposited 2016-12-21	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–89（89 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；20 % PEG3350, 0.17 M MgFormate	Resolution 2.30 Å R-free 0.217
5WVI The resting state of yeast proteasome Deposited 2016-12-25	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric	Chain Y 1–89（89 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.30 Å
5WVK Yeast proteasome-ADP-AlFx Deposited 2016-12-25	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric	Chain Y 1–89（89 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
6FVT 26S proteasome, s1 state Deposited 2018-03-05	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric	Chain Y 1–89（89 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 5 MG MAGNESIUM ION × 6 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 4.10 Å
6FVU 26S proteasome, s2 state Deposited 2018-03-05	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric	Chain Y 1–89（89 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 5 MG MAGNESIUM ION × 6 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 4.50 Å
6FVV 26S proteasome, s3 state Deposited 2018-03-05	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric	Chain Y 1–89（89 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 6 ATP ADENOSINE-5'-TRIPHOSPHATE × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 5.40 Å
6FVW 26S proteasome, s4 state Deposited 2018-03-05	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric	Chain Y 1–89（89 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 6 ADP ADENOSINE-5'-DIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 4.50 Å
6FVX 26S proteasome, s5 state Deposited 2018-03-05	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric	Chain Y 1–89（89 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 5 MG MAGNESIUM ION × 6 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 4.90 Å
6FVY 26S proteasome, s6 state Deposited 2018-03-05	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric	Chain Y 1–89（89 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 6 ADP ADENOSINE-5'-DIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 6.10 Å
6J2C Yeast proteasome in translocation competent state (C3-a) Deposited 2019-01-01	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric	Chain Y 1–89（89 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.00 Å
6J2N yeast proteasome in substrate-processing state (C3-b) Deposited 2019-01-02	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric	Chain Y 1–89（89 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.50 Å
6J2Q Yeast proteasome in Ub-accepted state (C1-b) Deposited 2019-01-02	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric	Chain Y 1–89（89 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
6J2X Yeast proteasome in resting state (C1-a) Deposited 2019-01-03	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric	Chain Y 1–89（89 aa） Fragment：SEM1	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
6J30 yeast proteasome in Ub-engaged state (C2) Deposited 2019-01-03	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric	Chain Y 1–89（89 aa） Fragment：SEM1	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.50 Å
7EWF Selenomethionine-substituted structure of S. cerevisiae Csn12 in complex with Thp3 and Sem1 Deposited 2021-05-25	Different mutation/modification Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–89（89 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；12% PEG3350, 100 mM Sodium malonate buffer (pH 5.0) and 3% Methanol	Resolution 2.85 Å R-free 0.257
7QO3 Structure of the 26S proteasome-Ubp6 complex in the si state (Core Particle and Lid) Deposited 2021-12-23	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 41 PDB declaration: 41-meric	Chain Y 1–89（89 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.10 Å
7QO5 26S proteasome Rpt1-RK -Ubp6-UbVS complex in the si state Deposited 2021-12-23	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 49 PDB declaration: 49-meric	Chain Y 1–89（89 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 5 MG MAGNESIUM ION × 6 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.00 Å
7QO6 26S proteasome Rpt1-RK -Ubp6-UbVS complex in the s2 state Deposited 2021-12-23	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 49 PDB declaration: 49-meric	Chain Y 1–89（89 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 5 MG MAGNESIUM ION × 6 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.30 Å
8U8C Crystal structure of the TREX-2 complex in complex with the N-terminal motif of Sub2 Deposited 2023-09-17	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–89（89 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M MES, pH 6.5, and 20% PEG3350	Resolution 2.40 Å R-free 0.231
9IWR 26S proteasome trimer Deposited 2024-07-25	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric	Chain Y 1–89（89 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 6.8；YPD buffer cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 9.10 Å

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

View Construct and Data Evidence

UniProt name	SEM1_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–89； UniProt 1–89

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	7ewm
Deposition date deposition_date	2021-05-25
Structure title title	Native crystal structure of S. cerevisiae Csn12 in complex with Thp3 and Sem1
Keywords keywords	Complex, Nucleic acid binding, Transcription, mRNA splicing; TRANSCRIPTION
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	32.55 Å
Radius of gyration Rg (electron density) rg_electron	31.70 Å
Forward intensity I(0) i0	116020000.00
Molecular weight molecular_weight	86809.0 kDa
Excluded volume excluded_volume	109330 Å³
Envelope volume envelope_volume	145940 Å³
Hydration-shell volume shell_volume	38569 Å³
Envelope diameter envelope_diameter	117.6 Å
Shell Rg shell_rg	38.34 Å
Envelope Rg envelope_rg	31.88 Å
Shape Rg shape_rg	31.66 Å
Total Rg total_rg	32.41 Å
Total atoms total_atoms	6106
Residues n_residues	739
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	112.2 Å
Rg (real space) rg_real	32.50 Å
Rg uncertainty (real space) rg_real_error	0.83 Å
I(0) (real space) i0_real	1.1600e+08
I(0) uncertainty (real space) i0_real_error	1.8430e+06
Rg (reciprocal space) rg_reciprocal	32.53 Å
I(0) (reciprocal space) i0_reciprocal	116000000.0000
Solution quality estimate total_estimate	0.8841
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	41.2 Å
Skewness Skewness skewness	0.252
Kurtosis Kurtosis kurtosis	-0.449
Angular range angular_range	— – 0.2450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	29370000.0000
Real-space data points n_real_points	50
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.848; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.976; Smooth: 0.971

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Protein THP3
Molecular weight formula_weight	33959.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	6110

GSHMKIHVVGRCQTLEKSYLRLTSEPNPDLIRPPNILQKMYCLLMDKYQSKTATYTYLCDQFKSMRQDLRVQMIENSFTIKVYQTHARIALENGDLGEFNQCQNRIMALFENPTIPKKSYSEFICYSVLYSMLTEDYPSISHLKLKLIDDGSSEILEDEHVKMIFELSDMKLVGNYHYFMKNYLKLHKFEKCLINSFLNLEKLIFLTIICKSYNQVNLDFVKSEFNFNSIEETTNFLNEQNLTEFILNKQITDSNGKSSNIKILNTKGCRVQLIQNYMKSKKIDIKGQK

来源 Source

来源生物 organism	Saccharomyces cerevisiae S288C
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Cop9 signalosome complex subunit 12
Molecular weight formula_weight	49558.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MDVDIGCYFEEKRYDDKLLDFIRYDVKTPKKTKYILQRPTATDEESVRLQRFYQLGVDLKLKYSKRRSLKKQGRIKNATEELLRLANEQLKLFNRIVERETNWIIYPLWVMAKQLIRLANESSELNKDSIEECGRTIHRSFTICLNDRNPRLNENKKIGCYMFANLEFSIYHRLSNKDMIKNLVKVLESRVNARDIPPLNKSLAMEHKSQVVLYNYYLGQYYGCLENDHERGFFHLNEALLQCPMLYVESTGKFVLQGQMEKIMILLVPLALLTKRLYPHWDHPVIAGVITRSKRLSQVYPTLVRSVISGNLSLYEATAASHERFFLSQGLHVVITLLREVVFTRLVQRCWQWGNDRKSIMPLKILLATKQHDSSANEDEEEQLDALECRLASAIASGLLRAYLSHSNRCIVFSKKEPFPHSK

来源 Source

来源生物 organism	Saccharomyces cerevisiae S288C
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	26S proteasome complex subunit SEM1
Molecular weight formula_weight	10397.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MSTDVAAAQAQSKIDLTKKKNEEINKKSLEEDDEFEDFPIDTWANGETIKSNAVTQTNIWEENWDDVEVDDDFTNELKAELDRYKRENQ

来源 Source

来源生物 organism	Saccharomyces cerevisiae S288C
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	4

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	7ewmA01
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	990 —

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8. Citations (1)

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Unit-cell length a length_a	115.575 Å
Unit-cell length b length_b	115.575 Å
Unit-cell length c length_c	126.825 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	32.290 Å
R factor r_factor	0.2236
R_work r_work	0.2220
R_free r_free	0.2510

fit	/app/data/saxs_computation/ew/7ewm/7ewm.fit
pddf	/app/data/pr_computation/ew/7ewm/7ewm.pr.out
profile	/app/data/saxs_computation/ew/7ewm/7ewm.dat

Native crystal structure of S. cerevisiae Csn12 in complex with Thp3 and Sem1

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

Protein THP3

State in the Current Structure

Other States of the Same Protein in the Database

Cop9 signalosome complex subunit 12

State in the Current Structure

Other States of the Same Protein in the Database

26S proteasome complex subunit SEM1

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 (4)

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 water

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)