SAXSdb — 8e8q

▼

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

ATP-dependent Clp protease ATP-binding subunit ClpX

Escherichia coli

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 × 20 PDB declaration: eicosameric（20） Consistent with protein copy count	Chain A； UniProt 62–424 Chain B； UniProt 62–424 Chain C； UniProt 62–424 Chain D； UniProt 62–424 Chain E； UniProt 62–424 Chain F； UniProt 62–424	Fragment：UNP residues 62-424 Mutation：C169S, K408E	ATP-dependent Clp protease proteolytic subunit × 14 （P0A6G7） ATP ADENOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.12 Å

Other States of the Same Protein in the Database

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

Other PDB	Difference from Current Entry 8E8Q	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1OVX NMR structure of the E. coli ClpX chaperone zinc binding domain dimer Deposited 2003-03-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–60（60 aa） Fragment：N-terminal domain (residues 1-60) Chain B 1–60（60 aa） Fragment：N-terminal domain (residues 1-60)	Not recorded	ZN ZINC ION × 2	SOLUTION NMR NMR measurement conditions pH 7.5；303 K；Ionic strength (raw mmCIF value) 150 mM NaCl；Pressure ambient NMR sample composition 1.3 mM ClpX U-15N,13C \| 20 mM sodium phosphate buffer, 0.03% sodium azide, pH 7.5; 150 mM sodium chloride; 90% H2O, 10% H2O	Resolution not provided
2DS5 Structure of the ZBD in the orthorhomibic crystal from Deposited 2006-06-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–51（51 aa） Fragment：Zinc binding domain(ZBD) Chain B 1–51（51 aa） Fragment：Zinc binding domain(ZBD)	Not recorded	ZN ZINC ION × 2 CA CALCIUM ION × 1 PG4 TETRAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；100mM Hepes-NaOH, pH 7.5, 200mM calcium chloride, 30% PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.50 Å R-free 0.221
2DS6 Structure of the ZBD in the tetragonal crystal form Deposited 2006-06-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–51（51 aa） Fragment：Zinc binding domain(ZBD) Chain B 1–51（51 aa） Fragment：Zinc binding domain(ZBD)	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；295 K；100mM tri-sodium citrate, pH 5.6, 2% ethyleneimine polymer, 500mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.00 Å R-free 0.313
2DS7 Structure of the ZBD in the hexagonal crystal form Deposited 2006-06-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–51（51 aa） Fragment：Zinc binding domain(ZBD)	Mutation：C43M Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；295 K；100mM sodium acetate, pH 4.6, 200mM lithium sulfate, 12% 2-propanol, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.50 Å R-free 0.272
2DS8 Structure of the ZBD-XB complex Deposited 2006-06-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–51（51 aa） Fragment：Zinc binding domain(ZBD) Chain B 1–51（51 aa） Fragment：Zinc binding domain(ZBD)	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；1.6M tri-sodium citrate, pH 6.5, 10-fold molar excess of XB peptide addition, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.60 Å R-free 0.226
3HTE Crystal structure of nucleotide-free hexameric ClpX Deposited 2009-06-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 62–424（363 aa） Fragment：Covalently linked ClpX residues 62-424 Chain B 62–424（363 aa） Fragment：Covalently linked ClpX residues 62-424 Chain C 62–424（363 aa） Fragment：Covalently linked ClpX residues 62-424 Chain D 62–424（363 aa） Fragment：Covalently linked ClpX residues 62-424 Chain E 62–424（363 aa） Fragment：Covalently linked ClpX residues 62-424 Chain F 62–424（363 aa） Fragment：Covalently linked ClpX residues 62-424	Not recorded	SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.8；298 K；75 mM Sodium acetate, 1.9 M ammonium sulfate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 4.03 Å R-free 0.313
3HWS Crystal structure of nucleotide-bound hexameric ClpX Deposited 2009-06-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 62–424（363 aa） Fragment：covalently linked ClpX lacking N-terminal domain Chain B 62–424（363 aa） Fragment：covalently linked ClpX lacking N-terminal domain Chain C 62–424（363 aa） Fragment：covalently linked ClpX lacking N-terminal domain Chain D 62–424（363 aa） Fragment：covalently linked ClpX lacking N-terminal domain Chain E 62–424（363 aa） Fragment：covalently linked ClpX lacking N-terminal domain Chain F 62–424（363 aa） Fragment：covalently linked ClpX lacking N-terminal domain	Mutation：E185Q, K408E Mutation：E185Q, K408E Mutation：E185Q, K408E Mutation：E185Q, K408E Mutation：E185Q, K408E Mutation：E185Q, K408E	ADP ADENOSINE-5'-DIPHOSPHATE × 4 SO4 SULFATE ION × 13 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.8；298 K；Sodium acetate, ammonium sulfate Soaked overnight in mother liquor plus 5 mM ATP-G-S / 5 mM magnesium chloride, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.25 Å R-free 0.282
3HWS Crystal structure of nucleotide-bound hexameric ClpX Deposited 2009-06-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 62–424（363 aa） Fragment：covalently linked ClpX lacking N-terminal domain Chain E 62–424（363 aa） Fragment：covalently linked ClpX lacking N-terminal domain Chain F 62–424（363 aa） Fragment：covalently linked ClpX lacking N-terminal domain	Mutation：E185Q, K408E Mutation：E185Q, K408E Mutation：E185Q, K408E	ADP ADENOSINE-5'-DIPHOSPHATE × 2 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.8；298 K；Sodium acetate, ammonium sulfate Soaked overnight in mother liquor plus 5 mM ATP-G-S / 5 mM magnesium chloride, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.25 Å R-free 0.282
3HWS Crystal structure of nucleotide-bound hexameric ClpX Deposited 2009-06-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain B 62–424（363 aa） Fragment：covalently linked ClpX lacking N-terminal domain Chain C 62–424（363 aa） Fragment：covalently linked ClpX lacking N-terminal domain Chain D 62–424（363 aa） Fragment：covalently linked ClpX lacking N-terminal domain	Mutation：E185Q, K408E Mutation：E185Q, K408E Mutation：E185Q, K408E	ADP ADENOSINE-5'-DIPHOSPHATE × 2 SO4 SULFATE ION × 9 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.8；298 K；Sodium acetate, ammonium sulfate Soaked overnight in mother liquor plus 5 mM ATP-G-S / 5 mM magnesium chloride, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.25 Å R-free 0.282
4I34 Crystal Structure of W-W-W ClpX Hexamer Deposited 2012-11-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 62–424（363 aa） Chain B 62–424（363 aa） Chain C 62–424（363 aa） Chain D 62–424（363 aa） Chain E 62–424（363 aa） Chain F 62–424（363 aa）	Not recorded	SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.8；298 K；75 mM sodium acetate, 1.9 M ammonium sulfate, pH 4.8, VAPOR DIFFUSION, temperature 298K	Resolution 4.12 Å R-free 0.308
4I4L Crystal Structure of Nucleotide-Bound W-W-W ClpX Hexamer Deposited 2012-11-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 62–424（363 aa） Chain B 62–424（363 aa） Chain C 62–424（363 aa） Chain D 62–424（363 aa） Chain E 62–424（363 aa） Chain F 62–424（363 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.8；298 K；75 mM sodium acetate, 1.9 M ammonium sulfate, pH 4.8, VAPOR DIFFUSION, temperature 298K	Resolution 3.70 Å R-free 0.323
4I5O Crystal Structure of W-W-R ClpX Hexamer Deposited 2012-11-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 62–424（363 aa） Chain B 62–424（363 aa） Chain C 62–424（363 aa） Chain D 62–424（363 aa） Chain E 62–424（363 aa） Chain F 62–424（363 aa）	Not recorded	SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 9；298 K；2.2 M ammonium sulfate, 0.2 M ammonium bromide, 0.1 M Bicine, pH 9.0, VAPOR DIFFUSION, temperature 298K	Resolution 4.48 Å R-free 0.323
4I63 Crystal Structure of E-R ClpX Hexamer Deposited 2012-11-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 62–424（363 aa） Chain B 62–424（363 aa） Chain C 62–424（363 aa） Chain D 62–424（363 aa） Chain E 62–424（363 aa） Chain F 62–424（363 aa）	Not recorded	SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 9；298 K；2.2 M ammonium sulfate, 0.2 M ammonium bromide, 0.1 M bicine, pH 9.0, VAPOR DIFFUSION, temperature 298K	Resolution 5.71 Å R-free 0.315
4I81 Crystal Structure of ATPgS bound ClpX Hexamer Deposited 2012-12-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 62–424（363 aa） Chain B 62–424（363 aa） Chain C 62–424（363 aa） Chain D 62–424（363 aa） Chain E 62–424（363 aa） Chain F 62–424（363 aa）	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 4 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.8；298 K；75 mM sodium acetate, 1.9 M ammonium sulfate, pH 4.8, VAPOR DIFFUSION, temperature 298K	Resolution 3.82 Å R-free 0.295
4I9K Crystal structure of symmetric W-W-W ClpX Hexamer Deposited 2012-12-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 62–424（363 aa） Chain B 62–424（363 aa）	Not recorded	SO4 SULFATE ION × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；298 K；2 M ammonium sulfate, 0.15 M potassium sulfate, 4 mM ATP, 4 mM magnesium sulfate, 50 mM EDTA, pH 7.5, VAPOR DIFFUSION, temperature 298K	Resolution 5.00 Å R-free 0.354
6WR2 ClpP and ClpX IGF loop in ClpX-ClpP complex bound to ssrA tagged GFP Deposited 2020-04-29	Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric	Chain A 62–424（363 aa） Chain B 62–424（363 aa） Chain C 62–424（363 aa） Chain D 62–424（363 aa） Chain E 62–424（363 aa） Chain F 62–424（363 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.88 Å
6WRF ClpX-ClpP complex bound to GFP-ssrA, recognition complex Deposited 2020-04-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain A 62–424（363 aa） Chain B 62–424（363 aa） Chain C 62–424（363 aa） Chain D 62–424（363 aa） Chain E 62–424（363 aa） Chain F 62–424（363 aa）	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 5 MG MAGNESIUM ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.14 Å
6WSG ClpX-ClpP complex bound to ssrA-tagged GFP, intermediate complex Deposited 2020-04-30	Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain A 62–424（363 aa） Fragment：UNP residues 62-424 Chain B 62–424（363 aa） Fragment：UNP residues 62-424 Chain C 62–424（363 aa） Fragment：UNP residues 62-424 Chain D 62–424（363 aa） Fragment：UNP residues 62-424 Chain E 62–424（363 aa） Fragment：UNP residues 62-424 Chain F 62–424（363 aa） Fragment：UNP residues 62-424	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 5 MG MAGNESIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.16 Å
8E7V Cryo-EM structure of substrate-free DNClpX.ClpP from singly capped particles Deposited 2022-08-24	Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric	Chain A 62–424（363 aa） Fragment：UNP residues 62-424 Chain B 62–424（363 aa） Fragment：UNP residues 62-424 Chain C 62–424（363 aa） Fragment：UNP residues 62-424 Chain D 62–424（363 aa） Fragment：UNP residues 62-424 Chain E 62–424（363 aa） Fragment：UNP residues 62-424 Chain F 62–424（363 aa） Fragment：UNP residues 62-424	Mutation：C169S, K408E Mutation：C169S, K408E Mutation：C169S, K408E Mutation：C169S, K408E Mutation：C169S, K408E Mutation：C169S, K408E	ATP ADENOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
8V9R Cryo-EM Structure of a Proteolytic ClpXP AAA+ Machine Poised to Unfold a Branched-Degron DHFR-ssrA Substrate Bound with MTX Deposited 2023-12-09	Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 21 PDB declaration: 21-meric	Chain A 62–424（363 aa） Fragment：UNP residues 62-424 Chain B 62–424（363 aa） Fragment：UNP residues 62-424 Chain C 62–424（363 aa） Fragment：UNP residues 62-424 Chain D 62–424（363 aa） Fragment：UNP residues 62-424 Chain E 62–424（363 aa） Fragment：UNP residues 62-424 Chain F 62–424（363 aa） Fragment：UNP residues 62-424	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 3 MG MAGNESIUM ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 3 MTX METHOTREXATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
9C87 Cryo-EM Structure of a Proteolytic ClpXP AAA+ Machine Poised to Unfold a Linear-Degron DHFR-ssrA Substrate Bound with MTX Deposited 2024-06-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 21 PDB declaration: 21-meric	Chain A 62–424（363 aa） Chain B 62–424（363 aa） Chain C 62–424（363 aa） Chain D 62–424（363 aa） Chain E 62–424（363 aa） Chain F 62–424（363 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 3 MG MAGNESIUM ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 3 MTX METHOTREXATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
9C88 Cryo-EM Structure of a Proteolytic ClpXP AAA+ Machine Translocating a Portion of a Branched-Degron DHFR Substrate Deposited 2024-06-12	Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 21 PDB declaration: 21-meric	Chain A 62–424（363 aa） Fragment：UNP residues 62-424 Chain B 62–424（363 aa） Fragment：UNP residues 62-424 Chain C 62–424（363 aa） Fragment：UNP residues 62-424 Chain D 62–424（363 aa） Fragment：UNP residues 62-424 Chain E 62–424（363 aa） Fragment：UNP residues 62-424 Chain F 62–424（363 aa） Fragment：UNP residues 62-424	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 3 MG MAGNESIUM ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.60 Å

20 other PDB entries and 22 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CLPX_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 26–388； UniProt 62–424 Author chain B； PDBConstruct 26–388； UniProt 62–424 Author chain C； PDBConstruct 26–388； UniProt 62–424 Author chain D； PDBConstruct 26–388； UniProt 62–424 Author chain E； PDBConstruct 26–388； UniProt 62–424 Author chain F； PDBConstruct 26–388； UniProt 62–424

ATP-dependent Clp protease proteolytic subunit

Escherichia coli

UniProt P0A6G7

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 × 20 PDB declaration: eicosameric（20） Consistent with protein copy count	Chain H； UniProt 16–207 Chain I； UniProt 16–207 Chain J； UniProt 16–207 Chain K； UniProt 16–207 Chain L； UniProt 16–207 Chain M； UniProt 16–207 Chain N； UniProt 16–207 Chain h； UniProt 16–207 Chain i； UniProt 16–207 Chain j； UniProt 16–207 Chain k； UniProt 16–207 Chain l； UniProt 16–207 Chain m； UniProt 16–207 Chain n； UniProt 16–207	Fragment：UNP residues 16-207	ATP-dependent Clp protease ATP-binding subunit ClpX × 6 （P0A6H1） ATP ADENOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.12 Å

Other States of the Same Protein in the Database

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

Other PDB	Difference from Current Entry 8E8Q	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1TYF THE STRUCTURE OF CLPP AT 2.3 ANGSTROM RESOLUTION SUGGESTS A MODEL FOR ATP-DEPENDENT PROTEOLYSIS Deposited 1997-10-13	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 14 PDB declaration: tetradecameric	Chain A 15–207（193 aa） Chain B 15–207（193 aa） Chain C 15–207（193 aa） Chain D 15–207（193 aa） Chain E 15–207（193 aa） Chain F 15–207（193 aa） Chain G 15–207（193 aa） Chain H 15–207（193 aa） Chain I 15–207（193 aa） Chain J 15–207（193 aa） Chain K 15–207（193 aa） Chain L 15–207（193 aa） Chain M 15–207（193 aa） Chain N 15–207（193 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å R-free 0.292
1YG6 ClpP Deposited 2005-01-04	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 14 PDB declaration: tetradecameric	Chain A 15–207（193 aa） Chain B 15–207（193 aa） Chain C 15–207（193 aa） Chain D 15–207（193 aa） Chain E 15–207（193 aa） Chain F 15–207（193 aa） Chain G 15–207（193 aa） Chain H 15–207（193 aa） Chain I 15–207（193 aa） Chain J 15–207（193 aa） Chain K 15–207（193 aa） Chain L 15–207（193 aa） Chain M 15–207（193 aa） Chain N 15–207（193 aa）	Not recorded	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 14	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.2；298 K；mpd, mes, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.90 Å R-free 0.251
2FZS Crystal structure of E. coli ClpP with a Peptide Chloromethyl Ketone Covalently Bound at the Active Site Deposited 2006-02-10	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 14 PDB declaration: tetradecameric	Chain A 15–207（193 aa） Chain B 15–207（193 aa） Chain C 15–207（193 aa） Chain D 15–207（193 aa） Chain E 15–207（193 aa） Chain F 15–207（193 aa） Chain G 15–207（193 aa） Chain H 15–207（193 aa） Chain I 15–207（193 aa） Chain J 15–207（193 aa） Chain K 15–207（193 aa） Chain L 15–207（193 aa） Chain M 15–207（193 aa） Chain N 15–207（193 aa）	Not recorded	CMQ N~2~-[(BENZYLOXY)CARBONYL]-N-[(1S,2S)-2-HYDROXY-1-(4-HYDROXYBENZYL)PROPYL]-L-LEUCINAMIDE × 14 PGE TRIETHYLENE GLYCOL × 15 GOL GLYCEROL × 11	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；0.1M tri-sodium citrate, 0.15M ammonium acetate, 30% PEG 4000 , pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.90 Å R-free 0.233
3HLN Crystal structure of ClpP A153C mutant with inter-heptamer disulfide bonds Deposited 2009-05-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 14 PDB declaration: tetradecameric	Chain A 15–207（193 aa） Fragment：UNP residues 15-207 Chain B 15–207（193 aa） Fragment：UNP residues 15-207 Chain C 15–207（193 aa） Fragment：UNP residues 15-207 Chain D 15–207（193 aa） Fragment：UNP residues 15-207 Chain E 15–207（193 aa） Fragment：UNP residues 15-207 Chain F 15–207（193 aa） Fragment：UNP residues 15-207 Chain G 15–207（193 aa） Fragment：UNP residues 15-207 Chain H 15–207（193 aa） Fragment：UNP residues 15-207 Chain I 15–207（193 aa） Fragment：UNP residues 15-207 Chain J 15–207（193 aa） Fragment：UNP residues 15-207 Chain K 15–207（193 aa） Fragment：UNP residues 15-207 Chain L 15–207（193 aa） Fragment：UNP residues 15-207 Chain M 15–207（193 aa） Fragment：UNP residues 15-207 Chain N 15–207（193 aa） Fragment：UNP residues 15-207	Mutation：A153C Mutation：A153C Mutation：A153C Mutation：A153C Mutation：A153C Mutation：A153C Mutation：A153C Mutation：A153C Mutation：A153C Mutation：A153C Mutation：A153C Mutation：A153C Mutation：A153C Mutation：A153C	CA CALCIUM ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；1 M 1,6-hexanediol, 0.1 M Sodium acetate pH 4.6, 10 mM CoCl2, 100 mM CaCl2, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.20 Å R-free 0.253
3HLN Crystal structure of ClpP A153C mutant with inter-heptamer disulfide bonds Deposited 2009-05-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 14 PDB declaration: tetradecameric	Chain 1 15–207（193 aa） Fragment：UNP residues 15-207 Chain 2 15–207（193 aa） Fragment：UNP residues 15-207 Chain O 15–207（193 aa） Fragment：UNP residues 15-207 Chain P 15–207（193 aa） Fragment：UNP residues 15-207 Chain Q 15–207（193 aa） Fragment：UNP residues 15-207 Chain R 15–207（193 aa） Fragment：UNP residues 15-207 Chain S 15–207（193 aa） Fragment：UNP residues 15-207 Chain T 15–207（193 aa） Fragment：UNP residues 15-207 Chain U 15–207（193 aa） Fragment：UNP residues 15-207 Chain V 15–207（193 aa） Fragment：UNP residues 15-207 Chain W 15–207（193 aa） Fragment：UNP residues 15-207 Chain X 15–207（193 aa） Fragment：UNP residues 15-207 Chain Y 15–207（193 aa） Fragment：UNP residues 15-207 Chain Z 15–207（193 aa） Fragment：UNP residues 15-207	Mutation：A153C Mutation：A153C Mutation：A153C Mutation：A153C Mutation：A153C Mutation：A153C Mutation：A153C Mutation：A153C Mutation：A153C Mutation：A153C Mutation：A153C Mutation：A153C Mutation：A153C Mutation：A153C	CA CALCIUM ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；1 M 1,6-hexanediol, 0.1 M Sodium acetate pH 4.6, 10 mM CoCl2, 100 mM CaCl2, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.20 Å R-free 0.253
3MT6 Structure of ClpP from Escherichia coli in complex with ADEP1 Deposited 2010-04-30	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 28 PDB declaration: 28-meric	Chain O 1–207（207 aa） Chain P 1–207（207 aa） Chain Q 1–207（207 aa） Chain R 1–207（207 aa） Chain S 1–207（207 aa） Chain T 1–207（207 aa） Chain U 1–207（207 aa） Chain V 1–207（207 aa） Chain W 1–207（207 aa） Chain X 1–207（207 aa） Chain Y 1–207（207 aa） Chain Z 1–207（207 aa） Chain a 1–207（207 aa） Chain b 1–207（207 aa）	Not recorded	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 27	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；295.15 K；25-35% (v/v) MPD and 0.1 M sodium acetate at pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 295.15K	Resolution 1.90 Å R-free 0.204
3MT6 Structure of ClpP from Escherichia coli in complex with ADEP1 Deposited 2010-04-30	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 28 PDB declaration: 28-meric	Chain A 1–207（207 aa） Chain B 1–207（207 aa） Chain C 1–207（207 aa） Chain D 1–207（207 aa） Chain E 1–207（207 aa） Chain F 1–207（207 aa） Chain G 1–207（207 aa） Chain H 1–207（207 aa） Chain I 1–207（207 aa） Chain J 1–207（207 aa） Chain K 1–207（207 aa） Chain L 1–207（207 aa） Chain M 1–207（207 aa） Chain N 1–207（207 aa）	Not recorded	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 28	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；295.15 K；25-35% (v/v) MPD and 0.1 M sodium acetate at pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 295.15K	Resolution 1.90 Å R-free 0.204
6NB1 Crystal structure of Escherichia coli ClpP protease complexed with small molecule activator, ACP1-06 Deposited 2018-12-06	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 14 PDB declaration: tetradecameric	Chain A 1–207（207 aa） Chain B 1–207（207 aa） Chain C 1–207（207 aa） Chain D 1–207（207 aa） Chain E 1–207（207 aa） Chain F 1–207（207 aa） Chain G 1–207（207 aa） Chain H 1–207（207 aa） Chain I 1–207（207 aa） Chain J 1–207（207 aa） Chain K 1–207（207 aa） Chain L 1–207（207 aa） Chain M 1–207（207 aa） Chain N 1–207（207 aa）	Not recorded	KHS N-{2-[(2-chlorophenyl)sulfanyl]ethyl}-2-methyl-2-{[5-(trifluoromethyl)pyridin-2-yl]sulfonyl}propanamide × 14 GOL GLYCEROL × 14	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；294 K；51-63% MPD 0.1 M sodium acetate pH 5.0	Resolution 1.90 Å R-free 0.244
6WR2 ClpP and ClpX IGF loop in ClpX-ClpP complex bound to ssrA tagged GFP Deposited 2020-04-29	Different construct Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric	Chain H 16–207（192 aa） Chain I 16–207（192 aa） Chain J 16–207（192 aa） Chain K 16–207（192 aa） Chain L 16–207（192 aa） Chain M 16–207（192 aa） Chain N 16–207（192 aa） Chain h 16–207（192 aa） Chain i 16–207（192 aa） Chain j 16–207（192 aa） Chain k 16–207（192 aa） Chain l 16–207（192 aa） Chain m 16–207（192 aa） Chain n 16–207（192 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.88 Å
6WRF ClpX-ClpP complex bound to GFP-ssrA, recognition complex Deposited 2020-04-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain H 16–207（192 aa） Chain I 16–207（192 aa） Chain J 16–207（192 aa） Chain K 16–207（192 aa） Chain L 16–207（192 aa） Chain M 16–207（192 aa） Chain N 16–207（192 aa）	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 5 MG MAGNESIUM ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.14 Å
6WSG ClpX-ClpP complex bound to ssrA-tagged GFP, intermediate complex Deposited 2020-04-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain H 16–207（192 aa） Fragment：UNP residues 16-207 Chain I 16–207（192 aa） Fragment：UNP residues 16-207 Chain J 16–207（192 aa） Fragment：UNP residues 16-207 Chain K 16–207（192 aa） Fragment：UNP residues 16-207 Chain L 16–207（192 aa） Fragment：UNP residues 16-207 Chain M 16–207（192 aa） Fragment：UNP residues 16-207 Chain N 16–207（192 aa） Fragment：UNP residues 16-207	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 5 MG MAGNESIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.16 Å
7MK5 Crystal structure of Escherichia coli ClpP covalently inhibited by clipibicyclene Deposited 2021-04-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 14 PDB declaration: tetradecameric	Chain A 15–207（193 aa） Chain B 15–207（193 aa） Chain C 15–207（193 aa） Chain D 15–207（193 aa） Chain E 15–207（193 aa） Chain F 15–207（193 aa） Chain G 15–207（193 aa） Chain H 15–207（193 aa） Chain I 15–207（193 aa） Chain J 15–207（193 aa） Chain K 15–207（193 aa） Chain L 15–207（193 aa） Chain M 15–207（193 aa） Chain N 15–207（193 aa）	Not recorded	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 25 ACT ACETATE ION × 6 ZGV 4-[(1E)-3-{[(2E,4E,6E,8S)-8-hydroxy-4-methyldeca-2,4,6-trienoyl]amino}-3-oxoprop-1-en-1-yl]azete-1(2H)-carboxylic acid × 14	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；0.1 M sodium acetate, 30% MPD	Resolution 2.95 Å R-free 0.248
7MK5 Crystal structure of Escherichia coli ClpP covalently inhibited by clipibicyclene Deposited 2021-04-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 14 PDB declaration: tetradecameric	Chain O 15–207（193 aa） Chain P 15–207（193 aa） Chain Q 15–207（193 aa） Chain R 15–207（193 aa） Chain S 15–207（193 aa） Chain T 15–207（193 aa） Chain U 15–207（193 aa） Chain V 15–207（193 aa） Chain W 15–207（193 aa） Chain X 15–207（193 aa） Chain Y 15–207（193 aa） Chain Z 15–207（193 aa） Chain a 15–207（193 aa） Chain b 15–207（193 aa）	Not recorded	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 25 ACT ACETATE ION × 4 ZGV 4-[(1E)-3-{[(2E,4E,6E,8S)-8-hydroxy-4-methyldeca-2,4,6-trienoyl]amino}-3-oxoprop-1-en-1-yl]azete-1(2H)-carboxylic acid × 14	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；0.1 M sodium acetate, 30% MPD	Resolution 2.95 Å R-free 0.248
8E7V Cryo-EM structure of substrate-free DNClpX.ClpP from singly capped particles Deposited 2022-08-24	Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric	Chain H 16–207（192 aa） Fragment：UNP residues 16-207 Chain I 16–207（192 aa） Fragment：UNP residues 16-207 Chain J 16–207（192 aa） Fragment：UNP residues 16-207 Chain K 16–207（192 aa） Fragment：UNP residues 16-207 Chain L 16–207（192 aa） Fragment：UNP residues 16-207 Chain M 16–207（192 aa） Fragment：UNP residues 16-207 Chain N 16–207（192 aa） Fragment：UNP residues 16-207 Chain h 16–207（192 aa） Fragment：UNP residues 16-207 Chain i 16–207（192 aa） Fragment：UNP residues 16-207 Chain j 16–207（192 aa） Fragment：UNP residues 16-207 Chain k 16–207（192 aa） Fragment：UNP residues 16-207 Chain l 16–207（192 aa） Fragment：UNP residues 16-207 Chain m 16–207（192 aa） Fragment：UNP residues 16-207 Chain n 16–207（192 aa） Fragment：UNP residues 16-207	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
8E91 Cryo-EM structure of substrate-free ClpX.ClpP Deposited 2022-08-26	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric	Chain H 16–207（192 aa） Fragment：UNP residues 16-207 Chain I 16–207（192 aa） Fragment：UNP residues 16-207 Chain J 16–207（192 aa） Fragment：UNP residues 16-207 Chain K 16–207（192 aa） Fragment：UNP residues 16-207 Chain L 16–207（192 aa） Fragment：UNP residues 16-207 Chain M 16–207（192 aa） Fragment：UNP residues 16-207 Chain N 16–207（192 aa） Fragment：UNP residues 16-207 Chain h 16–207（192 aa） Fragment：UNP residues 16-207 Chain i 16–207（192 aa） Fragment：UNP residues 16-207 Chain j 16–207（192 aa） Fragment：UNP residues 16-207 Chain k 16–207（192 aa） Fragment：UNP residues 16-207 Chain l 16–207（192 aa） Fragment：UNP residues 16-207 Chain m 16–207（192 aa） Fragment：UNP residues 16-207 Chain n 16–207（192 aa） Fragment：UNP residues 16-207	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 4 MG MAGNESIUM ION × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.57 Å
8ET3 Cryo-EM structure of a delivery complex containing the SspB adaptor, an ssrA-tagged substrate, and the AAA+ ClpXP protease Deposited 2022-10-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain H 16–207（192 aa） Fragment：UNP residues 16-207 Chain I 16–207（192 aa） Fragment：UNP residues 16-207 Chain J 16–207（192 aa） Fragment：UNP residues 16-207 Chain K 16–207（192 aa） Fragment：UNP residues 16-207 Chain L 16–207（192 aa） Fragment：UNP residues 16-207 Chain M 16–207（192 aa） Fragment：UNP residues 16-207 Chain N 16–207（192 aa） Fragment：UNP residues 16-207	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
8V9R Cryo-EM Structure of a Proteolytic ClpXP AAA+ Machine Poised to Unfold a Branched-Degron DHFR-ssrA Substrate Bound with MTX Deposited 2023-12-09	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 21 PDB declaration: 21-meric	Chain h 16–207（192 aa） Fragment：UNP residues 16-207 Chain i 16–207（192 aa） Fragment：UNP residues 16-207 Chain j 16–207（192 aa） Fragment：UNP residues 16-207 Chain k 16–207（192 aa） Fragment：UNP residues 16-207 Chain l 16–207（192 aa） Fragment：UNP residues 16-207 Chain m 16–207（192 aa） Fragment：UNP residues 16-207 Chain n 16–207（192 aa） Fragment：UNP residues 16-207 Chain p 16–207（192 aa） Fragment：UNP residues 16-207 Chain q 16–207（192 aa） Fragment：UNP residues 16-207 Chain r 16–207（192 aa） Fragment：UNP residues 16-207 Chain s 16–207（192 aa） Fragment：UNP residues 16-207 Chain t 16–207（192 aa） Fragment：UNP residues 16-207 Chain u 16–207（192 aa） Fragment：UNP residues 16-207 Chain v 16–207（192 aa） Fragment：UNP residues 16-207	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 3 MG MAGNESIUM ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 3 MTX METHOTREXATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
9C87 Cryo-EM Structure of a Proteolytic ClpXP AAA+ Machine Poised to Unfold a Linear-Degron DHFR-ssrA Substrate Bound with MTX Deposited 2024-06-12	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 21 PDB declaration: 21-meric	Chain h 16–207（192 aa） Fragment：UNP residues 16-207 Chain i 16–207（192 aa） Fragment：UNP residues 16-207 Chain j 16–207（192 aa） Fragment：UNP residues 16-207 Chain k 16–207（192 aa） Fragment：UNP residues 16-207 Chain l 16–207（192 aa） Fragment：UNP residues 16-207 Chain m 16–207（192 aa） Fragment：UNP residues 16-207 Chain n 16–207（192 aa） Fragment：UNP residues 16-207 Chain p 16–207（192 aa） Fragment：UNP residues 16-207 Chain q 16–207（192 aa） Fragment：UNP residues 16-207 Chain r 16–207（192 aa） Fragment：UNP residues 16-207 Chain s 16–207（192 aa） Fragment：UNP residues 16-207 Chain t 16–207（192 aa） Fragment：UNP residues 16-207 Chain u 16–207（192 aa） Fragment：UNP residues 16-207 Chain v 16–207（192 aa） Fragment：UNP residues 16-207	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 3 MG MAGNESIUM ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 3 MTX METHOTREXATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
9C88 Cryo-EM Structure of a Proteolytic ClpXP AAA+ Machine Translocating a Portion of a Branched-Degron DHFR Substrate Deposited 2024-06-12	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 21 PDB declaration: 21-meric	Chain h 16–207（192 aa） Fragment：UNP residues 16-207 Chain i 16–207（192 aa） Fragment：UNP residues 16-207 Chain j 16–207（192 aa） Fragment：UNP residues 16-207 Chain k 16–207（192 aa） Fragment：UNP residues 16-207 Chain l 16–207（192 aa） Fragment：UNP residues 16-207 Chain m 16–207（192 aa） Fragment：UNP residues 16-207 Chain n 16–207（192 aa） Fragment：UNP residues 16-207 Chain p 16–207（192 aa） Fragment：UNP residues 16-207 Chain q 16–207（192 aa） Fragment：UNP residues 16-207 Chain r 16–207（192 aa） Fragment：UNP residues 16-207 Chain s 16–207（192 aa） Fragment：UNP residues 16-207 Chain t 16–207（192 aa） Fragment：UNP residues 16-207 Chain u 16–207（192 aa） Fragment：UNP residues 16-207 Chain v 16–207（192 aa） Fragment：UNP residues 16-207	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 3 MG MAGNESIUM ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.60 Å
9PIO Cryo-EM structure of the ClpXP AAA+ protease bound to lambdaO-tagged Arc in a recognition complex Deposited 2025-07-10	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 21 PDB declaration: 21-meric	Chain H 16–207（192 aa） Fragment：UNP residues 16-207 Chain I 16–207（192 aa） Fragment：UNP residues 16-207 Chain J 16–207（192 aa） Fragment：UNP residues 16-207 Chain K 16–207（192 aa） Fragment：UNP residues 16-207 Chain L 16–207（192 aa） Fragment：UNP residues 16-207 Chain M 16–207（192 aa） Fragment：UNP residues 16-207 Chain N 16–207（192 aa） Fragment：UNP residues 16-207 Chain O 16–207（192 aa） Fragment：UNP residues 16-207 Chain P 16–207（192 aa） Fragment：UNP residues 16-207 Chain Q 16–207（192 aa） Fragment：UNP residues 16-207 Chain R 16–207（192 aa） Fragment：UNP residues 16-207 Chain S 16–207（192 aa） Fragment：UNP residues 16-207 Chain T 16–207（192 aa） Fragment：UNP residues 16-207 Chain U 16–207（192 aa） Fragment：UNP residues 16-207	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 5 MG MAGNESIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.61 Å
9PJD Cryo-EM structure of the ClpXP AAA+ protease bound to an unidentified portion of lambdaO-tagged Arc substrate within a translocation complex Deposited 2025-07-13	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 20 PDB declaration: 21-meric	Chain H 16–207（192 aa） Fragment：UNP residues 16-207 Chain I 16–207（192 aa） Fragment：UNP residues 16-207 Chain J 16–207（192 aa） Fragment：UNP residues 16-207 Chain K 16–207（192 aa） Fragment：UNP residues 16-207 Chain L 16–207（192 aa） Fragment：UNP residues 16-207 Chain M 16–207（192 aa） Fragment：UNP residues 16-207 Chain N 16–207（192 aa） Fragment：UNP residues 16-207 Chain O 16–207（192 aa） Fragment：UNP residues 16-207 Chain P 16–207（192 aa） Fragment：UNP residues 16-207 Chain Q 16–207（192 aa） Fragment：UNP residues 16-207 Chain R 16–207（192 aa） Fragment：UNP residues 16-207 Chain S 16–207（192 aa） Fragment：UNP residues 16-207 Chain T 16–207（192 aa） Fragment：UNP residues 16-207 Chain U 16–207（192 aa） Fragment：UNP residues 16-207	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 6 MG MAGNESIUM ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.67 Å

18 other PDB entries and 21 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CLPP_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain H； PDBConstruct 1–192； UniProt 16–207 Author chain I； PDBConstruct 1–192； UniProt 16–207 Author chain J； PDBConstruct 1–192； UniProt 16–207 Author chain K； PDBConstruct 1–192； UniProt 16–207 Author chain L； PDBConstruct 1–192； UniProt 16–207 Author chain M； PDBConstruct 1–192； UniProt 16–207 Author chain N； PDBConstruct 1–192； UniProt 16–207 Author chain h； PDBConstruct 1–192； UniProt 16–207 Author chain i； PDBConstruct 1–192； UniProt 16–207 Author chain j； PDBConstruct 1–192； UniProt 16–207 Author chain k； PDBConstruct 1–192； UniProt 16–207 Author chain l； PDBConstruct 1–192； UniProt 16–207 Author chain m； PDBConstruct 1–192； UniProt 16–207 Author chain n； PDBConstruct 1–192； UniProt 16–207

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	8e8q
Deposition date deposition_date	2022-08-25
最后修订 last_revision	2023-11-08
Structure title title	Cryo-EM structure of substrate-free DNClpX.ClpP
Keywords keywords	AAA+ protease, ClpXP, CHAPERONE; CHAPERONE
Experimental Method method	ELECTRON MICROSCOPY

▼

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

Radius of gyration Rg (Guinier) rg_guinier	58.22 Å
Radius of gyration Rg (electron density) rg_electron	57.88 Å
Forward intensity I(0) i0	3985270000.00
Molecular weight molecular_weight	531160.0 kDa
Excluded volume excluded_volume	665810 Å³
Envelope volume envelope_volume	986020 Å³
Hydration-shell volume shell_volume	139990 Å³
Envelope diameter envelope_diameter	185.4 Å
Shell Rg shell_rg	62.28 Å
Envelope Rg envelope_rg	55.62 Å
Shape Rg shape_rg	57.92 Å
Total Rg total_rg	57.88 Å
Total atoms total_atoms	74879
Residues n_residues	4782
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

▼

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

Maximum dimension Dmax dmax	190.6 Å
Rg (real space) rg_real	58.09 Å
Rg uncertainty (real space) rg_real_error	1.80 Å
I(0) (real space) i0_real	3.9850e+09
I(0) uncertainty (real space) i0_real_error	7.6780e+07
Rg (reciprocal space) rg_reciprocal	58.31 Å
I(0) (reciprocal space) i0_reciprocal	3987000000.0000
Solution quality estimate total_estimate	0.8585
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	70.6 Å
Skewness Skewness skewness	0.264
Kurtosis Kurtosis kurtosis	-0.523
Angular range angular_range	— – 0.1350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	381200000.0000
Real-space data points n_real_points	28
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.786; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.810

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	ATP-dependent Clp protease ATP-binding subunit ClpX
Molecular weight formula_weight	42355.8 kDa
Mutation mutation	C169S, K408E
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	74891

MGSSHHHHHHDYDIPTTENLYFQGSSALPTPHEIRNHLDDYVIGQEQAKKVLAVAVYNHYKRLRNGDTSNGVELGKSNILLIGPTGSGKTLLAETLARLLDVPFTMADATTLTEAGYVGEDVENIIQKLLQKSDYDVQKAQRGIVYIDEIDKISRKSDNPSITRDVSGEGVQQALLKLIEGTVAAVPPQGGRKHPQQEFLQVDTSKILFICGGAFAGLDKVISHRVETGSGIGFGATVKAKSDKASEGELLAQVEPEDLIKFGLIPEFIGRLPVVATLNELSEEALIQILKEPKNALTKQYQALFNLEGVDLEFRDEALDAIAKKAMARKTGARGLRSIVEAALLDTMYDLPSMEDVEKVVIDESVIDGQSEPLLIYGKPEAQQASGE

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	ATP-dependent Clp protease proteolytic subunit
Molecular weight formula_weight	23468.9 kDa
EC 编号 ec_number	3.4.21.92
Source method src_method	man
Copy count entity_count	14

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H,I,J,K,L,M,N,h,i,j,k,l,m,n

LVPMVIEQTSRGERSFDIYSRLLKERVIFLTGQVEDHMANLIVAQMLFLEAENPEKDIYLYINSPGGVITAGMSIYDTMQFIKPDVSTICMGQAASMGAFLLTAGAKGKRFCLPNSRVMIHQPLGGYQGQATDIEIHAREILKVKGRMNELMALHTGQSLEQIERDTERDRFLSAPEAVEYGLVDSILTHRNENLYFQSLEHHHHHH

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	2

▶

8. Citations (1)

▶

Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

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

Resolution resolution	3.12 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	171869

fit	/app/data/saxs_computation/e8/8e8q/8e8q.fit
pddf	/app/data/pr_computation/e8/8e8q/8e8q.pr.out
profile	/app/data/saxs_computation/e8/8e8q/8e8q.dat

Cryo-EM structure of substrate-free DNClpX.ClpP

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

ATP-dependent Clp protease ATP-binding subunit ClpX

State in the Current Structure

Other States of the Same Protein in the Database

ATP-dependent Clp protease proteolytic subunit

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)