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8yd0

CryoEM structure of M. tuberculosis ClpXP1P2 complex bound to bortezomib

Method: ELECTRON MICROSCOPY
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1. Protein Identity and Related Structures Protein Identity & Related Structures

ATP-dependent Clp protease ATP-binding subunit ClpX

Mycobacterium tuberculosis H37Rv

UniProt P9WPB9

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 20 ATP-dependent Clp protease proteolytic subunit 2 × 7 （P9WPC3） ATP-dependent Clp protease proteolytic subunit 1 × 7 （P9WPC5） MAGNESIUM ION × 2 ADENOSINE-5'-TRIPHOSPHATE × 4 ADENOSINE-5'-DIPHOSPHATE × 2 N-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE × 14 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
8yd0

1 assemblies

View Construct and Data Evidence
UniProt name CLPX_MYCTU
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–355； UniProt 60–414 Author chain B； PDBConstruct 1–355； UniProt 60–414 Author chain C； PDBConstruct 1–355； UniProt 60–414 Author chain D； PDBConstruct 1–355； UniProt 60–414 Author chain E； PDBConstruct 1–355； UniProt 60–414 Author chain F； PDBConstruct 1–355； UniProt 60–414

ATP-dependent Clp protease proteolytic subunit 2

Mycobacterium tuberculosis H37Rv

UniProt P9WPC3

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 20 ATP-dependent Clp protease ATP-binding subunit ClpX × 6 （P9WPB9） ATP-dependent Clp protease proteolytic subunit 1 × 7 （P9WPC5） MAGNESIUM ION × 2 ADENOSINE-5'-TRIPHOSPHATE × 4 ADENOSINE-5'-DIPHOSPHATE × 2 N-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE × 14 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
4u0g 4u0g 6vgk 8ycx 8yd0 8yd1 8yd2 8yd4 9if4 9jvp 9jvz 9p53

13 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name CLPP2_MYCTU
Isoform —
PDB entities 2
Chains and sequence ranges Author chain H； PDBConstruct 1–196； UniProt 15–210 Author chain I； PDBConstruct 1–196； UniProt 15–210 Author chain K； PDBConstruct 1–196； UniProt 15–210 Author chain L； PDBConstruct 1–196； UniProt 15–210 Author chain M； PDBConstruct 1–196； UniProt 15–210 Author chain N； PDBConstruct 1–196； UniProt 15–210 Author chain V； PDBConstruct 1–196； UniProt 15–210

ATP-dependent Clp protease proteolytic subunit 1

Mycobacterium tuberculosis H37Rv

UniProt P9WPC5

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 20 ATP-dependent Clp protease ATP-binding subunit ClpX × 6 （P9WPB9） ATP-dependent Clp protease proteolytic subunit 2 × 7 （P9WPC3） MAGNESIUM ION × 2 ADENOSINE-5'-TRIPHOSPHATE × 4 ADENOSINE-5'-DIPHOSPHATE × 2 N-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE × 14 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers
4u0h

1 assemblies

Heteromeric or nucleic-acid complex
4u0g 4u0g 6vgk 6vgn 6vgq 8ycx 8yd0 8yd1 8yd2 8yd4 9if4 9jvp

15 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name CLPP1_MYCTU
Isoform —
PDB entities 3
Chains and sequence ranges Author chain O； PDBConstruct 1–178； UniProt 15–192 Author chain P； PDBConstruct 1–178； UniProt 15–192 Author chain Q； PDBConstruct 1–178； UniProt 15–192 Author chain R； PDBConstruct 1–178； UniProt 15–192 Author chain S； PDBConstruct 1–178； UniProt 15–192 Author chain T； PDBConstruct 1–178； UniProt 15–192 Author chain U； PDBConstruct 1–178； UniProt 15–192

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id8yd0
Deposition date deposition_date2024-02-18
Structure title titleCryoEM structure of M. tuberculosis ClpXP1P2 complex bound to bortezomib
Keywords keywordsMycobacterium tuberculosis, Caseinolytic protease system, Activation, HYDROLASE; HYDROLASE
Experimental Method methodELECTRON MICROSCOPY
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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

8yd0__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

8yd0__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 109 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

8yd0__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）54.50 Å
Rg (electron density)54.13 Å
Total Rg54.29 Å
Atom count36147
Residues4631
Excluded volume647400 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 8yd0__assembly_1__model_1 20-meric （20） Success 4.1.3-1-20251215 (887e7ef) View Download
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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (7)

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7. Citations (1)