8yd1

CryoEM structure of M. tuberculosis ClpC1P1P2 complex bound to bortezomib, conformation 1

Method: ELECTRON MICROSCOPY

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

ATP-dependent Clp protease ATP-binding subunit ClpC1

Mycobacterium tuberculosis H37Rv

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 21	ATP-dependent Clp protease proteolytic subunit 2 × 7 （P9WPC3） ATP-dependent Clp protease proteolytic subunit 1 × 7 （P9WPC5） Beta-casein × 1 （P02666） MAGNESIUM ION × 7 ADENOSINE-5'-TRIPHOSPHATE × 7 ADENOSINE-5'-DIPHOSPHATE × 3 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

View Construct and Data Evidence

UniProt name	CLPC1_MYCTU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–657； UniProt 168–824 Author chain B； PDBConstruct 1–657； UniProt 168–824 Author chain C； PDBConstruct 1–657； UniProt 168–824 Author chain D； PDBConstruct 1–657； UniProt 168–824 Author chain E； PDBConstruct 1–657； UniProt 168–824 Author chain F； PDBConstruct 1–657； UniProt 168–824

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 21	ATP-dependent Clp protease ATP-binding subunit ClpC1 × 6 （P9WPC9） ATP-dependent Clp protease proteolytic subunit 1 × 7 （P9WPC5） Beta-casein × 1 （P02666） MAGNESIUM ION × 7 ADENOSINE-5'-TRIPHOSPHATE × 7 ADENOSINE-5'-DIPHOSPHATE × 3 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

View Construct and Data Evidence

UniProt name	CLPP2_MYCTU
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain G； PDBConstruct 1–181； UniProt 30–210 Author chain H； PDBConstruct 1–181； UniProt 30–210 Author chain I； PDBConstruct 1–181； UniProt 30–210 Author chain J； PDBConstruct 1–181； UniProt 30–210 Author chain K； PDBConstruct 1–181； UniProt 30–210 Author chain L； PDBConstruct 1–181； UniProt 30–210 Author chain M； PDBConstruct 1–181； UniProt 30–210

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 21	ATP-dependent Clp protease ATP-binding subunit ClpC1 × 6 （P9WPC9） ATP-dependent Clp protease proteolytic subunit 2 × 7 （P9WPC3） Beta-casein × 1 （P02666） MAGNESIUM ION × 7 ADENOSINE-5'-TRIPHOSPHATE × 7 ADENOSINE-5'-DIPHOSPHATE × 3 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

View Construct and Data Evidence

UniProt name	CLPP1_MYCTU
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain N； PDBConstruct 1–178； UniProt 15–192 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

Beta-casein

OrganismNot specified

UniProt P02666

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 21	ATP-dependent Clp protease ATP-binding subunit ClpC1 × 6 （P9WPC9） ATP-dependent Clp protease proteolytic subunit 2 × 7 （P9WPC3） ATP-dependent Clp protease proteolytic subunit 1 × 7 （P9WPC5） MAGNESIUM ION × 7 ADENOSINE-5'-TRIPHOSPHATE × 7 ADENOSINE-5'-DIPHOSPHATE × 3 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

View Construct and Data Evidence

UniProt name	CASB_BOVIN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain a； PDBConstruct 1–24； UniProt 1–24

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_id	8yd1
Deposition date deposition_date	2024-02-19
Structure title title	CryoEM structure of M. tuberculosis ClpC1P1P2 complex bound to bortezomib, conformation 1
Keywords keywords	Mycobacterium tuberculosis, Caseinolytic protease system, Activation, HYDROLASE; HYDROLASE
Experimental Method method	ELECTRON 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.

8yd1__assembly_1__model_1

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

Download this curve (.dat)

8yd1__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8yd1__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	61.29 Å
Rg (electron density)	61.12 Å
Total Rg	61.26 Å
Atom count	43488
Residues	5512
Excluded volume	774980 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8yd1__assembly_1__model_1`	21-meric （21）	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 (8)

Entity 1 Entity 1 polymer

Description description	ATP-dependent Clp protease ATP-binding subunit ClpC1
Molecular weight formula_weight	73270.3 kDa
Mutation mutation	E288A, F444S, E626A
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	43488

SLVLDQFGRNLTAAAMEGKLDPVIGREKEIERVMQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQAIVHGEVPETLKDKQLYTLDLGSLVAGSRYRGDFEERLKKVLKEINTRGDIILFIDALHTLVGAGAAEGAIDAASILKPKLARGELQTIGATTLDEYRKYIEKDAALERRFQPVQVGEPTVEHTIEILKGLRDRYEAHHRVSITDAAMVAAATLADRYINDRFLPDKAIDLIDEAGARMRIRRMTAPPDLREFDEKIAEARREKESAIDAQDSEKAASLRDREKTLVAQRAEREKQWRSGDLDVVAEVDDEQIAEVLGNWTGIPVFKLTEAETTRLLRMEEELHKRIIGQEDAVKAVSKAIRRTRAGLKDPKRPSGSFIFAGPSGVGKTELSKALANFLFGDDDALIQIDMGEFHDRFTASRLFGAPPGYVGYEEGGQLTEKVRRKPFSVVLFDAIEKAHQEIYNSLLQVLEDGRLTDGQGRTVDFKNTVLIFTSNLGTSDISKPVGLGFSKGGGENDYERMKQKVNDELKKHFRPEFLNRIDDIIVFHQLTREEIIRMVDLMISRVAGQLKSKDMALVLTDAAKALLAKRGFDPVLGARPLRRTIQREIEDQLSEKILFEEVGPGQVVTVDVDNWDGEGPGEDAVFTFTGTR

Source Source

Source organism organism	Mycobacterium tuberculosis H37Rv
NCBI taxonomy ID ncbi_taxonomy_id	83332
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	ATP-dependent Clp protease proteolytic subunit 2
Molecular weight formula_weight	19869.7 kDa
EC 编号 ec_number	3.4.21.92
Source method src_method	man
Copy count entity_count	7

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,H,I,J,K,L,M

SNPYNKLFEERIIFLGVQVDDASANDIMAQLLVLESLDPDRDITMYINSPGGGFTSLMAIYDTMQYVRADIQTVCLGQAASAAAVLLAAGTPGKRMALPNARVLIHQPSLSGVIQGQFSDLEIQAAEIERMRTLMETTLARHTGKDAGVIRKDTDRDKILTAEEAKDYGIIDTVLEYRKLS

Source Source

Source organism organism	Mycobacterium tuberculosis H37Rv
NCBI taxonomy ID ncbi_taxonomy_id	83332
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	ATP-dependent Clp protease proteolytic subunit 1
Molecular weight formula_weight	19383.1 kDa
EC 编号 ec_number	3.4.21.92
Source method src_method	man
Copy count entity_count	7

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	N,O,P,Q,R,S,T

SLTDSVYERLLSERIIFLGSEVNDEIANRLCAQILLLAAEDASKDISLYINSPGGSISAGMAIYDTMVLAPCDIATYAMGMAASMGEFLLAAGTKGKRYALPHARILMHQPLGGVTGSAADIAIQAEQFAVIKKEMFRLNAEFTGQPIERIEADSDRDRWFTAAEALEYGFVDHIITR

Source Source

Source organism organism	Mycobacterium tuberculosis H37Rv
NCBI taxonomy ID ncbi_taxonomy_id	83332
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 4 Entity 4 polymer

Description description	Beta-casein
Molecular weight formula_weight	2624.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	a

MKVLILACLVALALARELEELNVP

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 6 Entity 6 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 7 Entity 7 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 8 Entity 8 non-polymer

Description description	N-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE
Molecular weight formula_weight	384.2 kDa
Source method src_method	syn
Copy count entity_count	14

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Resolution resolution	2.81 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	95184

CryoEM structure of M. tuberculosis ClpC1P1P2 complex bound to bortezomib, conformation 1

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

ATP-dependent Clp protease ATP-binding subunit ClpC1

State in the Current Structure

Other States of the Same Protein in the Database

ATP-dependent Clp protease proteolytic subunit 2

State in the Current Structure

Other States of the Same Protein in the Database

ATP-dependent Clp protease proteolytic subunit 1

State in the Current Structure

Other States of the Same Protein in the Database

Beta-casein

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8yd1__assembly_1__model_1

8yd1__assembly_1__model_1 | I(q)

8yd1__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

7. Citations (1)

CryoEM structure of M. tuberculosis ClpC1P1P2 complex bound to bortezomib, conformation 1

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

ATP-dependent Clp protease ATP-binding subunit ClpC1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

ATP-dependent Clp protease proteolytic subunit 2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

ATP-dependent Clp protease proteolytic subunit 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Beta-casein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8yd1__assembly_1__model_1

8yd1__assembly_1__model_1 | I(q)

8yd1__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

7. Citations (1)