SAXSdb — 9pjd

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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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 20 RNA 1	unidentified portion of the substrate × 1 ATP-dependent Clp protease proteolytic subunit × 14 （P0A6G7） PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 6 MAGNESIUM ION × 5	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	C3TLS7_ECOLX
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–424； UniProt 1–424 Author chain B； PDBConstruct 1–424； UniProt 1–424 Author chain C； PDBConstruct 1–424； UniProt 1–424 Author chain D； PDBConstruct 1–424； UniProt 1–424 Author chain E； PDBConstruct 1–424； UniProt 1–424 Author chain F； PDBConstruct 1–424； UniProt 1–424

ATP-dependent Clp protease proteolytic subunit

Escherichia coli

UniProt P0A6G7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 20 RNA 1	ATP-dependent Clp protease ATP-binding subunit ClpX × 6 （C3TLS7） unidentified portion of the substrate × 1 PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 6 MAGNESIUM ION × 5	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CLPP_ECOLI
Isoform	—
PDB entities	3
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 O； PDBConstruct 1–192； UniProt 16–207 Author chain P； PDBConstruct 1–192； UniProt 16–207 Author chain Q； PDBConstruct 1–192； UniProt 16–207 Author chain R； PDBConstruct 1–192； UniProt 16–207 Author chain S； PDBConstruct 1–192； UniProt 16–207 Author chain T； PDBConstruct 1–192； UniProt 16–207 Author chain U； 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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9pjd
Deposition date deposition_date	2025-07-13
Structure title title	Cryo-EM structure of the ClpXP AAA+ protease bound to an unidentified portion of lambdaO-tagged Arc substrate within a translocation complex
Keywords keywords	AAA+ protease, ClpXP, substrate-bound, CHAPERONE; CHAPERONE
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.

9pjd__assembly_1__model_1

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

Download this curve (.dat)

9pjd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9pjd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	58.16 Å
Rg (electron density)	57.82 Å
Total Rg	57.83 Å
Atom count	74278
Residues	4749
Excluded volume	660990 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9pjd__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 (5)

Entity 1 Entity 1 polymer

Description description	ATP-dependent Clp protease ATP-binding subunit ClpX
Molecular weight formula_weight	46414.8 kDa
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	74278

MTDKRKDGSGKLLYCSFCGKSQHEVRKLIAGPSVYICDECVDLCNDIIREEIKEVAPHRERSALPTPHEIRNHLDDYVIGQEQAKKVLAVAVYNHYKRLRNGDTSNGVELGKSNILLIGPTGSGKTLLAETLARLLDVPFTMADATTLTEAGYVGEDVENIIQKLLQKCDYDVQKAQRGIVYIDEIDKISRKSDNPSITRDVSGEGVQQALLKLIEGTVAAVPPQGGRKHPQQEFLQVDTSKILFICGGAFAGLDKVISHRVETGSGIGFGATVKAKSDKASEGELLAQVEPEDLIKFGLIPEFIGRLPVVATLNELSEEALIQILKEPKNALTKQYQALFNLEGVDLEFRDEALDAIAKKAMARKTGARGLRSIVEAALLDTMYDLPSMEDVEKVVIDESVIDGQSEPLLIYGKPEAQQASGE

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	unidentified portion of the substrate
Molecular weight formula_weight	465.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	G

XXXXXX

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 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,O,P,Q,R,S,T,U

LVPMVIEQTSRGERSFDIYSRLLKERVIFLTGQVEDHMANLIVAQMLFLEAENPEKDIYLYINSPGGVITAGMSIYDTMQFIKPDVSTICMGQAASMGAFLLTAGAKGKRFCLPNSRVMIHQPLGGYQGQATDIEIHAREILKVKGRMNELMALHTGQSLEQIERDTERDRFLSAPEAVEYGLVDSILTHRNENLYFQSLEHHHHHH

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 4 Entity 4 non-polymer

Description description	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
Molecular weight formula_weight	523.2 kDa
Source method src_method	syn
Copy count entity_count	6

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	5

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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	2.670 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	2.67 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	325578

Cryo-EM structure of the ClpXP AAA+ protease bound to an unidentified portion of lambdaO-tagged Arc substrate within a translocation complex

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9pjd__assembly_1__model_1

9pjd__assembly_1__model_1 | I(q)

9pjd__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (5)

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 non-polymer

Entity 5 Entity 5 non-polymer

7. Citations (1)

Cryo-EM structure of the ClpXP AAA+ protease bound to an unidentified portion of lambdaO-tagged Arc substrate within a translocation complex

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

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

ATP-dependent Clp protease proteolytic subunit

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

9pjd__assembly_1__model_1

9pjd__assembly_1__model_1 | I(q)

9pjd__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (5)

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 non-polymer

Entity 5 Entity 5 non-polymer

7. Citations (1)