8E7V | pdb_00008e7v

Cryo-EM structure of substrate-free DNClpX.ClpP from singly capped particles

PDB DOI: https://doi.org/10.2210/pdb8E7V/pdb
EM Map EMD-27941: EMDB EMDataResource

Classification: CHAPERONE
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2022-08-24 Released: 2023-11-08
Deposition Author(s): Ghanbarpour, A., Cohen, S., Davis, J.H., Sauer, R.T.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Cryo-EM structure of substrate-free DNClpX.ClpP

Ghanbarpour, A., Cohen, S., Davis, J.H., Sauer, R.T.

(2023) Nat Commun

Macromolecule Content

Total Structure Weight: 585.66 kDa
Atom Count: 37,246
Modeled Residue Count: 4,779
Deposited Residue Count: 5,226
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent Clp protease ATP-binding subunit ClpX	A, B, C, D, E A, B, C, D, E, F	388	Escherichia coli	Mutation(s): 2 Gene Names: clpX, lopC, b0438, JW0428
UniProt
Find proteins for P0A6H1 (Escherichia coli (strain K12)) Explore P0A6H1 Go to UniProtKB: P0A6H1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A6H1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent Clp protease proteolytic subunit	G [auth H] H [auth I] I [auth J] J [auth K] K [auth L] G [auth H], H [auth I], I [auth J], J [auth K], K [auth L], L [auth M], M [auth N], N [auth h], O [auth i], P [auth j], Q [auth k], R [auth l], S [auth m], T [auth n]	207	Escherichia coli	Mutation(s): 0 Gene Names: clpP, lopP, b0437, JW0427 EC: 3.4.21.92
UniProt
Find proteins for P0A6G7 (Escherichia coli (strain K12)) Explore P0A6G7 Go to UniProtKB: P0A6G7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A6G7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP (Subject of Investigation/LOI) Query on ATP Download:Ideal Coordinates CCD File SDF format, chain U [auth A] SDF format, chain V [auth B] SDF format, chain X [auth C] SDF format, chain Z [auth D] MOL2 format, chain U [auth A] MOL2 format, chain V [auth B] MOL2 format, chain X [auth C] MOL2 format, chain Z [auth D] mmCIF format, chain U [auth A] mmCIF format, chain V [auth B] mmCIF format, chain X [auth C] mmCIF format, chain Z [auth D]	U [auth A], V [auth B], X [auth C], Z [auth D]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain U [auth A] Focus chain V [auth B] Focus chain X [auth C] Focus chain Z [auth D] Interactions & Density Focus chain U [auth A] Focus chain V [auth B] Focus chain X [auth C] Focus chain Z [auth D]
ADP (Subject of Investigation/LOI) Query on ADP Download:Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain CA [auth F] MOL2 format, chain BA [auth E] MOL2 format, chain CA [auth F] mmCIF format, chain BA [auth E] mmCIF format, chain CA [auth F]	BA [auth E], CA [auth F]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain BA [auth E] Focus chain CA [auth F] Interactions & Density Focus chain BA [auth E] Focus chain CA [auth F]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain W [auth B] SDF format, chain Y [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain W [auth B] MOL2 format, chain Y [auth C] mmCIF format, chain AA [auth D] mmCIF format, chain W [auth B] mmCIF format, chain Y [auth C]	AA [auth D], W [auth B], Y [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain W [auth B] Focus chain Y [auth C] Interactions & Density Focus chain AA [auth D] Focus chain W [auth B] Focus chain Y [auth C]