8K93 | pdb_00008k93

CryoEM structure of LonC protease S582A open hexamer with lysozyme

PDB DOI: https://doi.org/10.2210/pdb8K93/pdb
EM Map EMD-36973: EMDB EMDataResource

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

Deposited: 2023-07-31 Released: 2024-08-07
Deposition Author(s): Li, M., Hsieh, K., Liu, H., Zhang, S., Gao, Y., Gong, Q., Zhang, K., Chang, C., Li, S.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.23 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 8K93

This is version 1.1 of the entry. See complete history.

Literature

Bifurcated assembly pathway and dual function of a Lon-like protease revealed by cryo-EM Analysis

Li, M., Liu, H., Hsieh, K.Y., Zhang, S., Gao, Y., Gong, Q., Zhang, K., Chang, C.I., Li, S.

(2024) Fundam Res

DOI: https://doi.org/10.1016/j.fmre.2024.02.020

Macromolecule Content

Total Structure Weight: 483.71 kDa
Atom Count: 33,470
Modeled Residue Count: 4,314
Deposited Residue Count: 4,392
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endopeptidase La	A, B, C, D, E A, B, C, D, E, F	732	Meiothermus taiwanensis	Mutation(s): 1 EC: 3.4.21.53
UniProt
Find proteins for C9DRU9 (Meiothermus taiwanensis) Explore C9DRU9 Go to UniProtKB: C9DRU9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C9DRU9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TS6 Query on TS6 Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain H [auth C] SDF format, chain I [auth D] SDF format, chain J [auth E] MOL2 format, chain G [auth B] MOL2 format, chain H [auth C] MOL2 format, chain I [auth D] MOL2 format, chain J [auth E] mmCIF format, chain G [auth B] mmCIF format, chain H [auth C] mmCIF format, chain I [auth D] mmCIF format, chain J [auth E]	G [auth B], H [auth C], I [auth D], J [auth E]	Monothiophosphate H₃ O₃ P S RYYWUUFWQRZTIU-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Focus chain H [auth C] Focus chain I [auth D] Focus chain J [auth E] Interactions & Density Focus chain G [auth B] Focus chain H [auth C] Focus chain I [auth D] Focus chain J [auth E]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.23 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC	3.2

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-08-07

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government	China	--

Revision History (Full details and data files)

Version 1.0: 2024-08-07
Type: Initial release
Version 1.1: 2025-06-18
Changes: Data collection, Database references, Structure summary

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.