8K8V | pdb_00008k8v

CryoEM structure of LonC protease hepatmer, apo state

PDB DOI: https://doi.org/10.2210/pdb8K8V/pdb
EM Map EMD-36965: EMDB EMDataResource

Classification: CHAPERONE
Organism(s): Meiothermus taiwanensis
Expression System: Escherichia coli
Mutation(s): No

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: 2.75 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 8K8V

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: 564.57 kDa
Atom Count: 39,067
Modeled Residue Count: 5,033
Deposited Residue Count: 5,124
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
endopeptidase La	A B [auth G] C [auth F] D [auth E] E [auth D] A, B [auth G], C [auth F], D [auth E], E [auth D], F [auth B], G [auth C]	732	Meiothermus taiwanensis	Mutation(s): 0 Gene Names: lon_2, Mcate_02721 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
PO4 (Subject of Investigation/LOI) Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain N [auth C] SDF format, chain M [auth B] SDF format, chain L [auth D] SDF format, chain K [auth E] SDF format, chain J [auth F] SDF format, chain I [auth G] SDF format, chain H [auth A] MOL2 format, chain N [auth C] MOL2 format, chain M [auth B] MOL2 format, chain L [auth D] MOL2 format, chain K [auth E] MOL2 format, chain J [auth F] MOL2 format, chain I [auth G] MOL2 format, chain H [auth A] mmCIF format, chain N [auth C] mmCIF format, chain M [auth B] mmCIF format, chain L [auth D] mmCIF format, chain K [auth E] mmCIF format, chain J [auth F] mmCIF format, chain I [auth G] mmCIF format, chain H [auth A]	H [auth A] I [auth G] J [auth F] K [auth E] L [auth D] H [auth A], I [auth G], J [auth F], K [auth E], L [auth D], M [auth B], N [auth C]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain H [auth A] Focus chain I [auth G] Focus chain J [auth F] Focus chain K [auth E] Focus chain L [auth D] Focus chain M [auth B] Focus chain N [auth C] Interactions & Density Focus chain H [auth A] Focus chain I [auth G] Focus chain J [auth F] Focus chain K [auth E] Focus chain L [auth D] Focus chain M [auth B] Focus chain N [auth C]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.75 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC	4.2

Structure Validation

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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: 2025-07-02
Changes: Data collection, Database references, Structure summary

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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.