9UKV | pdb_00009ukv

JM Complex - E. coli MurJ, Levivirus M lysis protein LysM (SglM)

PDB DOI: https://doi.org/10.2210/pdb9UKV/pdb
EM Map EMD-64256: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Escherichia coli, Enterobacteria phage M
Expression System: Escherichia coli
Mutation(s): No
Membrane Protein: Yes MemProtMD

Deposited: 2025-04-18 Released: 2025-09-10
Deposition Author(s): Kohga, H., Lertpreedakorn, N., Tsukazaki, T.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.05 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

JM Complex - E. coli MurJ, Levivirus M lysis protein LysM (SglM)

Kohga, H., Lertpreedakorn, N., Tsukazaki, T.

To be published.

Macromolecule Content

Total Structure Weight: 63.64 kDa
Atom Count: 4,188
Modeled Residue Count: 548
Deposited Residue Count: 581
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipid II flippase MurJ	A	534	Escherichia coli	Mutation(s): 0 Gene Names: murJ, mviN, yceN, b1069, JW1056 Membrane Entity: Yes
UniProt
Find proteins for P0AF16 (Escherichia coli (strain K12)) Explore P0AF16 Go to UniProtKB: P0AF16
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0AF16
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysis protein	B	47	Enterobacteria phage M	Mutation(s): 0 Gene Names: lys
UniProt
Find proteins for K7QK87 (Enterobacteria phage M) Explore K7QK87 Go to UniProtKB: K7QK87
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	K7QK87
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.05 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-09-10

Deposition Author(s):

Lertpreedakorn, N.

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	--

Revision History (Full details and data files)

Version 1.0: 2025-09-10
Type: Initial release

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.