9BJE | pdb_00009bje

Encapsulin 1 of a two-component Family 2B encapsulin shell from Streptomyces lydicus

PDB DOI: https://doi.org/10.2210/pdb9BJE/pdb
EM Map EMD-44632: EMDB EMDataResource

Classification: VIRUS LIKE PARTICLE
Organism(s): Streptomyces lydicus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-04-25 Released: 2025-04-30
Deposition Author(s): Andreas, M.P., Dutcher, C., Giessen, T.W.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.58 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

A two-component quasi-icosahedral protein nanocompartment with variable shell composition and irregular tiling

Dutcher, C., Andreas, M.P., Giessen, T.W.

To be published.

Macromolecule Content

Total Structure Weight: 52.26 kDa
Atom Count: 2,094
Modelled Residue Count: 266
Deposited Residue Count: 475
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Crp/Fnr family transcriptional regulator	A	475	Streptomyces lydicus	Mutation(s): 0 Gene Names: ADL29_33315
UniProt
Find proteins for A0A0N0GW33 (Streptomyces chattanoogensis) Explore A0A0N0GW33 Go to UniProtKB: A0A0N0GW33
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0N0GW33
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.58 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	v3.2.0+210511
MODEL REFINEMENT	Coot	0.8.9.1
MODEL REFINEMENT	PHENIX	1.20.1-4487

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-04-30

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM133325

Revision History (Full details and data files)

Version 1.0: 2025-04-30
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.