9HXD | pdb_00009hxd

Bacterial antiviral defense protein Ec2ApeA from Escherichia coli strain 2-156-04_S4_C1 (oligomerization mutant R551E)

PDB DOI: https://doi.org/10.2210/pdb9HXD/pdb
EM Map EMD-52464: EMDB EMDataResource

Classification: RNA BINDING PROTEIN
Organism(s): Escherichia coli 2-156-04_S4_C1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-01-07 Released: 2026-07-22
Deposition Author(s): Sasnauskas, G., Juozapaitis, J., Puteikiene, R., Tamulaitiene, G.
Funding Organization(s): Research Council of Lithuania

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.55 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: in silico
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This is version 1.0 of the entry. See complete history.

Literature

ApeA is a deoxyribodinucleotide binding antiviral defense system targeting tRNA

Juozapaitis, J., Silanskas, A., Ruksenaite, A., Puteikiene, R., Truncaite, L., Songailiene, I., Tamulaitiene, G., Siksnys, V., Sasnauskas, G.

To be published.

Macromolecule Content

Total Structure Weight: 138.49 kDa
Atom Count: 7,700
Modeled Residue Count: 1,120
Deposited Residue Count: 1,186
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bacterial antiviral defense protein Ec2ApeA from Escherichia coli strain 2-156-04_S4_C1 (oligomerization mutant R551E)	A, B	593	Escherichia coli 2-156-04_S4_C1	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.55 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21rc1_4903
RECONSTRUCTION	cryoSPARC	4.5.3

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-07-22

Deposition Author(s):

Juozapaitis, J.

Tamulaitiene, G.

Funding Organization	Location	Grant Number
Research Council of Lithuania	Lithuania	S-MIP-22-13

Revision History (Full details and data files)

Version 1.0: 2026-07-22
Type: Initial release

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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.