9BJ6 | pdb_00009bj6

Crystal structure of the HEPN family member AbiV, an RNase in a two-component antiphage system in Lactococcus lactis

PDB DOI: https://doi.org/10.2210/pdb9BJ6/pdb

Classification: RNA BINDING PROTEIN
Organism(s): Lactococcus cremoris
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-04-25 Released: 2025-08-13
Deposition Author(s): Picard, M.-E., Moineau, S., Shi, R.
Funding Organization(s): Fonds de Recherche du Quebec - Nature et Technologies (FRQNT)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.92 Å
R-Value Free:
0.254 (Depositor), 0.256 (DCC)
R-Value Work:
0.208 (Depositor), 0.214 (DCC)
R-Value Observed:
0.210 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

HEPN-AbiV is an RNase in the AbiV antiphage system

Zhu, X., Morency, C., Picard, M.-E., Mosterd, C., McAlister, J.A., Perrault-Jolicoeur, A., Geddes-McAlister, J., Shi, R., Moineau, S.

To be published.

Macromolecule Content

Total Structure Weight: 94.43 kDa
Atom Count: 5,383
Modeled Residue Count: 679
Deposited Residue Count: 828
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AbiV family abortive infection protein	A, B, C, D	207	Lactococcus cremoris	Mutation(s): 0
UniProt
Find proteins for A2RJ64 (Lactococcus lactis subsp. cremoris (strain MG1363)) Explore A2RJ64 Go to UniProtKB: A2RJ64
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A2RJ64
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLY Query on MLY	A, B, C, D	L-PEPTIDE LINKING	C₈ H₁₈ N₂ O₂		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.92 Å
R-Value Free: 0.254 (Depositor), 0.256 (DCC)
R-Value Work: 0.208 (Depositor), 0.214 (DCC)
R-Value Observed: 0.210 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.173	α = 90
b = 144.955	β = 95.53
c = 55.563	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
XDS	data reduction
MOLREP	phasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2025-08-13

Deposition Author(s):

Funding Organization	Location	Grant Number
Fonds de Recherche du Quebec - Nature et Technologies (FRQNT)	Canada	--

Revision History (Full details and data files)

Version 1.0: 2025-08-13
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.