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

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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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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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

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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.