9T38: Rhs2-CT endonuclease toxin

Rhs2-CT endonuclease toxin in complex with cognate immunity protein RhsI2 and EF-Tu. Determined by X-ray diffraction at 2.45 Å resolution. Released 24 Dec 2025.

Method: X-ray diffraction
Resolution: 2.45 Å
Organisms: Escherichia coli, Serratia marcescens
Chains: 6
Atoms: 10,491
Mol. weight: 160.9 kDa
Ligands: MG, GDP
Released: 24 Dec 2025

Explore 9T38 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9T38 contains 64 α-helices and 83 β-strands across 6 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 8 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	1294-1303	10
β-strand	1306	1	13
α-helix	1314-1323	10
β-strand	1326-1328	3	11
α-helix	1329-1331	3
α-helix	1332-1357	26
α-helix	1360-1362	3
β-strand	1365-1369	5	13
α-helix	1373-1375	3
α-helix	1381-1383	3
β-strand	1384-1388	5	13
α-helix	1418-1421	4
β-strand	1425-1427	3	11

Chain B: 8 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	6-14	9
β-strand	32-34	3	9
α-helix	39-43	5
β-strand	58-59	2	10
α-helix	60-61	2
α-helix	67-68	2
α-helix	79-94	16
α-helix	101-104	4
β-strand	105-106	2	11
β-strand	109-110	2	11
α-helix	112-132	21
α-helix	137-146	10
β-strand	151	1	9
β-strand	153-154	2	10
β-strand	155	1	12
β-strand	158	1	12
β-strand	159-161	3	9

Chain C: 16 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	12-16	5	1
β-strand	17-18	2	2
α-helix	25-39	15
α-helix	47-51	5
α-helix	53-54	2
β-strand	55-58	4	3
β-strand	61-64	4	3
β-strand	66-71	6	1
β-strand	76-81	6	1
α-helix	85-93	9
α-helix	98-99	2
β-strand	102-107	6	2
α-helix	114-126	13
β-strand	131-136	6	2
α-helix	144-160	17
α-helix	165-167	3
β-strand	170-172	3	2
α-helix	175-179	5
α-helix	183-199	17
α-helix	201-203	3
α-helix	206-208	3
α-helix	210-211	2
β-strand	212-214	3	4
β-strand	217-221	5	5
β-strand	225-231	7	5
β-strand	234	1	4
β-strand	236-238	3	6
β-strand	242-246	5	4
α-helix	251	1
β-strand	252-255	4	4
β-strand	256-261	6	5
β-strand	264-266	3	5
β-strand	268-270	3	6
β-strand	274-279	6	5
α-helix	284-286	3
β-strand	292-294	3	4
β-strand	301-311	11	7
β-strand	323	1	8
β-strand	330-332	3	7
β-strand	337-343	7	7
α-helix	344-345	2
β-strand	351	1	8
β-strand	356-368	13	7
β-strand	374-379	6	7
β-strand	382-392	11	7

Chain D: 9 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	1294-1303	10
β-strand	1306	1	23
α-helix	1314-1323	10
β-strand	1326-1328	3	22
α-helix	1329-1331	3
α-helix	1332-1357	26
α-helix	1360-1362	3
β-strand	1366-1369	4	23
α-helix	1373-1375	3
α-helix	1381-1383	3
β-strand	1384-1387	4	23
α-helix	1391-1393	3
α-helix	1418-1421	4
β-strand	1425-1427	3	22

Chain E: 8 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	6-14	9
β-strand	32-34	3	21
α-helix	39-43	5
β-strand	58-59	2	21
α-helix	60-61	2
α-helix	67-68	2
α-helix	79-94	16
α-helix	102-104	3
β-strand	105-106	2	22
β-strand	109-110	2	22
α-helix	112-132	21
α-helix	137-146	10
β-strand	151-155	5	21
β-strand	158-161	4	21

Chain F: 15 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	12-16	5	14
β-strand	17-18	2	15
α-helix	25-39	15
α-helix	47-51	5
β-strand	55-58	4	16
β-strand	61-64	4	16
β-strand	66-71	6	14
β-strand	76-81	6	14
α-helix	85-93	9
α-helix	98-99	2
β-strand	102-107	6	15
α-helix	114-126	13
β-strand	131-136	6	15
α-helix	138-140	3
α-helix	144-160	17
α-helix	165-167	3
β-strand	170-172	3	15
α-helix	175-180	6
α-helix	183-199	17
α-helix	201-203	3
α-helix	206-208	3
α-helix	210-211	2
β-strand	212-214	3	17
β-strand	217-221	5	5
β-strand	225-231	7	5
β-strand	234	1	17
β-strand	236-238	3	18
β-strand	242-246	5	17
β-strand	252-255	4	17
β-strand	258-261	4	5
β-strand	264-266	3	5
β-strand	268-270	3	18
β-strand	274-278	5	5
α-helix	284-286	3
β-strand	292-294	3	17
β-strand	301-311	11	19
β-strand	323	1	20
β-strand	330-332	3	19
β-strand	337-343	7	19
α-helix	344-345	2
β-strand	351	1	20
β-strand	356-368	13	19
β-strand	374-379	6	19
β-strand	382-392	11	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Elongation factor Tu 2	C, F	protein	394	Escherichia coli	P0CE48 (AlphaFold model)
Immunity protein RhsI2	B, E	protein	162	Serratia marcescens	A0ABF7SXG6 (AlphaFold model)
Rhs-family protein	A, D	protein	162	Serratia marcescens	A0ABC9II69

Sequence of entity 1 (C, F), FASTA

>9T38_1 Elongation factor Tu 2 (chains C, F)
MSKEKFERTKPHVNVGTIGHVDHGKTTLTAAITTVLAKTYGGAARAFDQIDNAPEEKARG
ITINTSHVEYDTPTRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHI
LLGRQVGVPYIIVFLNKCDMVDDEELLELVEMEVRELLSQYDFPGDDTPIVRGSALKALE
GDAEWEAKILELAGFLDSYIPEPERAIDKPFLLPIEDVFSISGRGTVVTGRVERGIIKVG
EEVEIVGIKETQKSTCTGVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQVLAKPGTIK
PHTKFESEVYILSKDEGGRHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMVMPGDNIKMV
VTLIHPIAMDDGLRFAIREGGRTVGAGVVAKVLS

Sequence of entity 2 (B, E), FASTA

>9T38_2 Immunity protein RhsI2 (chains B, E)
MNEFDFDSLLQRIDSSCFFSRMGLPDVLDSRVILIENVEKVFVNPTDAEFKGYYDSVEWL
PTSMTQEDPFYKVKEVLPKELTGLRIRVNKAVMNATKGLSKDKFNYGPHDFSLAARNGIC
FAFREYVSEQYLHLGNKWEEVVGIYFSGHWPVGIAKDKIVTI

Sequence of entity 3 (A, D), FASTA

>9T38_3 Rhs-family protein (chains A, D)
MGSSHHHHHHSSGENLYFQGGSNCSTLDRIIGDANKVASRGGAITAKQAQILRDNLPVVQ
RRSVFQNQMARKEFVRDQHYLMSQWEANTGRTWPTGATPHHIIPLESGGANKWWNLMPTH
GTLPNHSLPGVPGPHAAGGVLRTTVQQSRKALPPGTITDLRL

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	2

Water and common crystallization additives (IMD, EDO) are not listed.

Primary citation

An Rhs effector uses distinct target cell functions to intoxicate bacterial and fungal competitors. Avelar, G.M., Pankov, G., Sarapa, T. et al. bioRxiv (2025). DOI 10.1101/2025.10.28.685041

Other PDB entries of the same protein (UniProt P0CE48 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2BVN 2.3 Å, E. coli EF-Tu:GDPNP in complex with the antibiotic enacyloxin IIa
6EZE 2.47 Å, The open conformation of E.coli Elongation Factor Tu in complex with GDPNP.
1DG1 2.5 Å, Whole, unmodified, ef-tu(elongation factor tu).
1EFU 2.5 Å, Elongation factor complex ef-tu/ef-ts from escherichia coli
3MMP 2.5 Å, Structure of the Qb replicase, an RNA-dependent RNA polymerase consisting of viral and…
1EFM 2.7 Å, Structure of the GDP domain of ef-tu and location of the amino acids homologous to ras…
8QFS 2.7 Å, Cryo-EM structure of SidH from Legionella pneumophila
5AFI 2.9 Å, 2.9A Structure of E. coli ribosome-EF-TU complex by cs-corrected cryo-EM
5WDT 3.0 Å, 70S ribosome-EF-Tu H84A complex with GppNHp
5WFS 3.0 Å, 70S ribosome-EF-Tu H84A complex with GTP and near-cognate tRNA (Complex C4)
5WE4 3.1 Å, 70S ribosome-EF-Tu wt complex with GppNHp
8G7Q 3.1 Å, Structure of the Escherichia coli 70S ribosome in complex with EF-Tu and…

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