5I4R: Contact-dependent inhibitor A

Contact-dependent inhibition system from Escherichia coli NC101 - ternary CdiA/CdiI/EF-Tu complex (trypsin-modified). Determined by X-ray diffraction at 3.3 Å resolution. Released 28 Jun 2017.

Method: X-ray diffraction
Resolution: 3.3 Å
Organisms: Escherichia coli NC101, Escherichia coli
Chains: 8
Atoms: 8,941
Mol. weight: 133.84 kDa
Ligands: GDP
Released: 28 Jun 2017

Explore 5I4R in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5I4R contains 40 α-helices and 74 β-strands across 8 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.

Chains A and E: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	171-172	2	1
α-helix	173	1
β-strand	174-175	2	2
β-strand	179-182	4	2
β-strand	185-188	4	2
α-helix	189-197	9
α-helix	203-211	9
β-strand	216-219	4	2
β-strand	228-232	5	2
β-strand	235-240	6	2
β-strand	245-251	7	2
α-helix	252-253	2

Chains B and F: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	4-40	37
α-helix	44-66	23
α-helix	74-82	9
α-helix	88-99	12

Chain C: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	10-11	2
β-strand	12-19	8	3
α-helix	25-40	16

Chain D: 11 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	66-71	6	3
β-strand	76-81	6	3
α-helix	85-93	9
β-strand	101-107	7	3
β-strand	111	1	3
α-helix	114-126	13
β-strand	131-136	6	3
α-helix	138-140	3
α-helix	144-160	17
β-strand	170-172	3	3
α-helix	175-180	6
α-helix	183-199	17
α-helix	201-205	5
α-helix	206-208	3
β-strand	212-214	3	4
β-strand	217-221	5	1
β-strand	225-231	7	1
β-strand	234	1	4
β-strand	236-238	3	5
β-strand	242-247	6	4
β-strand	249-255	7	4
β-strand	256-261	6	1
β-strand	265-266	2	1
β-strand	268-270	3	5
β-strand	274-280	7	1
α-helix	284-286	3
β-strand	289	1	6
β-strand	291	1	6
β-strand	292-294	3	4
β-strand	300-311	12	7
α-helix	312-313	2
β-strand	323	1	8
β-strand	330-333	4	7
β-strand	336-343	8	7
α-helix	344-345	2
β-strand	351	1	8
β-strand	356-369	14	7
β-strand	374-379	6	7
β-strand	382-392	11	7

Chain G: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	12-19	8	11
α-helix	25-39	15

Chain H: 10 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	66-71	6	11
β-strand	76-81	6	11
α-helix	85-94	10
β-strand	101-107	7	11
β-strand	111	1	11
α-helix	114-126	13
β-strand	131-136	6	11
α-helix	144-160	17
β-strand	170-172	3	11
α-helix	175-180	6
α-helix	183-199	17
α-helix	201-205	5
α-helix	206-208	3
β-strand	212-214	3	12
β-strand	217-221	5	9
β-strand	225-231	7	9
β-strand	234	1	12
β-strand	236-238	3	13
β-strand	242-247	6	12
β-strand	249-255	7	12
β-strand	256-261	6	9
β-strand	265-266	2	9
β-strand	268-270	3	13
β-strand	274-279	6	9
α-helix	284-286	3
β-strand	289	1	14
β-strand	291	1	14
β-strand	292-294	3	12
β-strand	300-311	12	15
α-helix	312-313	2
β-strand	323	1	16
β-strand	330-333	4	15
β-strand	336-343	8	15
α-helix	344-345	2
β-strand	351	1	16
β-strand	356-369	14	15
β-strand	374-379	6	15
β-strand	382-392	11	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Contact-dependent inhibitor A	A, E	protein	92	Escherichia coli NC101	P0DSI1
Elongation factor Tu	C, G	protein	45	Escherichia coli	P0CE48 (AlphaFold model)
Elongation factor Tu	D, H	protein	335	Escherichia coli	P0CE47 (AlphaFold model)
Contact-dependent inhibitor I	B, F	protein	114	Escherichia coli NC101	P0DSM8 (AlphaFold model)

Sequence of entity 1 (A, E), FASTA

>5I4R_1 Contact-dependent inhibitor A (chains A, E)
LSYLGIGKKISFDGDFYTVDGMKFSKSYYEKLWEQGRPAPFVQAREVLNSNPKIEPDPRG
APGYLRYEGAGLEMIYNPKTGQVGHIQPVKVK

Sequence of entity 2 (C, G), FASTA

>5I4R_2 Elongation factor Tu (chains C, G)
MSKEKFERTKPHVNVGTIGHVDHGKTTLTAAITTVLAKTYGGAAR

Sequence of entity 3 (D, H), FASTA

>5I4R_3 Elongation factor Tu (chains D, H)
GITINTSHVEYDTPTRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREH
ILLGRQVGVPYIIVFLNKCDMVDDEELLELVEMEVRELLSQYDFPGDDTPIVRGSALKAL
EGDAEWEAKILELAGFLDSYIPEPERAIDKPFLLPIEDVFSISGRGTVVTGRVERGIIKV
GEEVEIVGIKETQKSTCTGVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQVLAKPGTI
KPHTKFESEVYILSKDEGGRHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMVMPGDNIKM
VVTLIHPIAMDDGLRFAIREGGRTVGAGVVAKVLG

Sequence of entity 4 (B, F), FASTA

>5I4R_4 Contact-dependent inhibitor I (chains B, F)
MDIWPEFQRDLEMYRDVVLSIKRNLRLYEECIESLVHQIGSTNFDNAQPLFDDLFRMQSE
LATMLYKYEYKPGKRIQDLIYHLDRDDFYSRKYWHKKFSDGLAWPEAGHHHHHH

Ligands and cofactors

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

Primary citation

Structure of a novel antibacterial toxin that exploits elongation factor Tu to cleave specific transfer RNAs. Michalska, K., Gucinski, G.C., Garza-Sanchez, F. et al. Nucleic Acids Res (2017) 45:10306-10320. DOI 10.1093/nar/gkx700 · PubMed

Other PDB entries of the same protein (UniProt P0DSI1), best resolution first:

5I4Q 2.35 Å, Contact-dependent inhibition system from Escherichia coli NC101 - ternary…

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