8FR3: E. coli EF-Tu

Name: PDB 8FR3: E. coli EF-Tu in complex with KKL-55
Published: 2023-09-20
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: translation

E. coli EF-Tu in complex with KKL-55. Determined by X-ray diffraction at 2.23 Å resolution. Released 20 Sept 2023.

Method: X-ray diffraction
Resolution: 2.23 Å
Organism: Escherichia coli K-12
Chains: 2
Atoms: 6,018
Mol. weight: 90.03 kDa
Ligands: Y7C, GDP, MG
Released: 20 Sept 2023

Explore 8FR3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8FR3 contains 33 α-helices and 58 β-strands across 2 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: 16 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	11-15	5	1
β-strand	16-17	2	2
α-helix	24-39	16
α-helix	46-50	5
α-helix	52-53	2
β-strand	54-57	4	3
β-strand	60-63	4	3
β-strand	65-70	6	1
β-strand	75-80	6	1
α-helix	84-93	10
α-helix	97-98	2
β-strand	101-106	6	2
α-helix	113-124	12
β-strand	130-135	6	2
α-helix	137-139	3
α-helix	143-159	17
β-strand	169-171	3	2
α-helix	174-178	5
α-helix	182-198	17
α-helix	200-204	5
α-helix	205-207	3
α-helix	209-210	2
β-strand	211-213	3	4
β-strand	216-220	5	5
β-strand	224-230	7	5
β-strand	233	1	4
β-strand	235-237	3	6
β-strand	241-246	6	4
β-strand	248-254	7	4
β-strand	255-260	6	5
β-strand	263-265	3	5
β-strand	267-269	3	6
β-strand	273-278	6	5
α-helix	283-285	3
β-strand	291-293	3	4
β-strand	300-310	11	7
α-helix	311-312	2
β-strand	322	1	8
β-strand	329-332	4	7
β-strand	335-342	8	7
α-helix	343-344	2
β-strand	350	1	8
β-strand	355-367	13	7
β-strand	373-378	6	7
β-strand	381-391	11	7

Chain B: 17 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	11-15	5	9
β-strand	16-17	2	10
α-helix	24-39	16
α-helix	46-50	5
α-helix	52-53	2
β-strand	54-57	4	11
β-strand	60-63	4	11
β-strand	65-70	6	9
β-strand	75-80	6	9
α-helix	84-93	10
α-helix	97-98	2
β-strand	101-106	6	10
α-helix	113-124	12
β-strand	130-135	6	10
α-helix	137-139	3
α-helix	143-159	17
α-helix	164-166	3
β-strand	169-171	3	10
α-helix	174-178	5
α-helix	182-198	17
α-helix	200-204	5
α-helix	205-207	3
α-helix	209-210	2
β-strand	211-213	3	12
β-strand	216-220	5	5
β-strand	224-230	7	5
β-strand	233	1	12
β-strand	235-237	3	13
β-strand	241-246	6	12
β-strand	248-254	7	12
β-strand	255-260	6	5
β-strand	263-265	3	5
β-strand	267-269	3	13
β-strand	273-278	6	5
α-helix	283-285	3
β-strand	291-293	3	12
β-strand	300-310	11	14
α-helix	311-312	2
β-strand	322	1	15
β-strand	329-332	4	14
β-strand	335-342	8	14
α-helix	343-344	2
β-strand	350	1	15
β-strand	355-367	13	14
β-strand	373-378	6	14
β-strand	381-391	11	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Elongation factor Tu	A, B	protein	402	Escherichia coli K-12	P0CE47 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8FR3_1 Elongation factor Tu (chains A, B)
MSKEKFERTKPHVNVGTIGHVDHGKTTLTAAITTVLAKTYGGAARAFDQIDNAPEEKARG
ITINTSHVEYDTPTRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHI
LLGRQVGVPYIIVFLNKCDMVDDEELLELVEMEVRELLSQYDFPGDDTPIVRGSALKALE
GDAEWEAKILELAGFLDSYIPEPERAIDKPFLLPIEDVFSISGRGTVVTGRVERGIIKVG
EEVEIVGIKETQKSTCTGVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQVLAKPGTIK
PHTKFESEVYILSKDEGGRHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMVMPGDNIKMV
VTLIHPIAMDDGLRFAIREGGRTVGAGVVAKVLGRSHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
Y7C	3-chloro-N-(1-propyl-1H-tetrazol-5-yl)benzamide	C11 H12 Cl N5 O	1
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	2
MG	Magnesium ion	Mg	2

Primary citation

Antibiotic that inhibits trans -translation blocks binding of EF-Tu to tmRNA but not to tRNA. Marathe, N., Nguyen, H.A., Alumasa, J.N. et al. mBio (2023) 14:e0146123-e0146123. DOI 10.1128/mbio.01461-23 · PubMed

Other PDB entries of the same protein (UniProt P0CE47 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9TBU 1.23 Å, E. coli EF-Tu-T62A:GDP AMPylated at T65
4PC3 1.83 Å, Elongation factor Tu:Ts complex with partially bound GDP
5JBQ 2.01 Å, Ef-tu (escherichia coli) in complex with thiomuracin analog
1EFC 2.05 Å, Intact elongation factor from e.coli
2HCJ 2.12 Å, Trypsin-modified Elongation Factor Tu in complex with tetracycline
3U6B 2.12 Å, Ef-tu (escherichia coli) in complex with nvp-ldi028
4P3Y 2.15 Å, Crystal structure of Acinetobacter baumannii DsbA in complex with EF-Tu
5MI8 2.18 Å, Structure of the phosphomimetic mutant of EF-Tu T383E
4G5G 2.3 Å, ef-tu (Escherichia coli) complexed with nvp-ldu796
1D8T 2.35 Å, Crystal structure of elongation factor, tu (ef-tu-mggdp) complexed with GE2270A, a…
5I4Q 2.35 Å, Contact-dependent inhibition system from Escherichia coli NC101 - ternary…
3U6K 2.45 Å, Ef-tu (escherichia coli) in complex with nvp-ldk733

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