5MI8: Phosphomimetic mutant of EF-Tu T383E

Structure of the phosphomimetic mutant of EF-Tu T383E. Determined by X-ray diffraction at 2.18 Å resolution. Released 20 Dec 2017.

Method: X-ray diffraction
Resolution: 2.18 Å
Organism: Escherichia coli HS
Chains: 2
Atoms: 6,015
Mol. weight: 90.6 kDa
Ligands: GDP, MG
Released: 20 Dec 2017

Explore 5MI8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5MI8 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: 17 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	10-11	2
β-strand	12-16	5	1
β-strand	17-18	2	2
α-helix	25-38	14
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	85-94	10
β-strand	102-107	6	2
α-helix	114-126	13
β-strand	131-136	6	2
α-helix	138-140	3
α-helix	144-160	17
β-strand	170-172	3	2
α-helix	175-179	5
α-helix	183-199	17
α-helix	201-205	5
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
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	300-311	12	7
α-helix	312-313	2
α-helix	314-316	3
β-strand	323-324	2	8
β-strand	330-332	3	7
β-strand	337-343	7	7
α-helix	344-345	2
β-strand	350-351	2	8
β-strand	356-369	14	7
β-strand	374-379	6	7
β-strand	382-392	11	7

Chain B: 16 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	10-11	2
β-strand	12-16	5	9
β-strand	17-18	2	10
α-helix	25-40	16
α-helix	47-51	5
α-helix	53-54	2
β-strand	55-58	4	11
β-strand	61-64	4	11
β-strand	66-71	6	9
β-strand	76-81	6	9
α-helix	85-94	10
β-strand	102-107	6	10
α-helix	114-126	13
β-strand	131-136	6	10
α-helix	138-140	3
α-helix	144-160	17
β-strand	170-172	3	10
α-helix	175-179	5
α-helix	183-199	17
α-helix	201-205	5
α-helix	206-208	3
α-helix	210-211	2
β-strand	212-214	3	12
β-strand	217-221	5	5
β-strand	225-231	7	5
β-strand	234	1	12
β-strand	236-238	3	13
β-strand	242-246	5	12
β-strand	252-255	4	12
β-strand	256-261	6	5
β-strand	264-266	3	5
β-strand	268-270	3	13
β-strand	274-279	6	5
α-helix	284-286	3
β-strand	292-294	3	12
β-strand	300-311	12	14
α-helix	312-313	2
α-helix	314-316	3
β-strand	323-324	2	15
β-strand	330-332	3	14
β-strand	337-343	7	14
β-strand	350-351	2	15
β-strand	356-369	14	14
β-strand	374-378	5	14
β-strand	383-392	10	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Elongation factor Tu 1	A, B	protein	402	Escherichia coli HS	P0CE47 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5MI8_1 Elongation factor Tu 1 (chains A, B)
MGSHHHHHHSKEKFERTKPHVNVGTIGHVDHGKTTLTAAITTVLAKTYGGAARAFDQIDN
APEEKARGITINTSHVEYDTPTRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGP
MPQTREHILLGRQVGVPYIIVFLNKCDMVDDEELLELVEMEVRELLSQYDFPGDDTPIVR
GSALKALEGDAEWEAKILELAGFLDSYIPEPERAIDKPFLLPIEDVFSICGRGTVVTGRV
ERGIIKVGEEVEIVGIKETQKSTCTGVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQV
LAKPGTIKPHTKFESEVYILSKDEGGRHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMVM
PGDNIKMVVTLIHPIAMDDGLRFAIREGGREVGAGVVAKVLG

Ligands and cofactors

ID	Name	Formula	Copies
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	2
MG	Magnesium ion	Mg	4

Water and common crystallization additives (CL, BME, EPE, ACT) are not listed.

Primary citation

Phosphorylation decelerates conformational dynamics in bacterial translation elongation factors. Talavera, A., Hendrix, J., Versees, W. et al. Sci Adv (2018) 4:eaap9714-eaap9714. DOI 10.1126/sciadv.aap9714 · 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
8FR3 2.23 Å, E. coli EF-Tu in complex with KKL-55
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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