5MI3: Elongation factor Tu 1

Structure of phosphorylated translation elongation factor EF-Tu from E. coli. Determined by X-ray diffraction at 2.8 Å resolution. Released 20 Dec 2017.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Escherichia coli (strain K12)
Chains: 2
Atoms: 6,130
Mol. weight: 89.72 kDa
Ligands: GDP, MG
Released: 20 Dec 2017

Explore 5MI3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5MI3 contains 29 α-helices and 57 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: 15 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	12-16	5	1
β-strand	17-18	2	2
α-helix	25-40	16
α-helix	47-51	5
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
α-helix	165-167	3
β-strand	170-172	3	2
α-helix	175-180	6
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	4
β-strand	225-231	7	4
β-strand	234	1	4
β-strand	236-238	3	5
β-strand	242-247	6	4
β-strand	249-261	13	4
β-strand	264-266	3	4
β-strand	268-270	3	5
β-strand	274-280	7	4
α-helix	284-286	3
β-strand	292-294	3	4
β-strand	300-311	12	6
α-helix	312-313	2
β-strand	323	1	7
β-strand	330-333	4	6
β-strand	336-343	8	6
α-helix	344-345	2
β-strand	351	1	7
β-strand	356-369	14	6
β-strand	374-379	6	6
β-strand	382-392	11	6

Chain B: 14 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	12-16	5	8
β-strand	17-18	2	9
α-helix	25-40	16
α-helix	47-51	5
β-strand	55-58	4	10
β-strand	61-64	4	10
β-strand	66-71	6	8
β-strand	76-81	6	8
α-helix	85-94	10
β-strand	102-107	6	9
α-helix	114-126	13
β-strand	131-136	6	9
α-helix	138-140	3
α-helix	144-160	17
β-strand	170-172	3	9
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	11
β-strand	217-221	5	4
β-strand	225-231	7	4
β-strand	234	1	11
β-strand	236-238	3	12
β-strand	242-246	5	11
β-strand	252-255	4	11
β-strand	256-261	6	4
β-strand	264-266	3	4
β-strand	268-270	3	12
β-strand	274-279	6	4
α-helix	284-286	3
β-strand	292-294	3	11
β-strand	300-311	12	13
α-helix	312-313	2
β-strand	323	1	14
β-strand	330-332	3	13
β-strand	337-343	7	13
α-helix	344-345	2
β-strand	351	1	14
β-strand	356-369	14	13
β-strand	374-379	6	13
β-strand	382-392	11	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Elongation factor Tu 1	A, B	protein	402	Escherichia coli (strain K12)	P0CE47 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5MI3_1 Elongation factor Tu 1 (chains A, B)
MGSHHHHHHSKEKFERTKPHVNVGTIGHVDHGKTTLTAAITTVLAKTYGGAARAFDQIDN
APEEKARGITINTSHVEYDTPTRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGP
MPQTREHILLGRQVGVPYIIVFLNKCDMVDDEELLELVEMEVRELLSQYDFPGDDTPIVR
GSALKALEGDAEWEAKILELAGFLDSYIPEPERAIDKPFLLPIEDVFSISGRGTVVTGRV
ERGIIKVGEEVEIVGIKETQKSTCTGVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQV
LAKPGTIKPHTKFESEVYILSKDEGGRHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMVM
PGDNIKMVVTLIHPIAMDDGLRFAIREGGRTVGAGVVAKVLG

Ligands and cofactors

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

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
5MI8 2.18 Å, Structure of the phosphomimetic mutant of EF-Tu T383E
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…

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