1D8T: Elongation factor, tu

Crystal structure of elongation factor, tu (ef-tu-mggdp) complexed with GE2270A, a thiazolyl peptide antibiotic. Determined by X-ray diffraction at 2.35 Å resolution. Released 25 Oct 2000.

Method: X-ray diffraction
Resolution: 2.35 Å
Organisms: ESCHERICHIA COLI, PLANOBISPORA ROSEA
Chains: 4
Atoms: 6,718
Mol. weight: 92.09 kDa
Ligands: GDP, MG
Released: 25 Oct 2000

Explore 1D8T in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1D8T contains 30 α-helices and 61 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, 31 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
β-strand	101-106	6	2
α-helix	113-125	13
β-strand	130-135	6	2
α-helix	137-139	3
α-helix	143-159	17
α-helix	164-166	3
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	241-245	5	4
β-strand	251-254	4	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	288	1	7
β-strand	290	1	7
β-strand	291-293	3	4
β-strand	299-310	12	8
α-helix	311-312	2
β-strand	322-323	2	9
β-strand	329-332	4	8
β-strand	335-342	8	8
β-strand	349-350	2	9
β-strand	355-368	14	8
β-strand	373-378	6	8
β-strand	381-391	11	8

Chain B: 15 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	11-17	7	10
α-helix	24-39	16
α-helix	46-50	5
α-helix	52-53	2
β-strand	54-55	2	11
β-strand	62-63	2	11
β-strand	65-70	6	10
β-strand	75-80	6	10
α-helix	84-93	10
β-strand	100-106	7	10
α-helix	113-125	13
β-strand	130-135	6	10
α-helix	137-139	3
α-helix	143-158	16
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	13
β-strand	224-230	7	13
β-strand	233	1	12
β-strand	235-237	3	14
β-strand	241-246	6	12
β-strand	248-254	7	12
β-strand	255-260	6	13
β-strand	263-265	3	13
β-strand	267-269	3	14
β-strand	273-278	6	13
α-helix	283-285	3
β-strand	288	1	15
β-strand	290	1	15
β-strand	291-293	3	12
β-strand	299-310	12	16
α-helix	311-312	2
β-strand	322-323	2	17
β-strand	329-332	4	16
β-strand	335-342	8	16
β-strand	349-350	2	17
β-strand	355-368	14	16
β-strand	373-378	6	16
β-strand	381-391	11	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Elongation factor tu	A, B	protein	393	ESCHERICHIA COLI	P0CE47 (AlphaFold model)
Thiocillin GE2270	C, D	protein	15	PLANOBISPORA ROSEA	Q7M0J8

Sequence of entity 1 (A, B), FASTA

>1D8T_1 ELONGATION FACTOR TU (chains A, B)
SKEKFERTKPHVNVGTIGHVDHGKTTLTAAITTVLAKTYGGAARAFDQIDNAPEEKARGI
TINTSHVEYDTPTRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHIL
LGRQVGVPYIIVFLNKCDMVDDEELLELVEMEVRELLSQYDFPGDDTPIVRGSALKALEG
DAEWEAKILELAGFLDSYIPEPERAIDKPFLLPIEDVFSISGRGTVVTGRVERGIIKVGE
EVEIVGIKETQKSTCTGVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQVLAKPGTIKP
HTKFESEVYILSKDEGGRHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMVMPGDNIKMVV
TLIHPIAMDDGLRFAIREGGRTVGAGVVAKVLG

Sequence of entity 2 (C, D), FASTA

>1D8T_2 THIOCILLIN GE2270 (chains C, D)
SCNCVCGFCCSCSPX

Ligands and cofactors

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

Water and common crystallization additives (ACT) are not listed.

Primary citation

Structure of an EF-TU Complex with a Thiazolyl Peptide Antibiotic Determined at 2.35 A Resolution: Atomic Basis for Ge2270A Inhibition of EF-TU. Heffron, S.E., Jurnak, F. Biochemistry (2000) 39:37. DOI 10.1021/BI9913597 · 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
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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