6EZE: Elongation factor Tu 2

The open conformation of E.coli Elongation Factor Tu in complex with GDPNP. Determined by X-ray diffraction at 2.47 Å resolution. Released 22 Aug 2018.

Method: X-ray diffraction
Resolution: 2.47 Å
Organism: Escherichia coli (strain K12)
Chains: 2
Atoms: 6,348
Mol. weight: 89.18 kDa
Ligands: MG, GNP
Released: 22 Aug 2018

Explore 6EZE in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6EZE contains 32 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: 15 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	11-15	5	1
β-strand	16-18	3	2
α-helix	24-39	16
α-helix	46-50	5
α-helix	52-53	2
β-strand	54-56	3	3
β-strand	61-63	3	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	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	216-219	4	5
β-strand	225-230	6	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	299-310	12	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	355-368	14	7
β-strand	373-378	6	7
β-strand	381-391	11	7

Chain B: 17 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	9-10	2
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	54-56	3	11
β-strand	61-63	3	11
β-strand	65-70	6	9
β-strand	75-80	6	9
α-helix	84-93	10
β-strand	101-106	6	10
α-helix	113-125	13
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	216-219	4	13
β-strand	225-230	6	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	291-293	3	12
β-strand	299-310	12	15
α-helix	311-312	2
β-strand	322	1	16
β-strand	329-332	4	15
β-strand	335-342	8	15
α-helix	343-344	2
β-strand	350	1	16
β-strand	355-368	14	15
β-strand	373-378	6	15
β-strand	381-391	11	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Elongation factor Tu 2	A, B	protein	394	Escherichia coli (strain K12)	P0CE48 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6EZE_1 Elongation factor Tu 2 (chains A, B)
MSKEKFERTKPHVNVGTIGHVDHGKTTLTAAITTVLAKTYGGAARAFDQIDNAPEEKARG
ITINTSHVEYDTPTRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHI
LLGRQVGVPYIIVFLNKCDMVDDEELLELVEMEVRELLSQYDFPGDDTPIVRGSALKALE
GDAEWEAKILELAGFLDSYIPEPERAIDKPFLLPIEDVFSISGRGTVVTGRVERGIIKVG
EEVEIVGIKETQKSTCTGVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQVLAKPGTIK
PHTKFESEVYILSKDEGGRHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMVMPGDNIKMV
VTLIHPIAMDDGLRFAIREGGRTVGAGVVAKVLS

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2
GNP	Phosphoaminophosphonic acid-guanylate ester	C10 H17 N6 O13 P3	2

Water and common crystallization additives (PEG, SO4, GOL) are not listed.

Primary citation

E. coli elongation factor Tu bound to a GTP analogue displays an open conformation equivalent to the GDP-bound form. Johansen, J.S., Kavaliauskas, D., Pfeil, S.H. et al. Nucleic Acids Res (2018) 46:8641-8650. DOI 10.1093/nar/gky697 · PubMed

Other PDB entries of the same protein (UniProt P0CE48 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2BVN 2.3 Å, E. coli EF-Tu:GDPNP in complex with the antibiotic enacyloxin IIa
9T38 2.45 Å, Rhs2-CT endonuclease toxin in complex with cognate immunity protein RhsI2 and EF-Tu
1DG1 2.5 Å, Whole, unmodified, ef-tu(elongation factor tu).
1EFU 2.5 Å, Elongation factor complex ef-tu/ef-ts from escherichia coli
3MMP 2.5 Å, Structure of the Qb replicase, an RNA-dependent RNA polymerase consisting of viral and…
1EFM 2.7 Å, Structure of the GDP domain of ef-tu and location of the amino acids homologous to ras…
8QFS 2.7 Å, Cryo-EM structure of SidH from Legionella pneumophila
5AFI 2.9 Å, 2.9A Structure of E. coli ribosome-EF-TU complex by cs-corrected cryo-EM
5WDT 3.0 Å, 70S ribosome-EF-Tu H84A complex with GppNHp
5WFS 3.0 Å, 70S ribosome-EF-Tu H84A complex with GTP and near-cognate tRNA (Complex C4)
5WE4 3.1 Å, 70S ribosome-EF-Tu wt complex with GppNHp
8G7Q 3.1 Å, Structure of the Escherichia coli 70S ribosome in complex with EF-Tu and…

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