Elongation factor

Elongation factors (EF) facilitate translational elongation during the formation of peptide bonds in the ribosome. EF-selB is selenocysteine-specific EF. EF-Tu or EF 1-α (elongation factor thermo unstable) is a prokaryotic EF. EF-Tu contributes to translational accuracy. It catalyzes the addition of aminoacyl tRNA. EF-Ts or EF 1-β (elongation factor thermo stable) catalyzes the release of GDP from EF-Tu. EF-G translocates the peptidyl tRNA from the A site to the P site while moving the mRNA through the ribosome. EF-SII helps RNA polymerase II to bypass blocks to elongation. EF-ELL2 enhances polyadenylation and exon skipping with the gene encoding the immunoglobulin heavy-chain complex. EF-GreA or GreB are cleavage factors allowing the resumption of elongation. EF-NusA recruits translesion DNA polymerases to gaps encountered during translation. EF-P alters the ribosome affinity to aminoacyl-tRNA. EF-1 gamma acts during the delivery of aminoacyl tRNA to the ribosome. EF-2 promotes the translocation of the nascent protein chain from the A site to the P site on the ribosome. EF-3 is unique EF in fungi hence it provides an anti-fungal drug target. EF Spt4, Spt5, Spt6 are conserved among eukaryotes. They modulate the chromatin structure. EF-CA150 is believed to play a role in coupling transcription and splicing. The elongin B and C complex is involved in the proteasomal degredation of target proteins.

3D structures of elongation factor

EF-Tu

1efm, 1efc, 1dg1, 2fx3 – EcEF – Escherichia coli
1qzd – EcEF – Cryo EM
3u2q – EcEF + drug
1mj1 – EcEF + Phe-tRNA + S12 + S13 + L11 – Cryo EM
1ttt, 1ob5 – TaEF + Phe-tRNA + GDPNP - Thermus aquaticus
1b23 - TaEF + Cys-tRNA
1ls2 – yEF + Phe-tRNA – yeast – Cryo EM
3agj – EF + plethora protein – Aeropyrum pernix

EF-Tu complex with antibiotics

1ob2 - yEF + Phe-tRNA + antibiotic

4abr - TtEF + antibiotic in 30S ribosome
1ha3 - TtEF + antibiotic + GDP
2c77, 2c78 - TtEF + antibiotic + GTP analog
3fic, 3fic – TtEF + antibiotic in 70S ribosome – Cryo EM
2bvn - EcEF + GDP
NP + antibiotic
1d8t, 2hcj, 2hdn, 3u6b, 3u6k – EcEF + antibiotic

EF-Tu complex with nucleotide

1efu – EcEF + GDP

1exm – TtEF + GTP analog
1eft – TaEF + GNP – Thermus aquaticus
1tui – TaEF + GDP
1d2e – bEF + GDP – bovine
1jny, 1skq – SsEF + GDP – Sulfolobus solfataricus

EF-Tu with EF-Ts

1efu – EcEF + EcEF-Ts

1aip - TtEF + TtEF-Ts - Thermus thermophilus
1xb2 – bEF + EF-Ts - bovine
1f60 – yEF + EF-Ts C terminal
1g7c - yEF + EF-Ts C terminal + GDPNP
1ije, 1ijf - yEF + EF-Ts C terminal + GDP
2b7b - yEF + EF-Ts C terminal (mutant) + GDP
2b7c - yEF + EF-Ts C terminal (mutant)

EF-Tu in the ribosome

3eq3, 3eq4 – EcEF in 80S ribosome – Cryo EM

3izv, 3izw - EcEF in 30S ribosome – Cryo EM
1zc8, 3dwu – TtEF in 70S ribosome – Cryo EM
2wrn, 2wrq, 2xqd, 2y0u, 2y0w, 2y0y, 2y10, 2y12, 2y14, 2y16, 2y18 - TtEF in 70S ribosome

EF-SII

1tfi – hEF – human – NMR
3ndq - hEF domain II
1enw – yEF domain II – NMR
1eo0 - yEF domain I – NMR
2xex – SaEF – Staphylococcus aureus
1pqv, 1y1v – yEF + RNA polymerase II
1y1y, 3gtm – yEF + RNA polymerase II + RNA
1wjt – mEF N terminal – mouse – NMR

EF-ELL2

2e5n – hEF N2 domain - NMR

EF-G

1efg, 1elo, 1ktv, 1wdt, 2dy1 – TtEF
1pn6, 3izp – TtEF – Cryo EM
1fnm, 2bm0, 2bm1 – TtEF (mutant)
2xex – SaEF
3zz0, 3zzt, 3zzu – SaEF (mutant)
2bv3 - TtEF (mutant) + GTP analog
2j7k - TtEF (mutant) + GDP analog
2om7, 2wri, 2wrk – TtEF in 70S ribosome – Cryo EM
2xsy, 2xuy - TtEF in 70S ribosome
1dar, 2efg – TtEF + GDP
1jqm, 1jqs – EcEF + L11 – Cryo EM
1zn0, 2rdo, 3j0e, 3j18 – EcEF in 30S ribosome – Cryo-EM

EF-GreA/GreB

2pn0 – EF – Nitrosomonas europaea
2p4v – EcEF-GreB

EF-NusA

1wcl, 1wcn – EcEF C terminal – NMR
2kwp - EcEF N terminal – NMR
2jzb – EcEF + RNA polymerase subunit α - NMR

EF-P

1ueb – TtEF
3huw, 3huy – TtEF in 70S ribosome
3oyy – EF – Pseudomonas aeruginosa
3a5z – EcEF + lysyl-tRNA synthetase

EF-Ts

1tfe – TtEF
1b64 – hEF guanine exchange factor domain – NMR
2cp9 – UBA domain – NMR
1gh8 – EF – Methanobacterium thermoautotrophicum – NMR
2yy3 – EF – Pyrococcus horikoshii
2uz8 – hEF (mutant)

EF-1G

1nhy – yEF N terminal 1pbu – hEF C terminal (mutant) - NMR

EF-2

1n0v – yEF
1u2r – yEF + GDP
1n0u, 2e1r, 2npf – yEF + antifungal drug
1zm2, 1zm3, 1zm4, 1zm9, 3b78, 3b82, 3b8h, 2zit – yEF + exotoxin
1s1h - yEF + antifungal drug in 40S ribosome – Cryo EM
2p8w, 2p8x, 3dny - yEF in 80S ribosome – Cryo EM
2p8y, 2p8z - yEF+ antifungal drug in 80S ribosome – Cryo EM

EF-3

2ix3 – yEF
2iwh – yEF + ADPNP
2iw3 – yEF + ADP
2ix8 – yEF in 80S ribosome – Cryo EM

EF-SelB

1lva – MtEF C terminal – Moorella thermoacetica
2v9v – MtEF winged helix domain
1wsu, 2uwm – MtEF + RNA
2ply – MtEF (mutant) + RNA
1wb2 – MmEF – Methanococcus maripaludis
1wb3 – MmEF + GTP analog
4ac9 – MmEF + GDP
2pjp – EcEF + RNA

EF-Spt5

2do3, 2e6z, 2e70 – hEF KOW motif – NMR
2exu – yEF
3h7h – hEF + hEF-Spt4

EF-Spt6

3gxw, 3gxx, 3pjp – EF SH2 domain – Candida glabrata
3psf, 3psi – yEF core domain
3psj, 3psk – yEF SH2 domain
2l3t - yEF SH2 domain]] - NMR
3oak – yEF + transcription factor IWS1

EF-CA150

2dod, 2doe, 2dof, 2e71, 2kiq, 2kis – hEF FF domain – NMR
3hfh – hEF FF domain
2ysi– mEF WW domain - NMR

Elongin BC complex

1lqb – hEloBC + von-Hippel Lindau disease tumor suppressor + hypoxia inducible factor 1 α
3zrc, 3ztc, 3ztd, 3zun - hEloBC + von-Hippel Lindau disease tumor suppressor + inhibitor
3zrf - hEloBC + von-Hippel Lindau disease tumor suppressor
2c9w, 2izv, 2jz3 – hEloBC + suppressor of cytokine signaling
3dcg – hEloBC + virion infectivity factor
2xai - hEloBC + ankyrin repeat
2fnj - mEloBC + GUSTAVUS