. Author manuscript; available in PMC: 2017 May 22.

Published in final edited form as: J Mol Biol. 2016 Feb 13;428(10 Pt B):2146–2164. doi: 10.1016/j.jmb.2016.02.009

Table 2.

Summary of molecular interactions of the intersubunit bridges

	T. thermophilus¹					E. coli²
Bridge	30S component(s)		50S component(s)		Interaction³	30S component(s)		50S component(s)		Interaction³
B1a	S13	Arg92, Arg93	H38	A887, C888	Side-P	S13	Arg91, Arg92	H38	Disordered
B1b	S13	Ile8	L5	Tyrl45	Side-side	S13	Ile8	L5	Tyrl42	Side-side
		Arg10		Asp146	Side-side		No interaction
		Disordered					Asp67		Arg114	Side-side
		Disordered					Arg69, Arg70		Asp112	Side-side
		No interaction					Arg2	L31	Asn33	Side-back
		Arg56	L31	Glu60	Side-side		Arg56	L31	Asp35	Side-side
B1c			L31 Disordered			S14	Trp42	L31	Val57, Phe60, Phe64	Side-side (Hydrophobic)
						S19	Pro8, Phe40, Pro41, Val66		Val57, Phe60, Phe64	Side-side (Hydrophobic)
						S19	Glu64		Arg56	Back-side
						h42	A1311, G1312		Arg63	Back-side
B2a/d	h44	U1406, U1495	H69	A1919 A1912	Base-ribose	Same as T. thermophilus
		C1407-G1494		A1912	A-minor
		A1408		A1916	Ribose-base
		A1410		C1914	P-base
		C1409		C1914, U1915	Ribose-base	Missing, distance change due to lack of A-site tRNA
	Missing, conformational change due to A-site tRNA binding					h44	A1492	H69	A1913	Base-base
	h24	U793, G1517	H69	C1920	Mg	No Mg
	h45	G1517		A1919	Base-ribose	Same as T. thermophilus
	S13	Argl24		A1912, A1913	Mg	No Mg, phylogenetic difference
B2b	h24	C783	H68	C1836	Ribose-P	Same as T. thermophilus
B2b	Missing, distance change due to A-site tRNA binding					h45	G1516	H71	U1931	P-ribose
B2c	h27	C899	H67	C1832	Minor-P	Same as T. thermophilus
	h24	C770		C1833	Mg	No Mg
	h24	C770, G771, C899		C1832, C1833	Mg
	h27	A900, A901		C1832	Mg
B3	h44	A1483	H71	C1947-G1959	A-minor	Same as T. thermophilus
		C1484		A1960	Ribose-ribose
		A1418		G1948-C1958	A-minor
		G1419		G1949	Ribose-ribose
		G1421		G1950, U1951	Mg	NoMg
		G1421	L14	Glu54	Mg	h44	G1421	L14	Lys54	P-side
		G1423	L14	Arg49	P-side	Same as T. thermophilusss
B4	S15	Ser39, His52	H34	G715	Side-base	S15	Gln39	H34	A715	Side-base
		Arg63		G715	Side-P		Arg88		U714, A715	Side-P
		Lys43		A716	Side-ribose		Gln39		A716	Side-ribose
B5	Missing, distance difference					h44	A1428	H62	C1686	Ribose-base
	Missing, distance difference						A1428		G1703	Ribose-ribose
	h44	C1429, C1430	H62	G1703, G1704	Mg		A1429		G1703	Ribose-ribose
							A1429		C1704	Ribose-P
		G1475		A1689	P-ribose	Missing, distance difference
		G1475		A1700	P-base	Same as T. thermophilus
B6	h44	G1432	L19	Argl08	P-back	h44	G1432	L19	Lysl05	P-back
B6	h44	No interaction	L19			h44	A1433	L19		P-side
B6	h44	G1464, C1465	L19	Argl08	P-side	h44	U1463, U1464	L19	Argl08	P-side
		C1463		Arg111, Arg115	P-side	Phylogenetic difference
		G1442, A1444		Arg118	Side-side
		G1443		Asp122	Ribose-side
		G1443	H101	C2864	Base-P
B6R⁴	H44	No interaction	L19			h44	A1431	L19	Thrl03	P-side
		No interaction					G1432		Glyl04, Lysl05	P-back
		G1443		Ilel21, Aspl22, Argl25	Base-back/side		A1441		Glu111	Base-side
		G1464		Arg111	P-side		U1463, U1464		Argl08	P-side
		C1465		Argl08	P-side
	Phylogenetic difference						U1471	L14	Argl7	P-side
B7a	h23	A702	H68	A1848	Stacking, P- ribose	Same as T. thermophilics
B7a	h23		H68	G1846-C1894	A-minor	Same as T. thermophilics
B7aR⁴	H23	A702	H68	G1846, A1847	Base-P	H23	A702	H68	G1846	Base-P
B7b	h23	A712	L2	Glnl63, Glnl65	P-side	H23	A712	L2	Glnl62	P-side
B7b	h23	No interaction	L2			H23	C680	L2	Arg268	Ribose-Side
B7b	h24	G774	L2	Lys201	P-side	h24	G774	L2	Met200	P-side
B7b	h24	No interaction					G775		Argl76	P-side
B7bR⁴	h23	C680	L2	Glnl65	Ribose-side	Missing, distance difference
		C681		Argl67	Ribose-back	Missing, distance difference
		G711		Glyl38	Ribose-back	h23	G711	L2	Glyl37	Ribose-back
		A712		Glnl63	Ribose-side	h23	A712	L2	Glnl62	Ribose-side
B7bR⁴	h24	G773		Asn202	P-side	h24	U772		Lys4	P-side
B7bR⁴	h24	G774, G775		Lys201	P-side	h24	G773, G774		Met200, Leu201	P-side
B8	h14	A338, C339	L14	Asn13, Arg97	P-side	h14	C339	L14	Asn13	P-side
		U340		Thr96	P-side		U340		Thr97	P-side
		No interaction					C341		Arg98	P-side
		C345		Val115, Ser116, Ala118	Mg	No Mg
		G346		Argl07	P-side	h14	G346	L14	Argl05	P-side
		No interaction	L19				C345	L19	Arg38	P-side
		G346	L19	Lys35, Arg41	P-side		G346	L19	Arg38, Gln40	P-side
B8R⁴	h14	C337, A338	L14	Arg97	P-side	h14	A338, C339	L14	Arg98	P-side
		C339		Thr96	P-side		U340		Thr97	P-side
		A338, C339		Asn13	P-side		No interaction
		C345		Arg107	P-side		C345		Argl08	Ribose-side
B8R⁴						h14	C345	L19	Ser35, Lys36	P-back/side
							G346	L14	Argl05, Argl08	P-side
	No interaction, phylogenetic difference							L19	Glu33	Ribose-side
									Gly34	P-back
						h8	G159		Arg38	P-side
NewR⁴	S7	Argl42	H76	G2115	Side-P	S7	Argl42	H78	A2147	Side-P

Classic-state T. thermophilus bridges are assigned according to the structure of ribosome in the pre-peptidyl-transfer state [PDB entries 2WDK and 2WDL, Voorhees et al. 2009].

Classic-state E.coli bridges are assigned according to the structure of ribosome bound with a P-site tRNA [PDB entries 3R8O and 3R8T, Dunkle et al. 2011], except that B1b, B1c, and B7b are inferred from the structure of a decoding complex bound with the ternary complex and P- and E-site tRNAs [EMDB entry EMD-2847, Fischer et al. 2015].

The detailed molecular interaction(s) between 30S-50S components. For protein components: side, side chains; back, backbone. For RNA components: P, phosphate backbone; A-minor, interaction of an adenine with the minor groove. Mg, Mg²⁺-coordinated interaction.

⁴

Bridge interactions in the rotated conformation are assigned according to the structure of RF3-bound [T. thermophilus, PDB entries 3ZVO and 3ZVP, Jin et al. 2011] or RRF-bound [E.coli, PDB entries 3R8N and 3R8S, Dunkle et al. 2011] ribosome with a P/E-site tRNA.