5VP2

Crystal structure of the Thermus thermophilus 70S ribosome in complex with madumycin II and bound to mRNA and A-, P- and E-site tRNAs at 2.8A resolution

This is a non-PDB format compatible entry.

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	1A, 2A	23S Ribosomal RNA	polymer	2915	948035.6	2	GenBank (55771382)	Thermus thermophilus HB8
2	1B, 2B	5S ribosomal RNA	polymer	121	39188.4	2	GenBank (55771382)	Thermus thermophilus HB8
3	1D, 2D	50S ribosomal protein L2	polymer	276	30532.6	2	UniProt (P60405) Pfam (PF00181) Pfam (PF03947) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
4	1E, 2E	50S ribosomal protein L3	polymer	206	22450.2	2	UniProt (Q5SHN8) Pfam (PF00297) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
5	1F, 2F	50S ribosomal protein L4	polymer	210	23271.9	2	UniProt (Q5SHN9) Pfam (PF00573) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	L1e
6	1G, 2G	50S ribosomal protein L5	polymer	182	21061.6	2	UniProt (Q5SHQ0) Pfam (PF00281) Pfam (PF00673) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
7	1H, 2H	50S ribosomal protein L6	polymer	180	19568.9	2	UniProt (P0DOY8) Pfam (PF00347) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
8	1I, 2I	50S ribosomal protein L9	polymer	148	16422.2	2	UniProt (Q5SLQ1) Pfam (PF01281) Pfam (PF03948) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
9	1N, 2N	50S ribosomal protein L13	polymer	140	15927.9	2	UniProt (P60488) Pfam (PF00572) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
10	1O, 2O	50S ribosomal protein L14	polymer	122	13323.6	2	UniProt (Q5SHP8) Pfam (PF00238) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
11	1P, 2P	50S ribosomal protein L15	polymer	150	16319.1	2	UniProt (Q5SHQ7) Pfam (PF00828) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
12	1Q, 2Q	50S ribosomal protein L16	polymer	141	15993.9	2	UniProt (P60489) Pfam (PF00252) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
13	1R, 2R	50S ribosomal protein L17	polymer	118	13750.1	2	UniProt (Q9Z9H5) Pfam (PF01196) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
14	1S, 2S	50S ribosomal protein L18	polymer	112	12639.8	2	UniProt (Q5SHQ4) Pfam (PF00861) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	TL24
15	1T, 2T	50S ribosomal protein L19	polymer	146	17188.8	2	UniProt (P60490) Pfam (PF01245) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
16	1U, 2U	50S ribosomal protein L20	polymer	118	13779.3	2	UniProt (P60491) Pfam (PF00453) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
17	1V, 2V	50S ribosomal protein L21	polymer	101	11069.2	2	UniProt (P60492) Pfam (PF00829) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
18	1W, 2W	50S ribosomal protein L22	polymer	113	12808.1	2	UniProt (Q5SHP3) Pfam (PF00237) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
19	1X, 2X	50S ribosomal protein L23	polymer	96	10759.8	2	UniProt (Q5SHP0) Pfam (PF00276) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
20	1Y, 2Y	50S ribosomal protein L24	polymer	110	12085.6	2	UniProt (Q5SHP9) Pfam (PF00467) Pfam (PF17136) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
21	1Z, 2Z	50S ribosomal protein L25	polymer	206	23238.6	2	UniProt (Q5SHZ1) Pfam (PF01386) Pfam (PF14693) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	TL5
22	10, 20	50S ribosomal protein L27	polymer	85	9529.1	2	UniProt (P60493) Pfam (PF01016) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
23	11, 21	50S ribosomal protein L28	polymer	98	11004.2	2	UniProt (P60494) Pfam (PF00830) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
24	12, 22	50S ribosomal protein L29	polymer	72	8670.3	2	UniProt (Q5SHP6) Pfam (PF00831) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
25	13, 23	50S ribosomal protein L30	polymer	60	6799.1	2	UniProt (Q5SHQ6) Pfam (PF00327) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
26	14, 24	50S ribosomal protein L31	polymer	71	8300.5	2	UniProt (Q5SJE1) Pfam (PF01197) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
27	15, 25	50S ribosomal protein L32	polymer	60	6722.1	2	UniProt (P80339) Pfam (PF01783) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
28	16, 26	50S ribosomal protein L33	polymer	54	6632.9	2	UniProt (P35871) Pfam (PF00471) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
29	17, 27	50S ribosomal protein L34	polymer	49	6132.4	2	UniProt (P80340) Pfam (PF00468) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
30	18, 28	50S ribosomal protein L35	polymer	65	7506.2	2	UniProt (Q5SKU1) Pfam (PF01632) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
31	19, 29	50S ribosomal protein L36	polymer	37	4435.4	2	UniProt (Q5SHR2) Pfam (PF00444) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Ribosomal protein B
32	1a, 2a	16S ribosomal RNA	polymer	1521	493864.6	2	GenBank (55771382)	Thermus thermophilus HB8
33	1b, 2b	30S ribosomal protein S2	polymer	256	29317.7	2	UniProt (P80371) Pfam (PF00318) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
34	1c, 2c	30S ribosomal protein S3	polymer	239	26751.1	2	UniProt (P80372) Pfam (PF07650) Pfam (PF00189) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
35	1d, 2d	30S ribosomal protein S4	polymer	209	24373.4	2	UniProt (P80373) Pfam (PF00163) Pfam (PF01479) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
36	1e, 2e	30S ribosomal protein S5	polymer	162	17583.4	2	UniProt (Q5SHQ5) Pfam (PF00333) Pfam (PF03719) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
37	1f, 2f	30S ribosomal protein S6	polymer	101	11988.8	2	UniProt (Q5SLP8) Pfam (PF01250) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	TS9
38	1g, 2g	30S ribosomal protein S7	polymer	156	18051.0	2	UniProt (P17291) Pfam (PF00177) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
39	1h, 2h	30S ribosomal protein S8	polymer	138	15868.6	2	UniProt (P0DOY9) Pfam (PF00410) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
40	1i, 2i	30S ribosomal protein S9	polymer	128	14410.6	2	UniProt (P80374) Pfam (PF00380) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
41	1j, 2j	30S ribosomal protein S10	polymer	105	11955.0	2	UniProt (Q5SHN7) Pfam (PF00338) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
42	1k, 2k	30S ribosomal protein S11	polymer	129	13737.9	2	UniProt (P80376) Pfam (PF00411) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
43	1l, 2l	30S ribosomal protein S12	polymer	132	14683.5	2	UniProt (Q5SHN3) Pfam (PF00164) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
44	1m, 2m	30S ribosomal protein S13	polymer	126	14338.9	2	UniProt (P80377) Pfam (PF00416) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
45	1n, 2n	30S ribosomal protein S14 type Z	polymer	61	7158.7	2	UniProt (P0DOY6) Pfam (PF00253) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
46	1o, 2o	30S ribosomal protein S15	polymer	89	10578.4	2	UniProt (Q5SJ76) Pfam (PF00312) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
47	1p, 2p	30S ribosomal protein S16	polymer	88	10410.0	2	UniProt (Q5SJH3) Pfam (PF00886) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
48	1q, 2q	30S ribosomal protein S17	polymer	105	12325.7	2	UniProt (P0DOY7) Pfam (PF00366) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
49	1r, 2r	30S ribosomal protein S18	polymer	88	10258.3	2	UniProt (Q5SLQ0) Pfam (PF01084) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
50	1s, 2s	30S ribosomal protein S19	polymer	93	10605.5	2	UniProt (Q5SHP2) Pfam (PF00203) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
51	1t, 2t	30S ribosomal protein S20	polymer	106	11736.1	2	UniProt (P80380) Pfam (PF01649) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
52	1u, 2u	30S ribosomal protein Thx	polymer	27	3350.0	2	UniProt (Q5SIH3) Pfam (PF17070) In PDB	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	S31
53	1v, 2v	mRNA	polymer	24	7804.7	2		Enterobacteria phage T4
54	1w, 1y, 2w, 2y	A-site and E-site tRNAs	polymer	76	24645.9	4		Escherichia coli
55	1x, 2x	P-site tRNA	polymer	77	24846.9	2		Escherichia coli
56	1A, 1X, 2A, 2a, 12...	MAGNESIUM ION	non-polymer		24.3	2803	Chemie (MG)
57	1A, 2A	POTASSIUM ION	non-polymer		39.1	2	Chemie (K)
58	1A, 2A	Madumycin II	non-polymer		503.6	2	Chemie (M2D)
59	24, 25, 14, 15, 1Y...	ZINC ION	non-polymer		65.4	12	Chemie (ZN)
60	2d, 1d	IRON/SULFUR CLUSTER	non-polymer		351.6	2	Chemie (SF4)
61		water	water		18.0	5149	Chemie (HOH)

Contents of the asymmetric unit

Polymers	Number of chains	112
	Total formula weight	4500875.7
Non-Polymers*	Number of molecules	2821
	Total formula weight	70700.5
All*	Total formula weight	4571576.2

*Water molecules are not included.