6Y69

Cryo-EM structure of an Escherichia coli 70S ribosome in complex with antibiotic TetracenomycinX

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	A (a)	16S ribosomal RNA	polymer	1539	498725.4	1	GenBank (1108591457)	Escherichia coli (strain K12)
2	B (b)	30S ribosomal protein S2	polymer	218	24253.9	1	UniProt (P0A7V0) Pfam (PF00318)	Escherichia coli (strain K12)	Small ribosomal subunit protein uS2
3	C (c)	30S ribosomal protein S3	polymer	206	23078.8	1	UniProt (P0A7V3) Pfam (PF07650) Pfam (PF00189)	Escherichia coli (strain K12)	Small ribosomal subunit protein uS3
4	D (d)	30S ribosomal protein S4	polymer	205	23383.0	1	UniProt (P0A7V8) Pfam (PF00163) Pfam (PF01479)	Escherichia coli (strain K12)	Small ribosomal subunit protein uS4
5	E (e)	30S ribosomal protein S5	polymer	157	16532.1	1	UniProt (P0A7W1) Pfam (PF00333) Pfam (PF03719)	Escherichia coli (strain K12)	Small ribosomal subunit protein uS5
6	F (f)	30S ribosomal protein S6	polymer	100	11669.4	1	UniProt (P02358) Pfam (PF01250)	Escherichia coli (strain K12)	Small ribosomal subunit protein bS6
7	G (g)	30S ribosomal protein S7	polymer	155	17506.2	1	UniProt (P02359) Pfam (PF00177)	Escherichia coli (strain K12)	Small ribosomal subunit protein uS7
8	H (h)	30S ribosomal protein S8	polymer	129	14015.4	1	UniProt (P0A7W7) Pfam (PF00410)	Escherichia coli (strain K12)	Small ribosomal subunit protein uS8
9	I (i)	30S ribosomal protein S9	polymer	127	14554.9	1	UniProt (P0A7X3) Pfam (PF00380)	Escherichia coli (strain K12)	Small ribosomal subunit protein uS9
10	J (j)	30S ribosomal protein S10	polymer	98	11197.0	1	UniProt (P0A7R5) Pfam (PF00338)	Escherichia coli (strain K12)	Small ribosomal subunit protein uS10
11	K (k)	30S ribosomal protein S11	polymer	116	12388.1	1	UniProt (P0A7R9) Pfam (PF00411)	Escherichia coli (strain K12)	Small ribosomal subunit protein uS11
12	L (l)	30S ribosomal protein S12	polymer	123	13637.0	1	UniProt (P0A7S3) Pfam (PF00164)	Escherichia coli (strain K12)	Small ribosomal subunit protein uS12
13	M (m)	30S ribosomal protein S13	polymer	114	12625.8	1	UniProt (P0A7S9) Pfam (PF00416)	Escherichia coli (strain K12)	Small ribosomal subunit protein uS13
14	N (n)	30S ribosomal protein S14	polymer	101	11546.4	1	UniProt (P0AG59) Pfam (PF00253)	Escherichia coli (strain K12)	Small ribosomal subunit protein uS14
15	O (o)	30S ribosomal protein S15	polymer	88	10159.6	1	UniProt (P0ADZ4) Pfam (PF00312)	Escherichia coli (strain K12)	Small ribosomal subunit protein uS15
16	P (p)	30S ribosomal protein S16	polymer	82	9207.6	1	UniProt (P0A7T3) Pfam (PF00886)	Escherichia coli (strain K12)	Small ribosomal subunit protein bS16
17	Q (q)	30S ribosomal protein S17	polymer	80	9263.9	1	UniProt (P0AG63) Pfam (PF00366)	Escherichia coli (strain K12)	Small ribosomal subunit protein uS17
18	R (r)	30S ribosomal protein S18	polymer	65	7606.8	1	UniProt (P0A7T7) Pfam (PF01084)	Escherichia coli (strain K12)	Small ribosomal subunit protein bS18
19	S (s)	30S ribosomal protein S19	polymer	79	9057.6	1	UniProt (P0A7U3) Pfam (PF00203)	Escherichia coli (strain K12)	Small ribosomal subunit protein uS19
20	T (t)	30S ribosomal protein S20	polymer	85	9506.2	1	UniProt (P0A7U7) Pfam (PF01649)	Escherichia coli (strain K12)	Small ribosomal subunit protein bS20
21	U (u)	30S ribosomal protein S21	polymer	65	7763.1	1	UniProt (P68679) Pfam (PF01165)	Escherichia coli (strain K12)	Small ribosomal subunit protein bS21
22	V (A)	23S ribosomal RNA	polymer	2903	941305.3	1	GenBank (939732440)	Escherichia coli (strain K12)
23	W (B)	5S ribosomal RNA	polymer	120	38813.1	1	GenBank (1373146531)	Escherichia coli (strain K12)
24	X (C)	50S ribosomal protein L2	polymer	271	29663.2	1	UniProt (P60422) Pfam (PF00181) Pfam (PF03947)	Escherichia coli (strain K12)	Large ribosomal subunit protein uL2
25	Y (D)	50S ribosomal protein L3	polymer	209	22277.5	1	UniProt (P60438) Pfam (PF00297)	Escherichia coli (strain K12)	Large ribosomal subunit protein uL3
26	Z (E)	50S ribosomal protein L4	polymer	201	22121.6	1	UniProt (P60723) Pfam (PF00573)	Escherichia coli (strain K12)	Large ribosomal subunit protein uL4
27	AA (F)	50S ribosomal protein L5	polymer	177	20073.2	1	UniProt (P62399) Pfam (PF00281) Pfam (PF00673)	Escherichia coli (strain K12)	Large ribosomal subunit protein uL5
28	BA (G)	50S ribosomal protein L6	polymer	176	18801.6	1	UniProt (P0AG55) Pfam (PF00347)	Escherichia coli (strain K12)	Large ribosomal subunit protein uL6
29	CA (H)	50S ribosomal protein L9	polymer	79	8258.3	1	UniProt (P0A7R1) Pfam (PF03948)	Escherichia coli (strain K12)	Large ribosomal subunit protein bL9
30	DA (J)	50S ribosomal protein L13	polymer	142	16050.6	1	UniProt (P0AA10) Pfam (PF00572)	Escherichia coli (strain K12)	Large ribosomal subunit protein uL13
31	EA (K)	50S ribosomal protein L14	polymer	122	13451.9	1	UniProt (P0ADY3) Pfam (PF00238)	Escherichia coli (strain K12)	Large ribosomal subunit protein uL14
32	FA (L)	50S ribosomal protein L15	polymer	143	14877.3	1	UniProt (P02413) Pfam (PF00828)	Escherichia coli (strain K12)	Large ribosomal subunit protein uL15
33	GA (M)	50S ribosomal protein L16	polymer	136	15312.3	1	UniProt (P0ADY7) Pfam (PF00252)	Escherichia coli (strain K12)	Large ribosomal subunit protein uL16
34	HA (N)	50S ribosomal protein L17	polymer	120	13721.9	1	UniProt (P0AG44) Pfam (PF01196)	Escherichia coli (strain K12)	Large ribosomal subunit protein bL17
35	IA (O)	50S ribosomal protein L18	polymer	116	12663.5	1	UniProt (P0C018) Pfam (PF00861)	Escherichia coli (strain K12)	Large ribosomal subunit protein uL18
36	JA (P)	50S ribosomal protein L19	polymer	114	13028.1	1	UniProt (P0A7K6) Pfam (PF01245)	Escherichia coli (strain K12)	Large ribosomal subunit protein bL19
37	KA (Q)	50S ribosomal protein L20	polymer	117	13396.8	1	UniProt (P0A7L3) Pfam (PF00453)	Escherichia coli (strain K12)	Large ribosomal subunit protein bL20
38	LA (R)	50S ribosomal protein L21	polymer	103	11586.4	1	UniProt (P0AG48) Pfam (PF00829)	Escherichia coli (strain K12)	Large ribosomal subunit protein bL21
39	MA (S)	50S ribosomal protein L22	polymer	110	12253.4	1	UniProt (P61175) Pfam (PF00237)	Escherichia coli (strain K12)	Large ribosomal subunit protein uL22
40	NA (T)	50S ribosomal protein L23	polymer	93	10546.5	1	UniProt (P0ADZ0) Pfam (PF00276)	Escherichia coli (strain K12)	Large ribosomal subunit protein uL23
41	OA (U)	50S ribosomal protein L24	polymer	102	11078.9	1	UniProt (P60624) Pfam (PF00467) Pfam (PF17136)	Escherichia coli (strain K12)	Large ribosomal subunit protein uL24
42	PA (V)	50S ribosomal protein L25	polymer	94	10713.5	1	UniProt (P68919) Pfam (PF01386)	Escherichia coli (strain K12)	Large ribosomal subunit protein bL25
43	QA (W)	50S ribosomal protein L27	polymer	75	8174.4	1	UniProt (P0A7L8) Pfam (PF01016)	Escherichia coli (strain K12)	Large ribosomal subunit protein bL27
44	RA (X)	50S ribosomal protein L28	polymer	77	8896.4	1	UniProt (P0A7M2) Pfam (PF00830)	Escherichia coli (strain K12)	Large ribosomal subunit protein bL28
45	SA (Y)	50S ribosomal protein L29	polymer	63	7286.5	1	UniProt (P0A7M6) Pfam (PF00831)	Escherichia coli (strain K12)	Large ribosomal subunit protein uL29
46	TA (Z)	50S ribosomal protein L30	polymer	58	6423.6	1	UniProt (P0AG51) Pfam (PF00327)	Escherichia coli (strain K12)	Large ribosomal subunit protein uL30
47	UA (0)	50S ribosomal protein L32	polymer	56	6332.2	1	UniProt (P0A7N4) Pfam (PF01783)	Escherichia coli (strain K12)	Large ribosomal subunit protein bL32
48	VA (1)	50S ribosomal protein L33	polymer	50	5814.8	1	UniProt (P0A7N9) Pfam (PF00471)	Escherichia coli (strain K12)	Large ribosomal subunit protein bL33
49	WA (2)	50S ribosomal protein L34	polymer	46	5397.5	1	UniProt (P0A7P5) Pfam (PF00468)	Escherichia coli (strain K12)	Large ribosomal subunit protein bL34
50	XA (3)	50S ribosomal protein L35	polymer	64	7181.8	1	UniProt (P0A7Q1) Pfam (PF01632)	Escherichia coli (strain K12)	Large ribosomal subunit protein bL35,Ribosomal protein A
51	YA (4)	50S ribosomal protein L36	polymer	38	4377.4	1	UniProt (P0A7Q6) Pfam (PF00444)	Escherichia coli (strain K12)	Large ribosomal subunit protein bL36-A,Ribosomal protein B
52	ZA (6)	50S ribosomal protein L31	polymer	66	7516.7	1	UniProt (P0A7M9) Pfam (PF01197)	Escherichia coli (strain K12)	Large ribosomal subunit protein bL31-A
53	AB (w)	E-site tRNA	polymer	77	24771.8	1	GenBank (1789840096)	Escherichia coli (strain K12)
54	BB (x)	Ribosome hibernation promoting factor	polymer	95	10768.2	1	UniProt (P0AFX0) Pfam (PF02482)	Escherichia coli (strain K12)	HPF,Hibernation factor HPF
55	CB (A)	Tetracenomycin X	non-polymer		486.4	1	Chemie (OCW)
56	DB, EB (A)	MAGNESIUM ION	non-polymer		24.3	2	Chemie (MG)

Sequence modifications

n: 1 - 101 (UniProt: P0AG59)

PDB	External Database	Details
Ala 35	-	insertion

A: 1 - 2903 (GenBank: 939732440)

PDB	External Database	Details
C 747	U 4191431	conflict
G 1847	A 4192531	conflict
A 2069	G 4192753	conflict

B: 1 - 120 (GenBank: 1373146531)

PDB	External Database	Details
A 120	U 4247873	conflict

w: 1 - 76 (GenBank: 1789840096)

PDB	External Database	Details
U 29	G 2435360	conflict
A 41	C 2435372	conflict

x: 1 - 95 (UniProt: P0AFX0)

PDB	External Database	Details
Asp 57	Asn 57	conflict
Leu 61	Ile 61	conflict

Contents of the asymmetric unit

Polymers	Number of chains	54
	Total formula weight	2140614.2
Non-Polymers*	Number of molecules	3
	Total formula weight	535.0
All*	Total formula weight	2141149.2

*Water molecules are not included.