Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

9ZNG

Cryo-EM structure of the Methanosarcina acetivorans 70S ribosome in complex with SriD

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 (1)	23S rRNA	polymer	2904	939362.9	1	GenBank (470469544)	Methanosarcina acetivorans
2	B (2)	5S rRNA	polymer	133	42646.3	1	GenBank (19918815)	Methanosarcina acetivorans
3	C (3)	16S rRNA	polymer	1478	478458.1	1	GenBank (470466243)	Methanosarcina acetivorans
4	D (7)	CBS domain-containing protein	polymer	280	31406.2	1	UniProt (Q8TH71)	Methanosarcina acetivorans
5	E (8)	E-site tRNA	polymer	75	24249.4	1		Methanosarcina acetivorans
6	F (AA)	Large ribosomal subunit protein uL2	polymer	238	25738.6	1	UniProt (Q8TRU4)	Methanosarcina acetivorans	50S ribosomal protein L2
7	G (AB)	Large ribosomal subunit protein uL3	polymer	337	36949.6	1	UniProt (Q8TRU7)	Methanosarcina acetivorans	50S ribosomal protein L3
8	H (AC)	Large ribosomal subunit protein uL4	polymer	253	27516.6	1	UniProt (Q8TRU6)	Methanosarcina acetivorans	50S ribosomal protein L4
9	I (AD)	Large ribosomal subunit protein uL5	polymer	165	18398.3	1	UniProt (Q8TRT4)	Methanosarcina acetivorans	50S ribosomal protein L5
10	J (AE)	Large ribosomal subunit protein uL6	polymer	176	19530.7	1	UniProt (Q8TRT1)	Methanosarcina acetivorans	50S ribosomal protein L6
11	K (AF)	Large ribosomal subunit protein eL8	polymer	120	12741.7	1	UniProt (Q8TQL9)	Methanosarcina acetivorans	50S ribosomal protein L7Ae,Ribosomal protein L8e
12	L (AG)	Large ribosomal subunit protein uL13	polymer	143	16085.8	1	UniProt (Q8TT43)	Methanosarcina acetivorans	50S ribosomal protein L13
13	M (AH)	Large ribosomal subunit protein uL14	polymer	132	14356.9	1	UniProt (Q8TRT7)	Methanosarcina acetivorans	50S ribosomal protein L14
14	N (AI)	Large ribosomal subunit protein uL15	polymer	140	15129.0	1	UniProt (Q8TRS5)	Methanosarcina acetivorans	50S ribosomal protein L15
15	O (AJ)	Large ribosomal subunit protein eL15	polymer	196	22650.1	1	UniProt (Q8TPX0)	Methanosarcina acetivorans	50S ribosomal protein L15e
16	P (AK)	Large ribosomal subunit protein uL16	polymer	173	19409.6	1	UniProt (Q8TU90)	Methanosarcina acetivorans	50S ribosomal protein L10e
17	Q (AL)	Large ribosomal subunit protein uL18	polymer	174	19233.7	1	UniProt (Q8TRS8)	Methanosarcina acetivorans	50S ribosomal protein L18
18	R (AM)	Large ribosomal subunit protein eL18	polymer	126	13715.0	1	UniProt (Q8TT44)	Methanosarcina acetivorans	50S ribosomal protein L18e
19	S (AN)	Large ribosomal subunit protein eL19	polymer	151	17062.0	1	UniProt (A0A832W9G6)	Methanosarcina acetivorans
20	T (AO)	Large ribosomal subunit protein eL20	polymer	61	6972.0	1	UniProt (Q8TIN5)	Methanosarcina acetivorans	50S ribosomal protein L18Ae,50S ribosomal protein L20e,50S ribosomal protein LX
21	U (AP)	Large ribosomal subunit protein eL21	polymer	97	11063.7	1	UniProt (Q8TQU3)	Methanosarcina acetivorans	50S ribosomal protein L21e
22	V (AQ)	Large ribosomal subunit protein uL22	polymer	151	16764.6	1	UniProt (Q8TRU2)	Methanosarcina acetivorans	50S ribosomal protein L22
23	W (AR)	Large ribosomal subunit protein uL23	polymer	82	9447.2	1	UniProt (Q8TRU5)	Methanosarcina acetivorans	50S ribosomal protein L23
24	X (AS)	Large ribosomal subunit protein uL24	polymer	119	13075.3	1	UniProt (Q8TRT6)	Methanosarcina acetivorans	50S ribosomal protein L24
25	Y (AT)	Large ribosomal subunit protein eL24	polymer	62	7204.6	1	UniProt (Q8TQL7)	Methanosarcina acetivorans	50S ribosomal protein L24e
26	Z (AU)	Large ribosomal subunit protein uL29	polymer	67	7622.6	1	UniProt (Q8TRU0)	Methanosarcina acetivorans	50S ribosomal protein L29
27	AA (AV)	Large ribosomal subunit protein uL30	polymer	153	17627.4	1	UniProt (Q8TRS6)	Methanosarcina acetivorans	50S ribosomal protein L30
28	BA (AW)	Large ribosomal subunit protein eL30	polymer	99	10316.2	1	UniProt (Q8TRB9)	Methanosarcina acetivorans	50S ribosomal protein L30e
29	CA (AX)	Large ribosomal subunit protein eL31	polymer	89	10331.1	1	UniProt (Q8TIN3)	Methanosarcina acetivorans	50S ribosomal protein L31e
30	DA (AY)	Large ribosomal subunit protein eL32	polymer	129	14335.6	1	UniProt (Q8TRT0)	Methanosarcina acetivorans	50S ribosomal protein L32e
31	EA (AZ)	Large ribosomal subunit protein eL37	polymer	56	6456.6	1	UniProt (Q8TL48)	Methanosarcina acetivorans	50S ribosomal protein L37e
32	FA (Aa)	Large ribosomal subunit protein eL39	polymer	51	6257.5	1	UniProt (Q8TIN2)	Methanosarcina acetivorans	50S ribosomal protein L39e
33	GA (Ab)	Large ribosomal subunit protein eL40	polymer	49	5602.7	1	UniProt (Q8TJ19)	Methanosarcina acetivorans	50S ribosomal protein L40e
34	HA (Ac)	Large ribosomal subunit protein eL42	polymer	92	10873.0	1	UniProt (A0A832W9V9)	Methanosarcina acetivorans
35	IA (Ad)	Large ribosomal subunit protein eL43	polymer	94	10557.5	1	UniProt (A0A832SMV9)	Methanosarcina acetivorans
36	JA (BA)	Small ribosomal subunit protein eS1	polymer	203	22938.7	1	UniProt (Q8TKI9)	Methanosarcina acetivorans	30S ribosomal protein S3Ae,Ribosomal protein S1e
37	KA (BB)	Small ribosomal subunit protein uS2	polymer	225	24807.1	1	UniProt (Q8TT39)	Methanosarcina acetivorans	30S ribosomal protein S2
38	LA (BC)	Small ribosomal subunit protein uS3	polymer	318	34780.4	1	UniProt (Q8TRU1)	Methanosarcina acetivorans	30S ribosomal protein S3
39	MA (BD)	Small ribosomal subunit protein uS4	polymer	218	24559.3	1	UniProt (Q8TRR1)	Methanosarcina acetivorans	30S ribosomal protein S4
40	NA (BE)	Small ribosomal subunit protein eS4	polymer	235	26301.4	1	UniProt (Q8TRT5)	Methanosarcina acetivorans	30S ribosomal protein S4e
41	OA (BF)	Small ribosomal subunit protein uS5	polymer	209	22732.3	1	UniProt (Q8TRS7)	Methanosarcina acetivorans	30S ribosomal protein S5
42	PA (BG)	Small ribosomal subunit protein eS6	polymer	136	14474.8	1	UniProt (Q8TQL4)	Methanosarcina acetivorans	30S ribosomal protein S6e
43	QA (BH)	Small ribosomal subunit protein uS7	polymer	189	21062.3	1	UniProt (Q8TRC2)	Methanosarcina acetivorans	30S ribosomal protein S7
44	RA (BI)	Small ribosomal subunit protein uS8	polymer	130	14085.3	1	UniProt (Q8TRT2)	Methanosarcina acetivorans	30S ribosomal protein S8
45	SA (BJ)	Small ribosomal subunit protein uS9	polymer	134	14512.7	1	UniProt (Q8TT42)	Methanosarcina acetivorans	30S ribosomal protein S9
46	TA (BK)	Small ribosomal subunit protein eS8	polymer	125	13802.0	1	UniProt (Q8TS82)	Methanosarcina acetivorans	30S ribosomal protein S8e
47	UA (BL)	Small ribosomal subunit protein uS10	polymer	102	11380.3	1	UniProt (P61929)	Methanosarcina acetivorans	30S ribosomal protein S10
48	VA (BM)	Small ribosomal subunit protein uS11	polymer	126	13324.3	1	UniProt (Q8TRR0)	Methanosarcina acetivorans	30S ribosomal protein S11
49	WA (BN)	Small ribosomal subunit protein uS12	polymer	142	15540.1	1	UniProt (Q8TRC1)	Methanosarcina acetivorans	30S ribosomal protein S12
50	XA (BO)	Small ribosomal subunit protein uS13	polymer	162	18315.2	1	UniProt (Q8TRR2)	Methanosarcina acetivorans	30S ribosomal protein S13
51	YA (BP)	Small ribosomal subunit protein uS14	polymer	50	5971.0	1	UniProt (Q8TRT3)	Methanosarcina acetivorans	30S ribosomal protein S14 type Z
52	ZA (BQ)	Small ribosomal subunit protein uS15	polymer	152	17503.6	1	UniProt (Q8TS56)	Methanosarcina acetivorans	30S ribosomal protein S15
53	AB (BR)	Small ribosomal subunit protein uS17A	polymer	109	12184.2	1	UniProt (Q8TRT8)	Methanosarcina acetivorans	30S ribosomal protein S17 1
54	BB (BS)	Small ribosomal subunit protein eS17	polymer	64	7477.7	1	UniProt (Q8THP2)	Methanosarcina acetivorans	30S ribosomal protein S17e
55	CB (BT)	Small ribosomal subunit protein uS19	polymer	136	15467.9	1	UniProt (Q8TRU3)	Methanosarcina acetivorans	30S ribosomal protein S19
56	DB (BU)	Small ribosomal subunit protein eS19	polymer	149	16563.2	1	UniProt (A0A832W9Q0)	Methanosarcina acetivorans
57	EB (BV)	Putative zinc finger domain-containing protein	polymer	56	6162.3	1	UniProt (A0A832S8D7)	Methanosarcina acetivorans
58	FB (BW)	Small ribosomal subunit protein eS24	polymer	101	11620.3	1	UniProt (Q8TJT2)	Methanosarcina acetivorans	30S ribosomal protein S24e
59	GB (BX)	Small ribosomal subunit protein eS27	polymer	62	6955.0	1	UniProt (P61931)	Methanosarcina acetivorans	30S ribosomal protein S27e
60	HB (BY)	Small ribosomal subunit protein eS28	polymer	76	8268.6	1	UniProt (Q8TQL8)	Methanosarcina acetivorans	30S ribosomal protein S28e
61	IB (BZ)	DUF5350 family protein	polymer	57	6434.7	1	UniProt (A0A832SMB7)	Methanosarcina acetivorans
62	AC, AD, AE, AF, AG... (1, 3, AA, AB, AH...)	MAGNESIUM ION	non-polymer		24.3	314	Chemie (MG)
63	IN, KN, LN, MN, NN... (AT, AZ, Ab, Ac, Ad...)	ZINC ION	non-polymer		65.4	11	Chemie (ZN)
64	AO, AP, AQ, BO, BP... (8, AZ, BV, AA, Aa...)	water	water		18.0	10476	Chemie (HOH)

Sequence modifications

1: 5 - 2903 (GenBank: 470469544)

PDB	External Database	Details
A 1	-	insertion
A 2	-	insertion
U 3	-	insertion
U 4	-	insertion
G 403	U 399	conflict
U 408	C 404	conflict
U 2716	C 2712	conflict
A 2721	G 2717	conflict
A 2904	-	insertion

7: 1 - 274 (UniProt: Q8TH71)

PDB	External Database	Details
His 275	-	insertion
His 276	-	insertion
His 277	-	insertion
His 278	-	insertion
His 279	-	insertion
His 280	-	insertion

BM: 1 - 126 (UniProt: Q8TRR0)

PDB	External Database	Details
Ias 116	Asp 116	conflict

Sequence viewer

Contents of the asymmetric unit

Polymers	Number of chains	61
Polymers	Total formula weight	2366373.1
Non-Polymers*	Number of molecules	325
Non-Polymers*	Total formula weight	8351.3
All*	Total formula weight	2374724.4

*Water molecules are not included.

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		Validation report (PDF)