4V5J

Structure of the 70S ribosome bound to Release factor 2 and a substrate analog provides insights into catalysis of peptide release

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, HB (AA, CA)	16S Ribosomal RNA	polymer	1522	493958.3	2	GenBank (55979969)	THERMUS THERMOPHILUS
2	B, IB (AB, CB)	30S RIBOSOMAL PROTEIN S2	polymer	256	29317.7	2	UniProt (P80371) Pfam (PF00318)	THERMUS THERMOPHILUS
3	C, JB (AC, CC)	30S RIBOSOMAL PROTEIN S3	polymer	239	26751.1	2	UniProt (P80372) Pfam (PF07650) Pfam (PF00189)	THERMUS THERMOPHILUS
4	D, KB (AD, CD)	30S RIBOSOMAL PROTEIN S4	polymer	209	24373.4	2	UniProt (P80373) Pfam (PF00163) Pfam (PF01479)	THERMUS THERMOPHILUS
5	E, LB (AE, CE)	30S RIBOSOMAL PROTEIN S5	polymer	162	17583.4	2	UniProt (Q5SHQ5) Pfam (PF00333) Pfam (PF03719)	THERMUS THERMOPHILUS
6	F, MB (AF, CF)	30S RIBOSOMAL PROTEIN S6	polymer	101	11988.8	2	UniProt (Q5SLP8) Pfam (PF01250)	THERMUS THERMOPHILUS	TS9
7	G, NB (AG, CG)	30S RIBOSOMAL PROTEIN S7	polymer	156	18051.0	2	UniProt (P17291) Pfam (PF00177)	THERMUS THERMOPHILUS
8	H, OB (AH, CH)	30S RIBOSOMAL PROTEIN S8	polymer	138	15868.6	2	UniProt (Q5SHQ2)	THERMUS THERMOPHILUS
9	I, PB (AI, CI)	30S RIBOSOMAL PROTEIN S9	polymer	128	14429.7	2	UniProt (P62669) Pfam (PF00380)	THERMUS THERMOPHILUS
10	J, QB (AJ, CJ)	30S RIBOSOMAL PROTEIN S10	polymer	105	11955.0	2	UniProt (Q5SHN7) Pfam (PF00338)	THERMUS THERMOPHILUS
11	K, RB (AK, CK)	30S RIBOSOMAL PROTEIN S11	polymer	129	13737.9	2	UniProt (P80376) Pfam (PF00411)	THERMUS THERMOPHILUS
12	L, SB (AL, CL)	30S RIBOSOMAL PROTEIN S12	polymer	132	14637.4	2	UniProt (Q5SHN3) Pfam (PF00164)	THERMUS THERMOPHILUS
13	M, TB (AM, CM)	30S RIBOSOMAL PROTEIN S13	polymer	126	14338.9	2	UniProt (P80377) Pfam (PF00416)	THERMUS THERMOPHILUS
14	N, UB (AN, CN)	30S RIBOSOMAL PROTEIN S14 TYPE Z	polymer	61	7158.7	2	UniProt (Q5SHQ1)	THERMUS THERMOPHILUS	30S RIBOSOMAL PROTEIN S14
15	O, VB (AO, CO)	30S RIBOSOMAL PROTEIN S15	polymer	89	10578.4	2	UniProt (Q5SJ76) Pfam (PF00312)	THERMUS THERMOPHILUS
16	P, WB (AP, CP)	30S RIBOSOMAL PROTEIN S16	polymer	88	10410.0	2	UniProt (Q5SJH3) Pfam (PF00886)	THERMUS THERMOPHILUS
17	Q, XB (AQ, CQ)	30S RIBOSOMAL PROTEIN S17	polymer	105	12325.7	2	UniProt (Q5SHP7)	THERMUS THERMOPHILUS
18	R, YB (AR, CR)	30S RIBOSOMAL PROTEIN S18	polymer	88	10258.3	2	UniProt (Q5SLQ0) Pfam (PF01084)	THERMUS THERMOPHILUS
19	S, ZB (AS, CS)	30S RIBOSOMAL PROTEIN S19	polymer	93	10605.5	2	UniProt (Q5SHP2) Pfam (PF00203)	THERMUS THERMOPHILUS
20	AC, T (AT, CT)	30S RIBOSOMAL PROTEIN S20	polymer	106	11736.1	2	UniProt (P80380) Pfam (PF01649)	THERMUS THERMOPHILUS
21	BC, U (AU, CU)	30S RIBOSOMAL PROTEIN THX	polymer	27	3350.0	2	UniProt (Q5SIH3) Pfam (PF17070)	THERMUS THERMOPHILUS	S31
22	CC, DC, V, W (AV, AW, CV, CW)	E-SITE TRNA PHE OR P-SITE TRNA PHE (UNMODIFIED BASES)	polymer	77	24615.7	4		ESCHERICHIA COLI
23	EC, X (AX, CX)	MRNA	polymer	8	2495.5	2		synthetic construct
24	FC, Y (AY, CY)	PEPTIDE CHAIN RELEASE FACTOR 2	polymer	351	39857.3	2	UniProt (Q5SM01) Pfam (PF03462) Pfam (PF00472)	THERMUS THERMOPHILUS
25	GC, Z (B0, D0)	50S RIBOSOMAL PROTEIN L27	polymer	85	9529.1	2	UniProt (P60493) Pfam (PF01016)	THERMUS THERMOPHILUS
26	AA, HC (B1, D1)	50S RIBOSOMAL PROTEIN L28	polymer	98	11004.2	2	UniProt (P60494) Pfam (PF00830)	THERMUS THERMOPHILUS
27	BA, IC (B2, D2)	50S RIBOSOMAL PROTEIN L29	polymer	72	8670.3	2	UniProt (Q5SHP6) Pfam (PF00831)	THERMUS THERMOPHILUS	TL5
28	CA, JC (B3, D3)	50S RIBOSOMAL PROTEIN L30	polymer	60	6799.1	2	UniProt (Q5SHQ6) Pfam (PF00327)	THERMUS THERMOPHILUS
29	DA, KC (B4, D4)	50S RIBOSOMAL PROTEIN L31	polymer	71	8300.5	2	UniProt (Q5SJE1) Pfam (PF01197)	THERMUS THERMOPHILUS
30	EA, LC (B5, D5)	50S RIBOSOMAL PROTEIN L32	polymer	60	6722.1	2	UniProt (P80339) Pfam (PF01783)	THERMUS THERMOPHILUS
31	FA, MC (B6, D6)	50S RIBOSOMAL PROTEIN L33	polymer	54	6632.9	2	UniProt (P35871) Pfam (PF00471)	THERMUS THERMOPHILUS
32	GA, NC (B7, D7)	50S RIBOSOMAL PROTEIN L34	polymer	49	6132.4	2	UniProt (P80340) Pfam (PF00468)	THERMUS THERMOPHILUS
33	HA, OC (B8, D8)	50S RIBOSOMAL PROTEIN L35	polymer	65	7506.2	2	UniProt (Q5SKU1) Pfam (PF01632)	THERMUS THERMOPHILUS
34	IA, PC (B9, D9)	50S RIBOSOMAL PROTEIN L36	polymer	37	4435.4	2	UniProt (Q5SHR2) Pfam (PF00444)	THERMUS THERMOPHILUS	RIBOSOMAL PROTEIN B
35	JA, QC (BA, DA)	23S RIBOSOMAL RNA	polymer	2915	947935.4	2	GenBank (55979969)	THERMUS THERMOPHILUS
36	KA, RC (BB, DB)	5S RIBOSOMAL RNA	polymer	122	39494.5	2	GenBank (55979969)	THERMUS THERMOPHILUS
37	LA, SC (BC, DC)	50S RIBOSOMAL PROTEIN L1	polymer	229	24872.7	2	UniProt (Q5SLP7) Pfam (PF00687)	THERMUS THERMOPHILUS
38	MA, TC (BD, DD)	50S RIBOSOMAL PROTEIN L2	polymer	276	30532.6	2	UniProt (P60405) Pfam (PF00181) Pfam (PF03947)	THERMUS THERMOPHILUS
39	NA, UC (BE, DE)	50S RIBOSOMAL PROTEIN L3	polymer	206	22450.2	2	UniProt (Q5SHN8) Pfam (PF00297)	THERMUS THERMOPHILUS
40	OA, VC (BF, DF)	50S RIBOSOMAL PROTEIN L4	polymer	210	23271.9	2	UniProt (Q5SHN9) Pfam (PF00573)	THERMUS THERMOPHILUS	L1E
41	PA, WC (BG, DG)	50S RIBOSOMAL PROTEIN L5	polymer	182	21061.6	2	UniProt (Q5SHQ0) Pfam (PF00281) Pfam (PF00673)	THERMUS THERMOPHILUS
42	QA, XC (BH, DH)	50S RIBOSOMAL PROTEIN L6	polymer	180	19568.9	2	UniProt (Q5SHQ3)	THERMUS THERMOPHILUS
43	RA, YC (BI, DI)	50S RIBOSOMAL PROTEIN L9	polymer	148	16422.2	2	UniProt (Q5SLQ1) Pfam (PF01281) Pfam (PF03948)	THERMUS THERMOPHILUS
44	SA, ZC (BJ, DJ)	50S RIBOSOMAL PROTEIN L10	polymer	130	11081.7	2		THERMUS THERMOPHILUS
45	AD, TA (BK, DK)	50S RIBOSOMAL PROTEIN L11	polymer	147	15526.1	2	UniProt (Q5SLP6) Pfam (PF03946) Pfam (PF00298)	THERMUS THERMOPHILUS
46	BD, UA (BN, DN)	50S RIBOSOMAL PROTEIN L13	polymer	140	15927.9	2	UniProt (P60488) Pfam (PF00572)	THERMUS THERMOPHILUS
47	CD, VA (BO, DO)	50S RIBOSOMAL PROTEIN L14	polymer	122	13323.6	2	UniProt (Q5SHP8) Pfam (PF00238)	THERMUS THERMOPHILUS
48	DD, WA (BP, DP)	50S RIBOSOMAL PROTEIN L15	polymer	150	16319.1	2	UniProt (Q5SHQ7) Pfam (PF00828)	THERMUS THERMOPHILUS
49	ED, XA (BQ, DQ)	50S RIBOSOMAL PROTEIN L16	polymer	141	15993.9	2	UniProt (P60489) Pfam (PF00252)	THERMUS THERMOPHILUS
50	FD, YA (BR, DR)	50S RIBOSOMAL PROTEIN L17	polymer	118	13750.1	2	UniProt (Q9Z9H5) Pfam (PF01196)	THERMUS THERMOPHILUS
51	GD, ZA (BS, DS)	50S RIBOSOMAL PROTEIN L18	polymer	112	12639.8	2	UniProt (Q5SHQ4) Pfam (PF00861)	THERMUS THERMOPHILUS	TL24
52	AB, HD (BT, DT)	50S RIBOSOMAL PROTEIN L19	polymer	146	17188.8	2	UniProt (P60490) Pfam (PF01245)	THERMUS THERMOPHILUS
53	BB, ID (BU, DU)	50S RIBOSOMAL PROTEIN L20	polymer	118	13779.3	2	UniProt (P60491) Pfam (PF00453)	THERMUS THERMOPHILUS
54	CB, JD (BV, DV)	50S RIBOSOMAL PROTEIN L21	polymer	101	11069.2	2	UniProt (P60492) Pfam (PF00829)	THERMUS THERMOPHILUS
55	DB, KD (BW, DW)	50S RIBOSOMAL PROTEIN L22	polymer	113	12808.1	2	UniProt (Q5SHP3) Pfam (PF00237)	THERMUS THERMOPHILUS
56	EB, LD (BX, DX)	50S RIBOSOMAL PROTEIN L23	polymer	96	10759.8	2	UniProt (Q5SHP0) Pfam (PF00276)	THERMUS THERMOPHILUS
57	FB, MD (BY, DY)	50S RIBOSOMAL PROTEIN L24	polymer	110	12085.6	2	UniProt (Q5SHP9) Pfam (PF00467) Pfam (PF17136)	THERMUS THERMOPHILUS
58	GB, ND (BZ, DZ)	50S RIBOSOMAL PROTEIN L25	polymer	206	23238.6	2	UniProt (Q5SHZ1) Pfam (PF01386) Pfam (PF14693)	THERMUS THERMOPHILUS	TL5
59	AAA, ABA, ACA, ADA, AE... (CA, AA, CV, DA, AV...)	MAGNESIUM ION	non-polymer		24.3	1094	Chemie (MG)
60	NK, OFA, TEA, TJ, VJ... (B9, D9, CD, AD, AN...)	ZINC ION	non-polymer		65.4	6	Chemie (ZN)
61	WTA, XTA, YTA (AV, AY, BA)	water	water		18.0	3	Chemie (HOH)

Sequence modifications

AY, CY: 6 - 17 (PDB: 4V5J)
AY, CY: 18 - 356 (UniProt: Q5SM01)

Contents of the asymmetric unit

Polymers	Number of chains	118
	Total formula weight	4623663.6
Non-Polymers*	Number of molecules	1100
	Total formula weight	26982.1
All*	Total formula weight	4650645.7

*Water molecules are not included.