6WOO

CryoEM structure of yeast 80S ribosome with Met-tRNAiMet, eIF5B, and GDP

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 (5)	25S ribosomal RNA	polymer	3271	1057318.6	1		Saccharomyces cerevisiae (Baker's yeast)
2	B (7)	5S ribosomal RNA	polymer	121	38951.1	1	GenBank (1039024045)	Saccharomyces cerevisiae (Baker's yeast)
3	C (8)	5.8S ribosomal rRNA	polymer	157	50376.8	1	GenBank (1675231216)	Saccharomyces cerevisiae (Baker's yeast)
4	D (A)	uL2	polymer	249	26858.9	1	UniProt (P0CX45) Pfam (PF00181) Pfam (PF03947)	Saccharomyces cerevisiae (Baker's yeast)
5	E (B)	uL3	polymer	384	43491.4	1	UniProt (P14126) Pfam (PF00297)	Saccharomyces cerevisiae (Baker's yeast)
6	F (C)	uL4	polymer	359	38825.8	1	UniProt (P10664) Pfam (PF00573) Pfam (PF14374)	Saccharomyces cerevisiae (Baker's yeast)
7	G (D)	uL18	polymer	295	33562.6	1	UniProt (P26321) Pfam (PF17144) Pfam (PF14204)	Saccharomyces cerevisiae (Baker's yeast)
8	H (E)	eL6	polymer	175	19869.4	1	UniProt (Q02326) Pfam (PF01159)	Saccharomyces cerevisiae (Baker's yeast)
9	I (F)	uL30	polymer	222	25240.4	1	UniProt (P05737) Pfam (PF08079) Pfam (PF00327)	Saccharomyces cerevisiae (Baker's yeast)
10	J (G)	eL8	polymer	233	25815.0	1	UniProt (P17076) Pfam (PF01248)	Saccharomyces cerevisiae (Baker's yeast)
11	K (H)	uL6	polymer	191	21691.1	1	UniProt (P51401) Pfam (PF00347)	Saccharomyces cerevisiae (Baker's yeast)
12	L (I)	uL16	polymer	216	24937.9	1	UniProt (P41805) Pfam (PF00252)	Saccharomyces cerevisiae (Baker's yeast)
13	M (J)	uL5	polymer	168	19136.9	1	UniProt (Q3E757) Pfam (PF00281) Pfam (PF00673)	Saccharomyces cerevisiae (Baker's yeast)
14	N (L)	eL13	polymer	198	22473.0	1	UniProt (Q12690) Pfam (PF01294)	Saccharomyces cerevisiae (Baker's yeast)
15	O (M)	eL14	polymer	136	14992.8	1	UniProt (P36105) Pfam (PF00467) Pfam (PF01929)	Saccharomyces cerevisiae (Baker's yeast)
16	P (N)	eL15	polymer	202	24222.0	1	UniProt (P05748) Pfam (PF00827)	Saccharomyces cerevisiae (Baker's yeast)
17	Q (O)	uL13	polymer	197	22029.0	1	UniProt (P26784) Pfam (PF00572)	Saccharomyces cerevisiae (Baker's yeast)
18	R (P)	uL22	polymer	180	20245.1	1	UniProt (P05740) Pfam (PF00237)	Saccharomyces cerevisiae (Baker's yeast)
19	S (Q)	eL18	polymer	184	20421.0	1	UniProt (P0CX49) Pfam (PF17135)	Saccharomyces cerevisiae (Baker's yeast)
20	T (R)	eL19	polymer	188	21631.1	1	UniProt (P0CX82) Pfam (PF01280) Pfam (PF25476)	Saccharomyces cerevisiae (Baker's yeast)
21	U (S)	eL20	polymer	169	20138.4	1	UniProt (P0CX23) Pfam (PF01775)	Saccharomyces cerevisiae (Baker's yeast)
22	V (T)	eL21	polymer	158	18034.9	1	UniProt (Q02753) Pfam (PF01157)	Saccharomyces cerevisiae (Baker's yeast)
23	W (U)	eL22	polymer	100	11263.9	1	UniProt (P05749) Pfam (PF01776)	Saccharomyces cerevisiae (Baker's yeast)
24	X (V)	uL14	polymer	132	14005.4	1	UniProt (P0CX41) Pfam (PF00238)	Saccharomyces cerevisiae (Baker's yeast)
25	Y (W)	eL24	polymer	62	7253.5	1	UniProt (P04449) Pfam (PF01246)	Saccharomyces cerevisiae (Baker's yeast)
26	Z (X)	uL23	polymer	121	13771.2	1	UniProt (P04456) Pfam (PF03939) Pfam (PF00276)	Saccharomyces cerevisiae (Baker's yeast)
27	AA (Y)	uL24	polymer	125	14063.5	1	UniProt (P05743) Pfam (PF16906) Pfam (PF00467)	Saccharomyces cerevisiae (Baker's yeast)
28	BA (Z)	eL27	polymer	134	15366.1	1	UniProt (P0C2H6) Pfam (PF01777)	Saccharomyces cerevisiae (Baker's yeast)
29	CA (a)	uL15	polymer	147	16559.4	1	UniProt (P02406) Pfam (PF00828)	Saccharomyces cerevisiae (Baker's yeast)
30	DA (b)	eL29	polymer	57	6489.6	1	UniProt (P05747) Pfam (PF01779)	Saccharomyces cerevisiae (Baker's yeast)
31	EA (c)	eL30	polymer	97	10558.3	1	UniProt (P14120) Pfam (PF01248)	Saccharomyces cerevisiae (Baker's yeast)
32	FA (d)	eL31	polymer	106	12292.4	1	UniProt (P0C2H8) Pfam (PF01198)	Saccharomyces cerevisiae (Baker's yeast)
33	GA (e)	eL32	polymer	122	14022.5	1	UniProt (P38061) Pfam (PF01655)	Saccharomyces cerevisiae (Baker's yeast)
34	HA (f)	eL33	polymer	105	11932.8	1	UniProt (P05744) Pfam (PF01247)	Saccharomyces cerevisiae (Baker's yeast)
35	IA (g)	eL34	polymer	121	13671.2	1	UniProt (P87262) Pfam (PF01199)	Saccharomyces cerevisiae (Baker's yeast)
36	JA (h)	uL29	polymer	116	13540.1	1	UniProt (P0CX84) Pfam (PF00831)	Saccharomyces cerevisiae (Baker's yeast)
37	KA (i)	eL36	polymer	98	10919.0	1	UniProt (P05745) Pfam (PF01158)	Saccharomyces cerevisiae (Baker's yeast)
38	LA (j)	eL37	polymer	85	9629.1	1	UniProt (P49166) Pfam (PF01907)	Saccharomyces cerevisiae (Baker's yeast)
39	MA (k)	eL38	polymer	76	8643.3	1	UniProt (P49167) Pfam (PF01781)	Saccharomyces cerevisiae (Baker's yeast)
40	NA (l)	eL39	polymer	49	6114.3	1	UniProt (P04650) Pfam (PF00832)	Saccharomyces cerevisiae (Baker's yeast)
41	OA (m)	eL40	polymer	51	5919.2	1	UniProt (P0CH08) Pfam (PF01020)	Saccharomyces cerevisiae (Baker's yeast)
42	PA (n)	eL41	polymer	23	3138.0	1		Saccharomyces cerevisiae (Baker's yeast)
43	QA (o)	eL42	polymer	101	11655.9	1	UniProt (P0CX27) Pfam (PF00935)	Saccharomyces cerevisiae (Baker's yeast)
44	RA (p)	eL43	polymer	87	9611.4	1	UniProt (P0CX25) Pfam (PF01780)	Saccharomyces cerevisiae (Baker's yeast)
45	SA (q)	uL1	polymer	217	24524.8	1	UniProt (P0CX43) Pfam (PF00687)	Saccharomyces cerevisiae (Baker's yeast)
46	TA (r)	uL10	polymer	195	21474.7	1	UniProt (P05317) Pfam (PF00466) Pfam (PF17777)	Saccharomyces cerevisiae (Baker's yeast)
47	UA (K)	L10	polymer	152	12954.0	1		Saccharomyces cerevisiae (Baker's yeast)
48	VA (AA)	uS2	polymer	206	22852.2	1	UniProt (P46654) Pfam (PF00318)	Saccharomyces cerevisiae (Baker's yeast)
49	WA (BB)	eS1	polymer	214	24410.3	1	UniProt (P23248) Pfam (PF01015)	Saccharomyces cerevisiae (Baker's yeast)
50	XA (CC)	uS5	polymer	217	23213.0	1	UniProt (P25443) Pfam (PF00333) Pfam (PF03719)	Saccharomyces cerevisiae (Baker's yeast)
51	YA (DD)	uS3	polymer	223	24702.8	1	UniProt (P05750) Pfam (PF07650) Pfam (PF00189)	Saccharomyces cerevisiae (Baker's yeast)
52	ZA (EE)	eS4	polymer	257	29039.8	1	UniProt (P0CX35) Pfam (PF08071) Pfam (PF01479) Pfam (PF00900) Pfam (PF00467) Pfam (PF16121)	Saccharomyces cerevisiae (Baker's yeast)
53	AB (FF)	uS7	polymer	206	22908.3	1	UniProt (A0A1L4AA68)	Saccharomyces cerevisiae (Baker's yeast)
54	BB (GG)	eS6	polymer	226	25895.1	1	UniProt (P0CX37) Pfam (PF01092)	Saccharomyces cerevisiae (Baker's yeast)
55	CB (HH)	eS7	polymer	184	21000.5	1	UniProt (P26786) Pfam (PF01251)	Saccharomyces cerevisiae (Baker's yeast)
56	DB (II)	eS8	polymer	199	22406.6	1	UniProt (P0CX39) Pfam (PF01201)	Saccharomyces cerevisiae (Baker's yeast)
57	EB (JJ)	uS4	polymer	182	20965.4	1	UniProt (P05755) Pfam (PF00163) Pfam (PF01479)	Saccharomyces cerevisiae (Baker's yeast)
58	FB (KK)	eS10	polymer	96	11585.1	1	UniProt (Q08745) Pfam (PF03501)	Saccharomyces cerevisiae (Baker's yeast)
59	GB (LL)	uS17	polymer	145	16561.4	1	UniProt (P0CX47) Pfam (PF16205) Pfam (PF00366)	Saccharomyces cerevisiae (Baker's yeast)
60	HB (MM)	eS12	polymer	124	13327.3	1	UniProt (P48589) Pfam (PF01248)	Saccharomyces cerevisiae (Baker's yeast)
61	IB (NN)	uS15	polymer	150	16928.7	1	UniProt (P05756) Pfam (PF08069) Pfam (PF00312)	Saccharomyces cerevisiae (Baker's yeast)
62	JB (OO)	uS11	polymer	127	13446.4	1	UniProt (P39516) Pfam (PF00411)	Saccharomyces cerevisiae (Baker's yeast)
63	KB (PP)	uS19	polymer	103	11651.8	1	UniProt (Q01855) Pfam (PF00203)	Saccharomyces cerevisiae (Baker's yeast)
64	LB (QQ)	uS19	polymer	141	15659.2	1	UniProt (P0CX51) Pfam (PF00380)	Saccharomyces cerevisiae (Baker's yeast)
65	MB (RR)	eS17	polymer	123	14110.4	1	UniProt (P14127) Pfam (PF00833)	Saccharomyces cerevisiae (Baker's yeast)
66	NB (SS)	uS13	polymer	136	15928.3	1	UniProt (P0CX55) Pfam (PF00416)	Saccharomyces cerevisiae (Baker's yeast)
67	OB (TT)	eS19	polymer	143	15810.9	1	UniProt (P07280) Pfam (PF01090)	Saccharomyces cerevisiae (Baker's yeast)
68	PB (UU)	uS10	polymer	106	12076.1	1	UniProt (P38701) Pfam (PF00338)	Saccharomyces cerevisiae (Baker's yeast)
69	QB (VV)	eS21	polymer	87	9758.8	1	UniProt (P0C0V8) Pfam (PF01249)	Saccharomyces cerevisiae (Baker's yeast)
70	RB (WW)	uS8	polymer	129	14518.9	1	UniProt (P0C0W1) Pfam (PF00410)	Saccharomyces cerevisiae (Baker's yeast)
71	SB (XX)	uS12	polymer	144	15986.8	1	UniProt (P0CX29) Pfam (PF00164)	Saccharomyces cerevisiae (Baker's yeast)
72	TB (YY)	eS24	polymer	134	15231.6	1	UniProt (P0CX31) Pfam (PF01282)	Saccharomyces cerevisiae (Baker's yeast)
73	UB (ZZ)	eS25	polymer	70	8001.4	1	UniProt (Q3E792) Pfam (PF03297)	Saccharomyces cerevisiae (Baker's yeast)
74	VB (aa)	eS26	polymer	97	11023.0	1	UniProt (P39939) Pfam (PF01283)	Saccharomyces cerevisiae (Baker's yeast)
75	WB (bb)	eS27	polymer	81	8762.2	1	UniProt (P35997) Pfam (PF01667)	Saccharomyces cerevisiae (Baker's yeast)
76	XB (cc)	eS28	polymer	63	7116.3	1	UniProt (Q3E7X9) Pfam (PF01200)	Saccharomyces cerevisiae (Baker's yeast)
77	YB (dd)	uS14	polymer	53	6335.3	1	UniProt (P41057) Pfam (PF00253)	Saccharomyces cerevisiae (Baker's yeast)
78	ZB (ee)	eS30	polymer	53	6084.3	1	UniProt (P0CX33) Pfam (PF04758)	Saccharomyces cerevisiae (Baker's yeast)
79	AC (ff)	eS31	polymer	57	6457.7	1	UniProt (P05759) Pfam (PF01599)	Saccharomyces cerevisiae (Baker's yeast)
80	BC (gg)	RACK1	polymer	318	34710.0	1	UniProt (P38011) Pfam (PF00400)	Saccharomyces cerevisiae (Baker's yeast)
81	CC (2)	18S ribosomal RNA	polymer	1796	578475.1	1	GenBank (1329886537)	Saccharomyces cerevisiae (Baker's yeast)
82	DC (1)	eIF5B	polymer	600	67068.3	1	UniProt (P39730) Pfam (PF00009) Pfam (PF11987) Pfam (PF14578)	Saccharomyces cerevisiae (Baker's yeast)
83	EC (3)	Met-tRNA-iMet	polymer	76	24583.7	1	GenBank (176433)	Saccharomyces cerevisiae (Baker's yeast)
84	FC (4)	mRNA	polymer	6	1923.2	1		Saccharomyces cerevisiae
85	GC, HC, IC, JC, KC... (j, m, o, aa, bb...)	ZINC ION	non-polymer		65.4	6	Chemie (ZN)
86	MC (1)	GUANOSINE-5'-DIPHOSPHATE	non-polymer		443.2	1	Chemie (GDP) PubChem (136073927) PubChem (135398619) PubChem (135402030) PubChem (135431654) PubChem (135566337) PubChem (135760556) PubChem (136026707) PubChem (136053418) PubChem (136663964) PubChem (136664748) PubChem (136759848) PubChem (136759849) PubChem (136759850) PubChem (136836636) PubChem (136847074) PubChem (172898537)
87	NC (3)	N-carboxy-L-threonine	non-polymer		163.1	1	Chemie (U6A) PubChem (21720368) PubChem (132280896)
88	OC (3)	METHIONINE	non-polymer		149.2	1	Chemie (MET) PubChem (876) PubChem (6137) PubChem (84815)

Sequence modifications

H: 1 - 190 (UniProt: P51401)

PDB	External Database	Details
Glu 191	-	insertion

g: 2 - 121 (UniProt: P87262)

PDB	External Database	Details
Lys 122	-	insertion

j: 2 - 83 (UniProt: P49166)

PDB	External Database	Details
Lys 84	-	insertion
Ala 85	-	insertion
Gln 86	-	insertion

KK: 1 - 96 (UniProt: Q08745)

PDB	External Database	Details
Ala 89	Gly 89	conflict

LL: 2 - 145 (UniProt: P0CX47)

PDB	External Database	Details
Thr 146	-	insertion

2: 1 - 1798 (GenBank: 1329886537)

PDB	External Database	Details
A 677	G 469479	conflict
U 678	A 469478	conflict

3: 1 - 76 (GenBank: 176433)

PDB	External Database	Details
G 17	-	insertion

Contents of the asymmetric unit

Polymers	Number of chains	84
	Total formula weight	3120152.6
Non-Polymers*	Number of molecules	9
	Total formula weight	1148.0
All*	Total formula weight	3121300.6

*Water molecules are not included.