3J7Q

Structure of the idle mammalian ribosome-Sec61 complex

This is a non-PDB format compatible entry.

Replaces:  3J72Replaces:  1VWYReplaces:  1VWZ

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	5	28S ribosomal RNA	polymer	3722	1206101.9	1		Sus scrofa (Pig)
2	7	5S ribosomal RNA	polymer	120	38691.9	1	GenBank (371913672)	Sus scrofa (Pig)
3	8	5.8S ribosomal RNA	polymer	156	50143.6	1	GenBank (115552481)	Sus scrofa (Pig)
4	A	Ribosomal protein uL2	polymer	257	28088.9	1	UniProt (A0A480Q387) In PDB	Sus scrofa (Pig)
5	B	Ribosomal protein uL3	polymer	394	44759.4	1	UniProt (A0A480L253) In PDB	Sus scrofa (Pig)
6	C	Ribosomal protein uL4	polymer	367	41635.1	1	UniProt (A0A287AE76) Pfam (PF00573) Pfam (PF14374) UniProt (by SIFTS) (F1SJJ5) In PDB	Sus scrofa (Pig)
7	D	Ribosomal protein uL18	polymer	297	34417.7	1	UniProt (A0A287ASD0) Pfam (PF17144) Pfam (PF14204) In PDB	Sus scrofa (Pig)
8	E	Ribosomal protein eL6	polymer	236	27052.2	1	UniProt (Q2YGT9) Pfam (PF03868) Pfam (PF01159) In PDB	Sus scrofa (Pig)
9	F	Ribosomal protein uL30	polymer	225	26590.7	1	UniProt (A0A480W0U3) In PDB	Sus scrofa (Pig)
10	G	Ribosomal protein eL8	polymer	266	30166.9	1	UniProt (A0A4X1W808) Pfam (PF01248) In PDB	Sus scrofa (Pig)
11	H	Ribosomal protein uL6	polymer	192	21899.5	1	UniProt (I3LP78) Pfam (PF00347) In PDB	Sus scrofa (Pig)
12	I	Ribosomal protein uL16	polymer	213	24465.8	1	UniProt (Q29195) Pfam (PF00252) In PDB	Sus scrofa (Pig)	Protein QM homolog,Ribosomal protein L10
13	J	Ribosomal protein uL5	polymer	178	20248.4	1	UniProt (Q29205) Pfam (PF00281) Pfam (PF00673) In PDB	Sus scrofa (Pig)
14	L	Ribosomal protein eL13	polymer	211	24365.8	1	UniProt (A0A4X1TBV3) Pfam (PF01294) In PDB	Sus scrofa (Pig)
15	M	Ribosomal protein eL14	polymer	213	23383.1	1	UniProt (A1XQU3) Pfam (PF01929) In PDB	Sus scrofa (Pig)
16	N	Ribosomal protein eL15	polymer	204	24207.3	1	UniProt (A0A286ZL65) Pfam (PF00827) In PDB	Sus scrofa (Pig)
17	O	Ribosomal protein uL13	polymer	201	23435.1	1	UniProt (A0A481CAM4) In PDB	Sus scrofa (Pig)
18	P	Ribosomal protein uL22	polymer	153	17757.6	1	UniProt (A0A287B386) Pfam (PF00237) In PDB	Sus scrofa (Pig)
19	Q	Ribosomal protein eL18	polymer	188	21588.6	1	UniProt (A0A4X1W0N5) Pfam (PF17135) In PDB	Sus scrofa (Pig)
20	R	Ribosomal protein eL19	polymer	196	23567.3	1	UniProt (A0A480VXS3) In PDB	Sus scrofa (Pig)
21	S	Ribosomal protein eL20	polymer	224	26103.4	1	UniProt (A0A287APR1) Pfam (PF01775) In PDB	Sus scrofa (Pig)
22	T	Ribosomal protein eL21	polymer	160	18610.0	1	UniProt (P49666) Pfam (PF01157) In PDB	Sus scrofa (Pig)
23	U	Ribosomal protein eL22	polymer	128	14785.0	1	UniProt (P67985) Pfam (PF01776) In PDB	Sus scrofa (Pig)	Heparin-binding protein HBp15
24	V	Ribosomal protein uL14	polymer	140	14892.5	1	UniProt (A0A480VZZ1) In PDB	Sus scrofa (Pig)
25	W	Ribosomal protein eL24	polymer	157	17825.1	1	UniProt (A0A4X1SH42) Pfam (PF01246) In PDB	Sus scrofa (Pig)
26	X	Ribosomal protein uL23	polymer	156	17740.2	1	UniProt (A0A480KZ98) In PDB	Sus scrofa (Pig)
27	Y	Ribosomal protein uL24	polymer	145	17303.4	1	UniProt (A0A4X1V977) Pfam (PF16906) Pfam (PF00467) In PDB	Sus scrofa (Pig)
28	Z	Ribosomal protein eL27	polymer	136	15835.8	1	UniProt (A1XQU5) Pfam (PF00467) Pfam (PF01777) In PDB	Sus scrofa (Pig)
29	a	Ribosomal protein uL15	polymer	148	16631.5	1	UniProt (A0A4X1SN08) Pfam (PF00828) In PDB	Sus scrofa (Pig)
30	b	Ribosomal protein eL29	polymer	160	17545.8	1	UniProt (Q95281) Pfam (PF01779) In PDB	Sus scrofa (Pig)
31	c	Ribosomal protein eL30	polymer	115	12805.1	1	UniProt (A0A4X1TXJ8) Pfam (PF01248) In PDB	Sus scrofa (Pig)
32	d	Ribosomal protein eL31	polymer	125	14494.9	1	UniProt (P62901) Pfam (PF01198) In PDB	Sus scrofa (Pig)
33	e	Ribosomal protein eL32	polymer	135	15898.9	1	UniProt (Q6QAT0) Pfam (PF01655) In PDB	Sus scrofa (Pig)
34	f	Ribosomal protein eL33	polymer	110	12564.7	1	UniProt (A0A480KUB2) In PDB	Sus scrofa (Pig)
35	g	Ribosomal protein eL34	polymer	117	13326.1	1	UniProt (Q29223) Pfam (PF01199) In PDB	Sus scrofa (Pig)
36	h	Ribosomal protein uL29	polymer	123	14591.6	1	UniProt (Q29361) Pfam (PF00831) In PDB	Sus scrofa (Pig)
37	i	Ribosomal protein eL36	polymer	105	12290.9	1	UniProt (A0A480QBP0) In PDB	Sus scrofa (Pig)
38	j	Ribosomal protein eL37	polymer	86	10102.9	1	UniProt (A0A480UVT3) In PDB	Sus scrofa (Pig)
39	k	Ribosomal protein eL38	polymer	70	8238.9	1	UniProt (F2Z568) Pfam (PF01781) UniProt (by SIFTS) (A0A4X1VLH7) In PDB	Sus scrofa (Pig)
40	l	Ribosomal protein eL39	polymer	51	6426.8	1	UniProt (A0A4X1VIM4) Pfam (PF00832) UniProt (by SIFTS) (K7GP63) In PDB	Sus scrofa (Pig)
41	m	Ribosomal protein eL40	polymer	128	14758.4	1	UniProt (P63053) Pfam (PF00240) Pfam (PF01020) In PDB	Sus scrofa (Pig)	CEP52,Ubiquitin A-52 residue ribosomal protein fusion product 1
42	n	Ribosomal protein eL41	polymer	25	3473.5	1		Sus scrofa (Pig)
43	o	Ribosomal protein eL42	polymer	106	12477.0	1	UniProt (A0A480LCM6) In PDB	Sus scrofa (Pig)
44	p	Ribosomal protein eL43	polymer	91	10168.2	1	UniProt (A0A480WPS5) In PDB	Sus scrofa (Pig)
45	r	Ribosomal protein eL28	polymer	125	14301.8	1	UniProt (A0A480YX24) In PDB	Sus scrofa (Pig)
46	1	Sec61 alpha subunit	polymer	476	52279.4	1	UniProt (A0A480EHF8) In PDB	Sus scrofa (Pig)
47	2	Sec61 gamma subunit	polymer	68	7752.3	1	UniProt (A0A480WFL1) In PDB	Sus scrofa (Pig)
48	3	Sec61 beta subunit	polymer	36	3081.8	1		Sus scrofa (Pig)
49	5, 7, 8, P, V	MAGNESIUM ION	non-polymer		24.3	130	Chemie (MG)
50	j, m, o	ZINC ION	non-polymer		65.4	3	Chemie (ZN)

Sequence modifications

B: 2 - 395 (UniProt: A0A480L253)

PDB	External Database	Details
Ile 85	Val 107	conflict
Val 86	Ile 108	conflict
Ala 140	Glu 162	conflict
Ala 141	Asp 163	conflict
Ala 143	Lys 165	conflict
Ala 144	Lys 166	conflict
Ala 145	Gln 167	conflict
Ala 147	Glu 169	conflict
Ala 148	Arg 170	conflict
Ala 155	Lys 177	conflict

C: 2 - 368 (UniProt: A0A287AE76)

PDB	External Database	Details
Ala 354	-	insertion
Ala 355	-	insertion
Ala 356	-	insertion

E: 38 - 284 (UniProt: Q2YGT9)

PDB	External Database	Details
Met 62	Lys 62	conflict
Met 64	Leu 64	conflict
-	Lys 73	deletion
-	Ser 74	deletion
-	Lys 75	deletion
-	Val 76	deletion
-	Glu 77	deletion
-	Lys 78	deletion
-	Lys 79	deletion
-	Lys 80	deletion
-	Lys 81	deletion
-	Val 82	deletion
-	Arg 83	deletion
Val 176	Ser 176	conflict
Lys 206	Glu 206	conflict

F: 26 - 250 (UniProt: A0A480W0U3)

PDB	External Database	Details
Lys 31	Arg 31	conflict

G: 1 - 266 (UniProt: A0A4X1W808)

PDB	External Database	Details
Arg 53	Cys 87	conflict
Ala 172	Ser 206	conflict
Lys 185	Asn 219	conflict
Asn 231	Asp 265	conflict

I: 2 - 214 (UniProt: Q29195)

PDB	External Database	Details
Gly 49	Cys 49	conflict
Arg 82	Lys 82	conflict
Met 87	Ile 87	conflict
Glu 145	Lys 145	conflict
Lys 187	Glu 187	conflict
Cys 189	Arg 189	conflict
Val 200	Ile 200	conflict
His 203	Arg 203	conflict
Val 211	Ala 211	conflict

O: 3 - 203 (UniProt: A0A481CAM4)

PDB	External Database	Details
Glu 3	-	variant
Gly 4	-	variant

R: 2 - 196 (UniProt: A0A480VXS3)

PDB	External Database	Details
Tyr 1	-	variant

j: 2 - 87 (UniProt: A0A480UVT3)

PDB	External Database	Details
Ile 82	Thr 82	conflict

r: 2 - 126 (UniProt: A0A480YX24)

PDB	External Database	Details
Ile 64	Met 94	conflict

1: 1 - 476 (UniProt: A0A480EHF8)

PDB	External Database	Details
His 343	Tyr 455	conflict

Contents of the asymmetric unit

Polymers	Number of chains	48
	Total formula weight	2168872.5
Non-Polymers*	Number of molecules	133
	Total formula weight	3355.9
All*	Total formula weight	2172228.4

*Water molecules are not included.