7TM3

Structure of the rabbit 80S ribosome stalled on a 2-TMD Rhodopsin intermediate in complex with the multipass translocon

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	uL2	polymer	257	28088.9	1	UniProt (G1TT27) Pfam (PF00181) Pfam (PF03947) In PDB	Oryctolagus cuniculus (rabbit)
2	B	Nascent chain	polymer	229	23488.7	1		Oryctolagus cuniculus (rabbit)
3	C	uL4	polymer	425	47727.6	1	UniProt (G1SVW5) Pfam (PF00573) Pfam (PF14374) In PDB	Oryctolagus cuniculus (rabbit)
4	D	uL18	polymer	297	34481.8	1	UniProt (G1SYJ6) UniProt (by SIFTS) (P19949) In PDB	Oryctolagus cuniculus (rabbit)
5	E	eL6	polymer	291	33028.3	1	UniProt (G1SKF7) Pfam (PF03868) Pfam (PF01159) In PDB	Oryctolagus cuniculus (rabbit)
6	F	uL30	polymer	247	29201.8	1	UniProt (G1TUB1) Pfam (PF08079) Pfam (PF00327) In PDB	Oryctolagus cuniculus (rabbit)
7	G	eL8	polymer	319	36221.5	1	UniProt (G1STW0) Pfam (PF01248) In PDB	Oryctolagus cuniculus (rabbit)
8	H	uL6	polymer	192	21871.4	1	UniProt (G1SWI6) Pfam (PF00347) In PDB	Oryctolagus cuniculus (rabbit)
9	I	uL16	polymer	214	24643.1	1	UniProt (B7NZQ2) Pfam (PF00252) In PDB	Oryctolagus cuniculus (rabbit)
10	J	uL5	polymer	178	20288.5	1	UniProt (G1TUB8) Pfam (PF00281) Pfam (PF00673) In PDB	Oryctolagus cuniculus (rabbit)
11	L	eL13	polymer	211	24331.7	1	UniProt (G1TPV0) In PDB	Oryctolagus cuniculus (rabbit)
12	M	eL14	polymer	218	23870.5	1	UniProt (G1SZ12) Pfam (PF01929) In PDB	Oryctolagus cuniculus (rabbit)
13	N	eL15	polymer	204	24207.3	1	UniProt (G1T0C1) Pfam (PF00827) In PDB	Oryctolagus cuniculus (rabbit)
14	O	uL13	polymer	203	23533.3	1		Oryctolagus cuniculus (rabbit)
15	P	uL22	polymer	184	21444.2	1	UniProt (G1TVT6) Pfam (PF00237) UniProt (by SIFTS) (G1SCJ6) In PDB	Oryctolagus cuniculus (rabbit)
16	Q	eL18	polymer	188	21653.6	1		Oryctolagus cuniculus (rabbit)
17	R	eL19	polymer	196	23535.3	1	UniProt (G1TJR3) Pfam (PF01280) In PDB	Oryctolagus cuniculus (rabbit)
18	S	eL20	polymer	176	20827.6	1		Oryctolagus cuniculus (rabbit)
19	T	eL21	polymer	160	18610.0	1	UniProt (G1SHQ2) Pfam (PF01157) In PDB	Oryctolagus cuniculus (rabbit)
20	U	eL22	polymer	128	14813.0	1	UniProt (G1TSG1) Pfam (PF01776) In PDB	Oryctolagus cuniculus (rabbit)
21	V	uL14	polymer	140	14892.5	1	UniProt (G1T6D1) Pfam (PF00238) In PDB	Oryctolagus cuniculus (rabbit)
22	W	eL24	polymer	157	17825.1	1	UniProt (G1SE28) Pfam (PF01246) In PDB	Oryctolagus cuniculus (rabbit)
23	X	uL23	polymer	156	17768.2	1	UniProt (G1SE76) Pfam (PF03939) Pfam (PF00276) In PDB	Oryctolagus cuniculus (rabbit)
24	Y	uL24	polymer	145	17303.4	1	UniProt (G1SQH0) Pfam (PF16906) Pfam (PF00467) In PDB	Oryctolagus cuniculus (rabbit)
25	Z	eL27	polymer	136	15835.8	1	UniProt (G1TXF6) Pfam (PF00467) Pfam (PF01777) In PDB	Oryctolagus cuniculus (rabbit)
26	a	uL15	polymer	148	16620.6	1	UniProt (G1SNY0) Pfam (PF00828) In PDB	Oryctolagus cuniculus (rabbit)
27	b	eL29	polymer	226	24931.6	1	UniProt (G1SGR6) Pfam (PF01779) In PDB	Oryctolagus cuniculus (rabbit)
28	c	eL30	polymer	115	12807.1	1	UniProt (G1TDL2) Pfam (PF01248) In PDB	Oryctolagus cuniculus (rabbit)
29	d	eL31	polymer	125	14494.9	1	UniProt (G1SHG0) Pfam (PF01198) In PDB	Oryctolagus cuniculus (rabbit)
30	e	eL32	polymer	135	15898.9	1	UniProt (G1U437) Pfam (PF01655) UniProt (by SIFTS) (G1TUN8) In PDB	Oryctolagus cuniculus (rabbit)
31	f	eL33	polymer	110	12580.8	1	UniProt (G1SF08) Pfam (PF01247) In PDB	Oryctolagus cuniculus (rabbit)
32	g	eL34	polymer	116	13196.9	1	UniProt (G1U945) Pfam (PF01199) UniProt (by SIFTS) (G1TXG5) In PDB	Oryctolagus cuniculus (rabbit)
33	h	uL29	polymer	123	14566.6	1	UniProt (G1SIT5) Pfam (PF00831) In PDB	Oryctolagus cuniculus (rabbit)
34	i	eL36	polymer	105	12263.8	1	UniProt (G1TTQ5) Pfam (PF01158) In PDB	Oryctolagus cuniculus (rabbit)
35	j	eL37	polymer	97	11111.0	1	UniProt (U3KPD5) Pfam (PF01907) In PDB	Oryctolagus cuniculus (rabbit)
36	k	eL38	polymer	70	8238.9	1	UniProt (G1U001) Pfam (PF01781) In PDB	Oryctolagus cuniculus (rabbit)
37	l	eL39	polymer	51	6455.8	1	UniProt (G1TTN1) Pfam (PF00832) In PDB	Oryctolagus cuniculus (rabbit)
38	m	eL40	polymer	102	11699.8	1		Oryctolagus cuniculus (rabbit)
39	n	eL41	polymer	25	3473.5	1	UniProt (A0A087WNH4) Pfam (PF05162) In PDB	Oryctolagus cuniculus (rabbit)	60s ribosomal protein l41
40	o	eL42	polymer	106	12477.0	1	UniProt (G1U344) Pfam (PF00935) UniProt (by SIFTS) (G1T040) In PDB	Oryctolagus cuniculus (rabbit)
41	p	eL43	polymer	92	10299.4	1	UniProt (G1SY53) Pfam (PF01780) In PDB	Oryctolagus cuniculus (rabbit)
42	q	P-site tRNA	polymer	77	24632.6	1		Oryctolagus cuniculus (rabbit)
43	r	eL28	polymer	137	15783.6	1	UniProt (G1U7L1) Pfam (PF01778) In PDB	Oryctolagus cuniculus (rabbit)
44	u	5S ribosomal RNA	polymer	120	38691.9	1	GenBank (X06789.1)	Oryctolagus cuniculus (rabbit)
45	v	5.8S ribosomal RNA	polymer	156	50143.6	1		Oryctolagus cuniculus (rabbit)
46	w	uL3	polymer	403	46108.0	1	UniProt (G1TL06) Pfam (PF00297) In PDB	Oryctolagus cuniculus (rabbit)
47	1	Protein transport protein Sec61 subunit alpha isoform 1	polymer	476	52279.4	1	UniProt (P38377) Pfam (PF10559) Pfam (PF00344) In PDB	Canis lupus (gray wolf)	Sec61 alpha-1
48	2	Protein transport protein Sec61 subunit beta	polymer	96	9987.5	1	UniProt (P60467) Pfam (PF03911) In PDB	Canis lupus (gray wolf)
49	3	Protein transport protein Sec61 gamma	polymer	68	7752.3	1		Canis lupus (gray wolf)
50	4	Coiled-coil domain containing 47	polymer	483	55803.5	1	UniProt (A0A8C0RJF2) Pfam (PF07946) In PDB	Canis lupus (gray wolf)
51	5	PAT complex subunit Asterix	polymer	106	12077.1	1	UniProt (A0A8C0TSD6) Pfam (PF03669) In PDB	Canis lupus (gray wolf)
52	7	Nicalin	polymer	563	63172.1	1	UniProt (A0A8C0S144) Pfam (PF04389) In PDB	Canis lupus (gray wolf)
53	6	Transmembrane protein 147	polymer	224	25309.9	1	UniProt (A0A8C0RUW0) Pfam (PF09767) In PDB	Canis lupus (gray wolf)
54	K	28S ribosomal RNA	polymer	3543	1148115.4	1		Oryctolagus cuniculus (rabbit)
55	K, P, V, a, g...	MAGNESIUM ION	non-polymer		24.3	220	Chemie (MG)
56	g, j, m, o, p	ZINC ION	non-polymer		65.4	5	Chemie (ZN)

Sequence modifications

C: 1 - 425 (UniProt: G1SVW5)

PDB	External Database	Details
Lys 378	-	insertion
Val 379	-	insertion
Lys 380	-	insertion
Lys 381	-	insertion
Pro 382	-	insertion
Arg 383	-	insertion
Ala 384	-	insertion
Val 385	-	insertion
Gly 386	-	insertion
Ile 387	-	insertion
Lys 388	-	insertion
Gln 389	-	insertion

F: 1 - 247 (UniProt: G1TUB1)

PDB	External Database	Details
Arg 61	Gly 61	conflict
Arg 93	Gly 93	conflict
Met 131	Val 131	conflict
Ile 153	Val 153	conflict

G: 1 - 319 (UniProt: G1STW0)

PDB	External Database	Details
Gly 244	Cys 244	conflict

L: 1 - 211 (UniProt: G1TPV0)

PDB	External Database	Details
Ile 46	-	insertion
Ala 47	-	insertion
Pro 48	-	insertion
Arg 49	-	insertion
Pro 50	-	insertion
Ala 51	-	insertion
Ala 52	-	insertion
Gly 53	-	insertion
Pro 54	-	insertion

R: 1 - 196 (UniProt: G1TJR3)

PDB	External Database	Details
Arg 38	Cys 38	conflict
Arg 64	Gln 64	conflict
Thr 94	Lys 94	conflict

U: 1 - 128 (UniProt: G1TSG1)

PDB	External Database	Details
Leu 18	Val 18	conflict
Gly 32	Arg 32	conflict
Ala 36	Glu 36	conflict
Phe 39	Ser 39	conflict
Gly 54	Arg 54	conflict
Val 60	Ala 60	conflict
Ser 62	Thr 62	conflict
Leu 63	Ile 63	conflict
Arg 97	His 97	conflict
Thr 106	Ser 106	conflict
Glu 126	Asp 126	conflict

k: 1 - 70 (UniProt: G1U001)

PDB	External Database	Details
Lys 24	Asn 24	conflict

u: 1 - 120 (GenBank: X06789.1)

PDB	External Database	Details
U 2	N 2	conflict
C 36	N 36	conflict
U 102	N 102	conflict
U 112	N 112	conflict
U 114	N 114	conflict
U 119	C 119	conflict
U 120	N 120	conflict

w: 2 - 403 (UniProt: G1TL06)

PDB	External Database	Details
Met 1	-	insertion

Contents of the asymmetric unit

Polymers	Number of chains	54
	Total formula weight	2350466.7
Non-Polymers*	Number of molecules	225
	Total formula weight	5674.1
All*	Total formula weight	2356140.9

*Water molecules are not included.