8RJC

Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in complex with Sec61-TRAP, open conformation 1

• PDB DOI: https://doi.org/10.2210/pdb8RJC/pdb
• EM Map EMD-19197: EMDB EMDataResource
• NAKB: 8RJC

• Classification: RIBOSOME
• Organism(s): Canis lupus familiaris, Oryctolagus cuniculus, Bos taurus, Oryctolagus, Sus scrofa
• Expression System: Oryctolagus cuniculus
• Mutation(s): No 


• Deposited: 2023-12-20 Released: 2024-01-24 
• Deposition Author(s): Lewis, A.J.O., Hegde, R.S.
• Funding Organization(s): Medical Research Council (MRC, United Kingdom)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in complex with Sec61-TRAP, open conformation 1

Lewis, A.J.O., Hegde, R.S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 52-mer - A1B1C1D1E1F1G1H1I1J1K1L1M1N1O1P1Q1R1S1T1U1V1W1X1Y1Z1a1b1c1d1e1f1g1h1i1j1k1l1m1n1o1p1q1r1s1t1u1v1w1x1y1z1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 52-mer - A2B1C1D1E1F1G1H1I1J1K1L1M1N1O1P1Q1R1S1T1U1V1W1X1Y1Z1a1b1c1d1e1f1g1h1i1j1k1l1m1n1o1p1q1r1s1t1u1v1w1x1y1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 2,366.69 kDa 
• Atom Count: 146,794 
• Modelled Residue Count: 11,717 
• Deposited Residue Count: 13,557 
• Unique protein chains: 52
• Unique nucleic acid chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein transport protein Sec61 subunit alpha isoform 1	A [auth 1]	476	Canis lupus familiaris	Mutation(s): 0
UniProt
Find proteins for P38377 (Canis lupus familiaris) Explore P38377  Go to UniProtKB:  P38377

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein transport protein Sec61 subunit beta	B [auth 2]	96	Canis lupus familiaris	Mutation(s): 0
UniProt
Find proteins for P60467 (Canis lupus familiaris) Explore P60467  Go to UniProtKB:  P60467

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein transport protein Sec61 subunit gamma	C [auth 3]	68	Canis lupus familiaris	Mutation(s): 0
UniProt
Find proteins for P60058 (Canis lupus familiaris) Explore P60058  Go to UniProtKB:  P60058

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Stress-associated endoplasmic reticulum protein	D [auth 4]	66	Canis lupus familiaris	Mutation(s): 0
UniProt
Find proteins for A0A8C0RGL8 (Canis lupus familiaris) Explore A0A8C0RGL8  Go to UniProtKB:  A0A8C0RGL8

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Translocon-associated protein subunit alpha	E [auth 5]	286	Canis lupus familiaris	Mutation(s): 0
UniProt
Find proteins for P16967 (Canis lupus familiaris) Explore P16967  Go to UniProtKB:  P16967

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Translocon-associated protein subunit beta	F [auth 6]	183	Canis lupus familiaris	Mutation(s): 0
UniProt
Find proteins for P23438 (Canis lupus familiaris) Explore P23438  Go to UniProtKB:  P23438

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Translocon-associated protein subunit gamma	G [auth 7]	185	Canis lupus familiaris	Mutation(s): 0
UniProt
Find proteins for A0A8C0T6I4 (Canis lupus familiaris) Explore A0A8C0T6I4  Go to UniProtKB:  A0A8C0T6I4

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Translocon-associated protein subunit delta	H [auth 8]	173	Canis lupus familiaris	Mutation(s): 0
UniProt
Find proteins for A0A8I3PXW2 (Canis lupus familiaris) Explore A0A8I3PXW2  Go to UniProtKB:  A0A8I3PXW2

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Calnexin	I [auth 9]	593	Canis lupus familiaris	Mutation(s): 0
UniProt
Find proteins for P24643 (Canis lupus familiaris) Explore P24643  Go to UniProtKB:  P24643

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein L8	J [auth A]	257	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1TT27 (Oryctolagus cuniculus) Explore G1TT27  Go to UniProtKB:  G1TT27

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Nascent chain	K [auth B]	229	Bos taurus	Mutation(s): 0

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL4	L [auth C]	425	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for A0A5F9C3C5 (Oryctolagus cuniculus) Explore A0A5F9C3C5  Go to UniProtKB:  A0A5F9C3C5

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal_L18_c domain-containing protein	M [auth D]	297	Oryctolagus cuniculus	Mutation(s): 0

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L6	N [auth E]	291	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1SKF7 (Oryctolagus cuniculus) Explore G1SKF7  Go to UniProtKB:  G1SKF7

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal Protein uL30	O [auth F]	247	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1TUB1 (Oryctolagus cuniculus) Explore G1TUB1  Go to UniProtKB:  G1TUB1

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L7a	P [auth G]	319	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1STW0 (Oryctolagus cuniculus) Explore G1STW0  Go to UniProtKB:  G1STW0

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L9	Q [auth H]	192	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1SWI6 (Oryctolagus cuniculus) Explore G1SWI6  Go to UniProtKB:  G1SWI6

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L10	R [auth I]	214	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for B7NZQ2 (Oryctolagus cuniculus) Explore B7NZQ2  Go to UniProtKB:  B7NZQ2

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L11	S [auth J]	178	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1TUB8 (Oryctolagus cuniculus) Explore G1TUB8  Go to UniProtKB:  G1TUB8

Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L13	U [auth L]	211	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1TKB3 (Oryctolagus cuniculus) Explore G1TKB3  Go to UniProtKB:  G1TKB3

Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L14	V [auth M]	218	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1SZ12 (Oryctolagus cuniculus) Explore G1SZ12  Go to UniProtKB:  G1SZ12

Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein L15	W [auth N]	204	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1T0C1 (Oryctolagus cuniculus) Explore G1T0C1  Go to UniProtKB:  G1T0C1

Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L13	X [auth O]	203	Oryctolagus cuniculus	Mutation(s): 0

Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
uL22	Y [auth P]	184	Oryctolagus cuniculus	Mutation(s): 0

Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein L18	Z [auth Q]	187	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1TFE0 (Oryctolagus cuniculus) Explore G1TFE0  Go to UniProtKB:  G1TFE0

Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein L19	AA [auth R]	196	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1TJR3 (Oryctolagus cuniculus) Explore G1TJR3  Go to UniProtKB:  G1TJR3

Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L18a	BA [auth S]	176	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for A0A287APR1 (Sus scrofa) Explore A0A287APR1  Go to UniProtKB:  A0A287APR1

Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L21	CA [auth T]	160	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1SHQ2 (Oryctolagus cuniculus) Explore G1SHQ2  Go to UniProtKB:  G1SHQ2

Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein L22	DA [auth U]	128	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1TSG1 (Oryctolagus cuniculus) Explore G1TSG1  Go to UniProtKB:  G1TSG1

Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein L23	EA [auth V]	140	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1T6D1 (Oryctolagus cuniculus) Explore G1T6D1  Go to UniProtKB:  G1T6D1

Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein L24	FA [auth W]	157	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1SE28 (Oryctolagus cuniculus) Explore G1SE28  Go to UniProtKB:  G1SE28

Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal_L23eN domain-containing protein	GA [auth X]	156	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1SE76 (Oryctolagus cuniculus) Explore G1SE76  Go to UniProtKB:  G1SE76

Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein L26	HA [auth Y]	145	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1SQH0 (Oryctolagus cuniculus) Explore G1SQH0  Go to UniProtKB:  G1SQH0

Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L27	IA [auth Z]	136	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1TXF6 (Oryctolagus cuniculus) Explore G1TXF6  Go to UniProtKB:  G1TXF6

Entity ID: 36
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L27a	JA [auth a]	148	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1SNY0 (Oryctolagus cuniculus) Explore G1SNY0  Go to UniProtKB:  G1SNY0

Entity ID: 37
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L29	KA [auth b]	226	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1SGR6 (Oryctolagus cuniculus) Explore G1SGR6  Go to UniProtKB:  G1SGR6

Entity ID: 38
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L30	LA [auth c]	115	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1TDL2 (Oryctolagus cuniculus) Explore G1TDL2  Go to UniProtKB:  G1TDL2

Entity ID: 39
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L31	MA [auth d]	125	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1SHG0 (Oryctolagus cuniculus) Explore G1SHG0  Go to UniProtKB:  G1SHG0

Entity ID: 40
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein L32	NA [auth e]	135	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1TUN8 (Oryctolagus cuniculus) Explore G1TUN8  Go to UniProtKB:  G1TUN8

Entity ID: 41
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L35a	OA [auth f]	110	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1SF08 (Oryctolagus cuniculus) Explore G1SF08  Go to UniProtKB:  G1SF08

Entity ID: 42
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L34	PA [auth g]	116	Oryctolagus cuniculus	Mutation(s): 0

Entity ID: 43
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L35	QA [auth h]	123	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1SIT5 (Oryctolagus cuniculus) Explore G1SIT5  Go to UniProtKB:  G1SIT5

Entity ID: 44
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L36	RA [auth i]	105	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1TTQ5 (Oryctolagus cuniculus) Explore G1TTQ5  Go to UniProtKB:  G1TTQ5

Entity ID: 45
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein L37	SA [auth j]	97	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for U3KPD5 (Oryctolagus cuniculus) Explore U3KPD5  Go to UniProtKB:  U3KPD5

Entity ID: 46
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L38	TA [auth k]	70	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1U001 (Oryctolagus cuniculus) Explore G1U001  Go to UniProtKB:  G1U001

Entity ID: 47
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L39-like	UA [auth l]	51	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1TTN1 (Oryctolagus cuniculus) Explore G1TTN1  Go to UniProtKB:  G1TTN1

Entity ID: 48
Molecule	Chains	Sequence Length	Organism	Details	Image
eL40	VA [auth m]	102	Oryctolagus cuniculus	Mutation(s): 0

Entity ID: 49
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L41	WA [auth n]	25	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for A0A087WNH4 (Oryctolagus cuniculus) Explore A0A087WNH4  Go to UniProtKB:  A0A087WNH4

Entity ID: 50
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L36a-like	XA [auth o]	106	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1T040 (Oryctolagus cuniculus) Explore G1T040  Go to UniProtKB:  G1T040

Entity ID: 51
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L37a	YA [auth p]	92	Oryctolagus	Mutation(s): 0
UniProt
Find proteins for G1SY53 (Oryctolagus cuniculus) Explore G1SY53  Go to UniProtKB:  G1SY53

Entity ID: 53
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L28	AB [auth r]	137	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1U7L1 (Oryctolagus cuniculus) Explore G1U7L1  Go to UniProtKB:  G1U7L1

Entity ID: 56
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein L3	DB [auth w]	403	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1TL06 (Oryctolagus cuniculus) Explore G1TL06  Go to UniProtKB:  G1TL06

Entity ID: 20
Molecule	Chains	Length	Organism	Image
28S rRNA	T [auth K]	3,543	Oryctolagus cuniculus

Entity ID: 52
Molecule	Chains	Length	Organism	Image
P-site tRNA	ZA [auth q]	76	Sus scrofa

Entity ID: 54
Molecule	Chains	Length	Organism	Image
5S rRNA	BB [auth u]	120	Oryctolagus cuniculus

Entity ID: 55
Molecule	Chains	Length	Organism	Image
5.8S rRNA	CB [auth v]	156	Oryctolagus cuniculus

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	BJ [auth g], DJ [auth j], EJ [auth m], FJ [auth o], GJ [auth p]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	AC [auth K], AD [auth K], AE [auth K], AF [auth K], AG [auth K], AH [auth K], AI [auth K], AJ [auth g], BC [auth K], BD [auth K], BE [auth K], BF [auth K], BG [auth K], BH [auth K], BI [auth K], CC [auth K], CD [auth K], CE [auth K], CF [auth K], CG [auth K], CH [auth K], CI [auth K], CJ [auth j], DC [auth K], DD [auth K], DE [auth K], DF [auth K], DG [auth K], DH [auth K], DI [auth K], EB [auth I], EC [auth K], ED [auth K], EE [auth K], EF [auth K], EG [auth K], EH [auth K], EI [auth K], FB [auth K], FC [auth K], FD [auth K], FE [auth K], FF [auth K], FG [auth K], FH [auth K], FI [auth K], GB [auth K], GC [auth K], GD [auth K], GE [auth K], GF [auth K], GG [auth K], GH [auth K], GI [auth K], HB [auth K], HC [auth K], HD [auth K], HE [auth K], HF [auth K], HG [auth K], HH [auth K], HI [auth K], HJ [auth u], IB [auth K], IC [auth K], ID [auth K], IE [auth K], IF [auth K], IG [auth K], IH [auth K], II [auth K], IJ [auth u], JB [auth K], JC [auth K], JD [auth K], JE [auth K], JF [auth K], JG [auth K], JH [auth K], JI [auth K], JJ [auth u], KB [auth K], KC [auth K], KD [auth K], KE [auth K], KF [auth K], KG [auth K], KH [auth K], KI [auth K], KJ [auth u], LB [auth K], LC [auth K], LD [auth K], LE [auth K], LF [auth K], LG [auth K], LH [auth K], LI [auth K], LJ [auth u], MB [auth K], MC [auth K], MD [auth K], ME [auth K], MF [auth K], MG [auth K], MH [auth K], MI [auth K], MJ [auth u], NB [auth K], NC [auth K], ND [auth K], NE [auth K], NF [auth K], NG [auth K], NH [auth K], NI [auth K], NJ [auth u], OB [auth K], OC [auth K], OD [auth K], OE [auth K], OF [auth K], OG [auth K], OH [auth K], OI [auth K], OJ [auth v], PB [auth K], PC [auth K], PD [auth K], PE [auth K], PF [auth K], PG [auth K], PH [auth K], PI [auth K], PJ [auth v], QB [auth K], QC [auth K], QD [auth K], QE [auth K], QF [auth K], QG [auth K], QH [auth K], QI [auth K], QJ [auth v], RB [auth K], RC [auth K], RD [auth K], RE [auth K], RF [auth K], RG [auth K], RH [auth K], RI [auth K], RJ [auth v], SB [auth K], SC [auth K], SD [auth K], SE [auth K], SF [auth K], SG [auth K], SH [auth K], SI [auth K], SJ [auth w], TB [auth K], TC [auth K], TD [auth K], TE [auth K], TF [auth K], TG [auth K], TH [auth K], TI [auth K], UB [auth K], UC [auth K], UD [auth K], UE [auth K], UF [auth K], UG [auth K], UH [auth K], UI [auth K], VB [auth K], VC [auth K], VD [auth K], VE [auth K], VF [auth K], VG [auth K], VH [auth K], VI [auth K], WB [auth K], WC [auth K], WD [auth K], WE [auth K], WF [auth K], WG [auth K], WH [auth K], WI [auth K], XB [auth K], XC [auth K], XD [auth K], XE [auth K], XF [auth K], XG [auth K], XH [auth K], XI [auth K], YB [auth K], YC [auth K], YD [auth K], YE [auth K], YF [auth K], YG [auth K], YH [auth K], YI [auth V], ZB [auth K], ZC [auth K], ZD [auth K], ZE [auth K], ZF [auth K], ZG [auth K], ZH [auth K], ZI [auth a]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-01-24 
Deposition Author(s): Lewis, A.J.O., Hegde, R.S.

---

Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	MC_UP_A022_1007

Revision History  

• Version 1.0: 2024-01-24
  Type: Initial release