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Structure of the RQT-bound 80S ribosome from S. cerevisiae (C1)

Analyse Structure of the RQT-bound 80S ribosome from S. cerevisiae (C1) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7ZPQ
Type: protein + RNA
Length: 18,603 residues
Chains: 82
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.47
Source: Saccharomyces cerevisiae
Molecule: 18S ribosomal RNA; 5.8S ribosomal RNA; 5S ribosomal RNA; 25S ribosomal RNA; tRNA; 40S…
UniProt: B3LI22, A0A6A5PRY4, A0A6A5PWF7, A0A6A5Q3Q1, P0CX35, A0A1L4AA68, P0CX37, P26786, A0A6A5Q1H1, O13516, Q08745, P0CX47, A0A6A5Q8I3, P05756, P39516, A0A6A5Q6F2, P0CX51, P14127, P0CX55, P07280, A0A6A5PVE9, P0C0V8, A0A6A5PSE9, P0CX29, P0CX31, A0A6A5PZ18, A0A6A5Q0E8, P35997, A0A6A5Q700, A0A6A5PV92, P0CX33, A0A6A5PU37, P38011, P0CX45, A0A6A5Q627, A0A6A5Q3W0, A0A6A5Q0W8, P05739, P05737, P17076, P05738, A0A6A5PUZ5, A0A6A5PYM2, Q12690, P36105, P05748, P26784, P05740, P0CX49, P0CX82, P0CX23, Q02753, P05749, P0CX41, A0A6A5PY83, P04456, P05743, P0C2H6, P02406, A0A6A5PWR1, P14120, P0C2H8, A0A6A5Q1M9, P05744, P87262, P0CX84, P05745, P49166, A0A6A5PUL8, P04650, P0CH08, A0A8H8UMB4, P0CX27, P0CX25, A0A8H8UL01, P53137, A0A8H4C0K6
Ligands: MG, ZN
Pockets: 20 · best druggability 0.90

Structure

electron microscopy · resolution 3.47 · 82 distinct chains · 32% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
2	18S ribosomal RNA	rna	1771	—	—
3	5.8S ribosomal RNA	rna	158	—	—
4	5S ribosomal RNA	rna	121	—	—
5	25S ribosomal RNA	rna	3184	—	—
6	tRNA	rna	76	—	—
AA	40S ribosomal protein S0-A	protein	206	33% helix, 11% strand	B3LI22
AB	40S ribosomal protein S1	protein	226	25% helix, 24% strand	A0A6A5PRY4
AC	RPS2 isoform 1	protein	216	32% helix, 26% strand	A0A6A5PWF7
AD	RPS3 isoform 1	protein	222	37% helix, 29% strand	A0A6A5Q3Q1
AE	40S ribosomal protein S4-A	protein	258	16% helix, 29% strand	P0CX35
AF	Rps5p	protein	206	46% helix, 9% strand	A0A1L4AA68
AG	40S ribosomal protein S6-A	protein	228	29% helix, 22% strand	P0CX37
AH	40S ribosomal protein S7-A	protein	184	38% helix, 19% strand	P26786
AI	40S ribosomal protein S8	protein	187	27% helix, 28% strand	A0A6A5Q1H1
AJ	40S ribosomal protein S9-A	protein	184	46% helix, 3% strand	O13516
AK	40S ribosomal protein S10-A	protein	92	40% helix, 12% strand	Q08745
AL	40S ribosomal protein S11-A	protein	144	6% helix, 32% strand	P0CX47
AM	40S ribosomal protein S12	protein	121	32% helix, 8% strand	A0A6A5Q8I3
AN	40S ribosomal protein S13	protein	150	55% helix, 0% strand	P05756
AO	40S ribosomal protein S14-B	protein	127	26% helix, 25% strand	P39516
AP	RPS15 isoform 1	protein	117	30% helix, 11% strand	A0A6A5Q6F2
AQ	40S ribosomal protein S16-A	protein	141	40% helix, 21% strand	P0CX51
AR	40S ribosomal protein S17-B	protein	121	53% helix, 2% strand	P14127
AS	40S ribosomal protein S18-A	protein	145	38% helix, 8% strand	P0CX55
AT	40S ribosomal protein S19-A	protein	143	48% helix, 10% strand	P07280
AU	RPS20 isoform 1	protein	100	25% helix, 36% strand	A0A6A5PVE9
AV	40S ribosomal protein S21-A	protein	87	17% helix, 26% strand	P0C0V8
AW	RPS22A isoform 1	protein	129	34% helix, 26% strand	A0A6A5PSE9
AX	40S ribosomal protein S23-A	protein	144	24% helix, 26% strand	P0CX29
AY	40S ribosomal protein S24-A	protein	134	35% helix, 25% strand	P0CX31
AZ	40S ribosomal protein S25	protein	82	29% helix, 15% strand	A0A6A5PZ18
Aa	RPS26B isoform 1	protein	97	11% helix, 18% strand	A0A6A5Q0E8
Ab	40S ribosomal protein S27-A	protein	81	7% helix, 21% strand	P35997
Ac	RPS28A isoform 1	protein	63	0% helix, 48% strand	A0A6A5Q700
Ad	RPS29A isoform 1	protein	53	32% helix, 9% strand	A0A6A5PV92
Ae	40S ribosomal protein S30-A	protein	60	35% helix, 0% strand	P0CX33
Af	RPS31 isoform 1	protein	73	0% helix, 3% strand	A0A6A5PU37
Ag	Guanine nucleotide-binding protein subunit beta-like protein	protein	312	1% helix, 48% strand	P38011
BA	60S ribosomal protein L2-A	protein	251	8% helix, 23% strand	P0CX45
BB	60S ribosomal protein L3	protein	386	13% helix, 26% strand	A0A6A5Q627
BC	RPL4A isoform 1	protein	361	32% helix, 8% strand	A0A6A5Q3W0
BD	RPL5 isoform 1	protein	294	41% helix, 11% strand	A0A6A5Q0W8
BE	60S ribosomal protein L6-B	protein	167	21% helix, 17% strand	P05739
BF	60S ribosomal protein L7-A	protein	222	49% helix, 15% strand	P05737
BG	60S ribosomal protein L8-A	protein	233	45% helix, 8% strand	P17076
BH	60S ribosomal protein L9-A	protein	191	20% helix, 39% strand	P05738
BI	RPL10 isoform 1	protein	218	27% helix, 23% strand	A0A6A5PUZ5
BJ	RPL11B isoform 1	protein	169	28% helix, 21% strand	A0A6A5PYM2
BK	60S ribosomal protein L13-A	protein	193	39% helix, 8% strand	Q12690
BL	60S ribosomal protein L14-A	protein	136	43% helix, 26% strand	P36105
BM	60S ribosomal protein L15-A	protein	203	38% helix, 17% strand	P05748
BN	60S ribosomal protein L16-A	protein	197	53% helix, 11% strand	P26784
BO	60S ribosomal protein L17-A	protein	183	35% helix, 27% strand	P05740
BP	60S ribosomal protein L18-A	protein	185	31% helix, 15% strand	P0CX49
BQ	60S ribosomal protein L19-A	protein	188	71% helix, 0% strand	P0CX82
BR	60S ribosomal protein L20-A	protein	171	23% helix, 32% strand	P0CX23
BS	60S ribosomal protein L21-A	protein	159	19% helix, 25% strand	Q02753
BT	60S ribosomal protein L22-A	protein	100	29% helix, 30% strand	P05749
BU	60S ribosomal protein L23-A	protein	136	9% helix, 33% strand	P0CX41
BV	RPL24A isoform 1	protein	126	40% helix, 10% strand	A0A6A5PY83
BW	60S ribosomal protein L25	protein	121	26% helix, 21% strand	P04456
BX	60S ribosomal protein L26-A	protein	125	30% helix, 32% strand	P05743
BY	60S ribosomal protein L27-A	protein	135	19% helix, 22% strand	P0C2H6
BZ	60S ribosomal protein L28	protein	148	22% helix, 14% strand	P02406
Ba	60S ribosomal protein L29	protein	58	48% helix, 0% strand	A0A6A5PWR1
Bb	60S ribosomal protein L30	protein	96	43% helix, 19% strand	P14120
Bc	60S ribosomal protein L31-A	protein	109	28% helix, 28% strand	P0C2H8
Bd	RPL32 isoform 1	protein	127	19% helix, 9% strand	A0A6A5Q1M9
Be	60S ribosomal protein L33-A	protein	106	7% helix, 48% strand	P05744
Bf	60S ribosomal protein L34-A	protein	112	35% helix, 11% strand	P87262
Bg	60S ribosomal protein L35-A	protein	119	58% helix, 2% strand	P0CX84
Bh	60S ribosomal protein L36-A	protein	99	63% helix, 0% strand	P05745
Bi	60S ribosomal protein L37-A	protein	85	24% helix, 7% strand	P49166
Bj	RPL38 isoform 1	protein	77	18% helix, 42% strand	A0A6A5PUL8
Bk	60S ribosomal protein L39	protein	50	32% helix, 0% strand	P04650
Bl	60S ribosomal protein L40-A	protein	52	27% helix, 15% strand	P0CH08
Bm	RPL41A isoform 1	protein	25	84% helix, 0% strand	A0A8H8UMB4
Bn	60S ribosomal protein L42-A	protein	103	10% helix, 32% strand	P0CX27
Bo	60S ribosomal protein L43-A	protein	91	41% helix, 18% strand	P0CX25
CA	SLH1 isoform 1	protein	1742	39% helix, 15% strand	A0A8H8UL01
CB	RQC trigger complex subunit CUE3	protein	297	62% helix, 0% strand	P53137
CC	RQT4 isoform 1	protein	114	29% helix, 5% strand	A0A8H4C0K6

Ligands and binding sites

MG · Magnesium ion · metal · 86 copies · chains 2, AC, AN, AQ, AS, AT, AX, AU, AE, AF
ZN · Zinc ion · metal · 9 copies · chains 2, Ad, Af, Bf, Bi, Bl, Bn, Bo, CC

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	900	0.90	0.94	115	MG
2	1002	0.89	0.91	107	empty
3	837	0.88	0.92	112	empty
4	1080	0.88	0.91	104	empty
5	643	0.88	0.93	78	MG

Interfaces

246 interfaces between chains.

5–BB · 9123 Å² buried · 216 hydrogen bonds · protein-nucleic
5–BC · 8247 Å² buried · 168 hydrogen bonds · protein-nucleic
5–BM · 7460 Å² buried · 149 hydrogen bonds · protein-nucleic
5–BA · 7106 Å² buried · 187 hydrogen bonds · protein-nucleic
3–5 · 5182 Å² buried · 274 hydrogen bonds · nucleic-nucleic

Compared structures

P0CX45 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L2-a (P0CX45) · a predicted model of the same protein · chain BA against A, TM-score 0.99
P14120 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L30 (P14120) · a predicted model of the same protein · chain Bb against A, TM-score 0.98
P39516 · AlphaFold monomer V2.0 prediction for 40S ribosomal protein S14-B (P39516) · a predicted model of the same protein · chain AO against A, TM-score 0.98
P0CX25 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L43-a (P0CX25) · a predicted model of the same protein · chain Bo against A, TM-score 0.98
P05756 · AlphaFold monomer V2.0 prediction for 40S ribosomal protein S13 (P05756) · a predicted model of the same protein · chain AN against A, TM-score 0.98
P05743 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L26-a (P05743) · a predicted model of the same protein · chain BX against A, TM-score 0.98
P38011 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein subunit… · a predicted model of the same protein · chain Ag against A, TM-score 0.98
B3LI22 · AlphaFold monomer V2.0 prediction for 40S ribosomal protein S0-a (B3LI22) · a predicted model of the same protein · chain AA against A, TM-score 0.97
P0CX27 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L42-a (P0CX27) · a predicted model of the same protein · chain Bn against A, TM-score 0.97
P0CX49 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L18-a (P0CX49) · a predicted model of the same protein · chain BP against A, TM-score 0.97
P05739 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L6-B (P05739) · a predicted model of the same protein · chain BE against A, TM-score 0.97
P02406 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L28 (P02406) · a predicted model of the same protein · chain BZ against A, TM-score 0.97

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