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Structure of yeast disome (di-ribosome) stalled on poly(A) tract.

Analyse Structure of yeast disome (di-ribosome) stalled on poly(A) tract. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6T83
Type: protein + RNA
Length: 32,931 residues
Chains: 159
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 4.0
Source: Saccharomyces cerevisiae
Molecule: 18S rRNA; 40S ribosomal protein S0-A; 40S ribosomal protein S1-A; 40S ribosomal protein…
UniProt: P32905, P33442, Q01855, P25443, P05750, P0CX35, A0A1L4AA68, P0CX37, P26786, P0CX39, O13516, Q08745, P0CX47, P48589, P05756, P06367, P0CX51, P14127, P0CX55, P07280, P38701, P0C0V8, P0C0W1, P0CX29, P0CX31, Q3E792, P39938, P35997, P41057, P0CX33, P05759, P38011, P0C0X0, P0CX45, P14126, P10664, P26321, Q02326, P05737, P17076, P05738, P41805, P0C0W9, Q12690, P36105, P05748, P26784, P05740, P0CX49, P0CX82, P0CX23, Q02753, P05749, P0CX41, P04449, P04456, P05743, P0C2H6, P02406, P05747, P14120, P0C2H8, P38061, P05744, P87262, P0CX84, P05745, P49166, P49167, P04650, P0CH08, P0CX27, P0CX25, P05317
Pockets: 20 · best druggability 0.90

Structure

electron microscopy · resolution 4.0 · 118 distinct chains · 30% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
2b	18S rRNA	rna	1771	—	—
Ab, b	40S ribosomal protein S0-A	protein	206	35% helix, 11% strand	P32905
Ba	40S ribosomal protein S1-A	protein	226	26% helix, 25% strand	P33442
Pb	40S ribosomal protein S15	protein	117	32% helix, 15% strand	Q01855
Cb	40S ribosomal protein S2	protein	216	34% helix, 26% strand	P25443
Db	40S ribosomal protein S3	protein	222	38% helix, 27% strand	P05750
Eb	40S ribosomal protein S4-A	protein	258	15% helix, 30% strand	P0CX35
Fb, g	Rps5p	protein	206	48% helix, 5% strand	A0A1L4AA68
Gb	40S ribosomal protein S6-A	protein	228	29% helix, 21% strand	P0CX37
Hb	40S ribosomal protein S7-A	protein	184	34% helix, 19% strand	P26786
Ib	40S ribosomal protein S8-A	protein	187	28% helix, 28% strand	P0CX39
Jb	40S ribosomal protein S9-A	protein	184	53% helix, 2% strand	O13516
Kb, l	40S ribosomal protein S10-A	protein	92	42% helix, 11% strand	Q08745
Lb	40S ribosomal protein S11-A	protein	144	3% helix, 28% strand	P0CX47
Mb	40S ribosomal protein S12	protein	121	40% helix, 6% strand	P48589
Nb, o	40S ribosomal protein S13	protein	150	55% helix, 0% strand	P05756
Ob	40S ribosomal protein S14-A	protein	127	26% helix, 26% strand	P06367
Qb, r	40S ribosomal protein S16-A	protein	141	39% helix, 21% strand	P0CX51
Rb	40S ribosomal protein S17-B	protein	121	53% helix, 2% strand	P14127
Sb, t	40S ribosomal protein S18-A	protein	145	36% helix, 8% strand	P0CX55
Tb, u	40S ribosomal protein S19-A	protein	143	45% helix, 11% strand	P07280
Ub	40S ribosomal protein S20	protein	100	26% helix, 38% strand	P38701
Vb, w	40S ribosomal protein S21-A	protein	87	21% helix, 24% strand	P0C0V8
Wb, x	40S ribosomal protein S22-A	protein	129	29% helix, 22% strand	P0C0W1
Xb, y	40S ribosomal protein S23-A	protein	144	18% helix, 23% strand	P0CX29
Yb, z	40S ribosomal protein S24-A	protein	134	34% helix, 24% strand	P0CX31
Zb	40S ribosomal protein S25-A	protein	82	35% helix, 20% strand	Q3E792
ab, 1	40S ribosomal protein S26-A	protein	97	14% helix, 18% strand	P39938
bb, 2	40S ribosomal protein S27-A	protein	81	6% helix, 16% strand	P35997
db, 4	40S ribosomal protein S29-A	protein	53	32% helix, 11% strand	P41057
eb, 5	40S ribosomal protein S30-A	protein	60	35% helix, 0% strand	P0CX33
fb, 6	Ubiquitin-40S ribosomal protein S31	protein	73	0% helix, 0% strand	P05759
gb	Guanine nucleotide-binding protein subunit beta-like protein	protein	312	1% helix, 52% strand	P38011
cb, 3	40S ribosomal protein S28-B	protein	63	0% helix, 35% strand	P0C0X0
4b, Bb	5S rRNA	rna	121	—	—
3b	5.8S rRNA	rna	158	—	—
Ay	60S ribosomal protein L2-A	protein	251	8% helix, 22% strand	P0CX45
By, Ea	60S ribosomal protein L3	protein	386	12% helix, 24% strand	P14126
Cy, Fa	60S ribosomal protein L4-A	protein	361	32% helix, 6% strand	P10664
Dy, Ga	60S ribosomal protein L5	protein	294	40% helix, 11% strand	P26321
Ey	60S ribosomal protein L6-A	protein	167	20% helix, 18% strand	Q02326
Fy	60S ribosomal protein L7-A	protein	222	49% helix, 14% strand	P05737
Gy	60S ribosomal protein L8-A	protein	233	46% helix, 6% strand	P17076
Hy	60S ribosomal protein L9-A	protein	191	23% helix, 42% strand	P05738
Iy	60S ribosomal protein L10	protein	218	26% helix, 24% strand	P41805
Jy, Ma	60S ribosomal protein L11-A	protein	169	25% helix, 20% strand	P0C0W9
Ly	60S ribosomal protein L13-A	protein	193	42% helix, 8% strand	Q12690
My	60S ribosomal protein L14-A	protein	136	40% helix, 18% strand	P36105
Ny, Pa	60S ribosomal protein L15-A	protein	203	34% helix, 17% strand	P05748
Oy, Qa	60S ribosomal protein L16-A	protein	197	48% helix, 8% strand	P26784
Py	60S ribosomal protein L17-A	protein	183	36% helix, 26% strand	P05740
Qy, B	60S ribosomal protein L18-A	protein	185	27% helix, 12% strand	P0CX49
Ry	60S ribosomal protein L19-A	protein	188	72% helix, 1% strand	P0CX82
Sy	60S ribosomal protein L20-A	protein	171	20% helix, 32% strand	P0CX23
Ty, E	60S ribosomal protein L21-A	protein	159	14% helix, 25% strand	Q02753
Uy	60S ribosomal protein L22-A	protein	100	32% helix, 28% strand	P05749
Vy	60S ribosomal protein L23-A	protein	136	9% helix, 27% strand	P0CX41
Wy	60S ribosomal protein L24-A	protein	126	39% helix, 8% strand	P04449
Xy	60S ribosomal protein L25	protein	121	28% helix, 22% strand	P04456
Yy	60S ribosomal protein L26-A	protein	125	29% helix, 28% strand	P05743
Zy, K	60S ribosomal protein L27-A	protein	135	24% helix, 21% strand	P0C2H6
ay, L	60S ribosomal protein L28	protein	148	21% helix, 11% strand	P02406
by, M	60S ribosomal protein L29	protein	58	43% helix, 0% strand	P05747
cy	60S ribosomal protein L30	protein	96	43% helix, 21% strand	P14120
dy, O	60S ribosomal protein L31-A	protein	109	22% helix, 27% strand	P0C2H8
ey, P	60S ribosomal protein L32	protein	127	22% helix, 3% strand	P38061
fy, Q	60S ribosomal protein L33-A	protein	106	4% helix, 41% strand	P05744
gy, R	60S ribosomal protein L34-A	protein	112	33% helix, 11% strand	P87262
hb, S	60S ribosomal protein L35-A	protein	119	52% helix, 3% strand	P0CX84
ib, T	60S ribosomal protein L36-A	protein	99	56% helix, 0% strand	P05745
jb	60S ribosomal protein L37-A	protein	85	24% helix, 4% strand	P49166
kb, V	60S ribosomal protein L38	protein	77	22% helix, 36% strand	P49167
lb, W	60S ribosomal protein L39	protein	50	28% helix, 0% strand	P04650
mb, X	Ubiquitin-60S ribosomal protein L40	protein	52	21% helix, 13% strand	P0CH08
nb, Y	60S ribosomal protein L41-A	protein	25	52% helix, 0% strand	—
ob	60S ribosomal protein L42-A	protein	103	10% helix, 24% strand	P0CX27
pb, aa	60S ribosomal protein L43-A	protein	91	25% helix, 13% strand	P0CX25
1b	25S rRNA	rna	3184	—	—
6b, 8	tRNA	rna	76	—	—
a	18S rRNA	rna	1758	—	—
c	40S ribosomal protein S1-A	protein	216	32% helix, 31% strand	P33442
d	40S ribosomal protein S2	protein	217	31% helix, 25% strand	P25443
e	40S ribosomal protein S3	protein	223	37% helix, 22% strand	P05750
f	40S ribosomal protein S4-A	protein	260	17% helix, 29% strand	P0CX35
h	40S ribosomal protein S6-A	protein	218	26% helix, 24% strand	P0CX37
i	40S ribosomal protein S7-A	protein	185	35% helix, 21% strand	P26786
j	40S ribosomal protein S8-A	protein	188	31% helix, 24% strand	P0CX39
k	40S ribosomal protein S9-A	protein	185	58% helix, 3% strand	O13516
m	40S ribosomal protein S11-A	protein	146	3% helix, 30% strand	P0CX47
n	40S ribosomal protein S12	protein	124	40% helix, 7% strand	P48589
p	40S ribosomal protein S14-A	protein	128	27% helix, 23% strand	P06367
q	40S ribosomal protein S15	protein	119	29% helix, 18% strand	Q01855
s	40S ribosomal protein S17-B	protein	125	50% helix, 3% strand	P14127
v	40S ribosomal protein S20	protein	101	27% helix, 40% strand	P38701
0	40S ribosomal protein S25-A	protein	69	45% helix, 12% strand	Q3E792
7	Guanine nucleotide-binding protein subunit beta-like protein	protein	313	0% helix, 53% strand	P38011
Aa	25S rRNA	rna	3127	—	—
Ca	5.8S rRNA	rna	157	—	—
Da	60S ribosomal protein L2-A	protein	252	10% helix, 27% strand	P0CX45
Ha	60S ribosomal protein L6-A	protein	157	20% helix, 15% strand	Q02326
Ia	60S ribosomal protein L7-A	protein	223	54% helix, 14% strand	P05737
Ja	60S ribosomal protein L8-A	protein	231	50% helix, 6% strand	P17076
Ka	60S ribosomal protein L9-A	protein	190	21% helix, 39% strand	P05738
La	60S ribosomal protein L10	protein	209	26% helix, 24% strand	P41805
Na	60S ribosomal protein L13-A	protein	194	40% helix, 8% strand	Q12690
Oa	60S ribosomal protein L14-A	protein	137	41% helix, 23% strand	P36105
A	60S ribosomal protein L17-A	protein	175	39% helix, 25% strand	P05740
C	60S ribosomal protein L19-A	protein	183	74% helix, 3% strand	P0CX82
D	60S ribosomal protein L20-A	protein	172	23% helix, 33% strand	P0CX23
F	60S ribosomal protein L22-A	protein	98	32% helix, 34% strand	P05749
G	60S ribosomal protein L23-A	protein	134	10% helix, 30% strand	P0CX41
H	60S ribosomal protein L24-A	protein	135	43% helix, 10% strand	P04449
I	60S ribosomal protein L25	protein	120	28% helix, 23% strand	P04456
J	60S ribosomal protein L26-A	protein	124	29% helix, 26% strand	P05743
N	60S ribosomal protein L30	protein	100	44% helix, 20% strand	P14120
U	60S ribosomal protein L37-A	protein	82	28% helix, 4% strand	P49166
Z	60S ribosomal protein L42-A	protein	105	10% helix, 28% strand	P0CX27
ba	60S acidic ribosomal protein P0	protein	138	49% helix, 18% strand	P05317

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	980	0.90	0.93	93	empty
2	1555	0.89	0.92	151	empty
3	1887	0.89	0.91	175	empty
4	1033	0.89	0.92	81	empty
5	1260	0.89	0.91	85	empty

Interfaces

488 interfaces between chains.

Aa–Ea · 9167 Å² buried · 235 hydrogen bonds · protein-nucleic
By–1b · 9147 Å² buried · 210 hydrogen bonds · protein-nucleic
Cy–1b · 8281 Å² buried · 208 hydrogen bonds · protein-nucleic
Aa–Fa · 8046 Å² buried · 194 hydrogen bonds · protein-nucleic
Ny–1b · 7589 Å² buried · 178 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 7 disulfide (disulfide).

Compared structures

P25443 · AlphaFold monomer V2.0 prediction for 40S ribosomal protein S2 (P25443) · a predicted model of the same protein · chain Cb against A, TM-score 0.99
P0CX45 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L2-a (P0CX45) · a predicted model of the same protein · chain Ay against A, TM-score 0.99
P38011 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein subunit… · a predicted model of the same protein · chain 7 against A, TM-score 0.99
P0CX35 · AlphaFold monomer V2.0 prediction for 40S ribosomal protein S4-a (P0CX35) · a predicted model of the same protein · chain Eb against A, TM-score 0.99
P14126 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L3 (P14126) · a predicted model of the same protein · chain By against A, TM-score 0.99
O13516 · AlphaFold monomer V2.0 prediction for 40S ribosomal protein S9-a (O13516) · a predicted model of the same protein · chain Jb against A, TM-score 0.98
P05748 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L15-a (P05748) · a predicted model of the same protein · chain Ny against A, TM-score 0.98

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