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Cryo-EM reconstruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GDP+AlF4/sordarin)

Analyse Cryo-EM reconstruction of yeast 80S ribosome in complex with mRNA, tRNA and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6GQB
Type: protein + RNA
Length: 17,734 residues
Chains: 84
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.9
Source: Saccharomyces cerevisiae (strain ATCC 204508 / S288c); SYNTHETIC CONSTRUCT
Molecule: Saccharomyces cerevisiae S288C 35S pre-ribosomal RNA (RDN37-1), miscRNA; 5S ribosomal…
UniProt: P05317, P0CX53, P0CX45, P14126, P10664, P26321, Q02326, P05737, P17076, P05738, P41805, Q3E757, 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, P0CX87, P0CX27, P0CX25, P32905, P33442, P25443, P05750, P0CX35, P26783, P0CX37, P26786, P0CX39, O13516, Q08745, P0CX47, P48589, P05756, P39516, Q01855, P0CX51, P14127, P0CX55, P07280, P38701, P0C0V8, P0C0W1, P0CX29, P0CX31, Q3E792, P39939, P35997, Q3E7X9, P41057, P0CX33, P38011, P05759, P0CX43, P32324
Ligands: SO1, GDP, ALF, ZN
Pockets: 20 · best druggability 0.90

Structure

electron microscopy · resolution 3.9 · 84 distinct chains · 18% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
1	Saccharomyces cerevisiae S288C 35S pre-ribosomal RNA (RDN37-1), miscRNA	rna	3223	—	—
3	5S ribosomal RNA	rna	121	—	—
4	5.8S ribosomal RNA	rna	158	—	—
P0	60S acidic ribosomal protein P0	protein	189	10% helix, 8% strand	P05317
P2	60S ribosomal protein L12-A	protein	94	4% helix, 2% strand	P0CX53
A	60S ribosomal protein L2-A	protein	252	5% helix, 22% strand	P0CX45
B	60S ribosomal protein L3	protein	386	9% helix, 22% strand	P14126
C	60S ribosomal protein L4-A	protein	361	19% helix, 7% strand	P10664
D	60S ribosomal protein L5	protein	296	31% helix, 8% strand	P26321
E	60S ribosomal protein L6-A	protein	156	12% helix, 16% strand	Q02326
F	60S ribosomal protein L7-A	protein	222	37% helix, 8% strand	P05737
G	60S ribosomal protein L8-A	protein	233	27% helix, 3% strand	P17076
H	60S ribosomal protein L9-A	protein	191	7% helix, 16% strand	P05738
I	60S ribosomal protein L10	protein	211	18% helix, 20% strand	P41805
J	60S ribosomal protein L11-B	protein	169	13% helix, 15% strand	Q3E757
L	60S ribosomal protein L13-A	protein	193	26% helix, 9% strand	Q12690
M	60S ribosomal protein L14-A	protein	136	32% helix, 18% strand	P36105
N	60S ribosomal protein L15-A	protein	203	21% helix, 16% strand	P05748
O	60S ribosomal protein L16-A	protein	197	34% helix, 11% strand	P26784
P	60S ribosomal protein L17-A	protein	183	21% helix, 22% strand	P05740
Q	60S ribosomal protein L18-A	protein	185	19% helix, 10% strand	P0CX49
R	60S ribosomal protein L19-A	protein	188	44% helix, 0% strand	P0CX82
S	60S ribosomal protein L20-A	protein	172	17% helix, 28% strand	P0CX23
T	60S ribosomal protein L21-A	protein	159	9% helix, 20% strand	Q02753
U	60S ribosomal protein L22-A	protein	100	21% helix, 22% strand	P05749
V	60S ribosomal protein L23-A	protein	136	5% helix, 19% strand	P0CX41
W	60S ribosomal protein L24-A	protein	64	27% helix, 9% strand	P04449
X	60S ribosomal protein L25	protein	121	12% helix, 17% strand	P04456
Y	60S ribosomal protein L26-A	protein	126	13% helix, 29% strand	P05743
Z	60S ribosomal protein L27-A	protein	135	21% helix, 17% strand	P0C2H6
a	60S ribosomal protein L28	protein	148	13% helix, 9% strand	P02406
b	60S ribosomal protein L29	protein	58	38% helix, 0% strand	P05747
c	60S ribosomal protein L30	protein	97	34% helix, 15% strand	P14120
d	60S ribosomal protein L31-A	protein	109	14% helix, 18% strand	P0C2H8
e	60S ribosomal protein L32	protein	127	13% helix, 7% strand	P38061
f	60S ribosomal protein L33-A	protein	106	0% helix, 34% strand	P05744
g	60S ribosomal protein L34-A	protein	112	13% helix, 5% strand	P87262
h	60S ribosomal protein L35-A	protein	119	38% helix, 3% strand	P0CX84
i	60S ribosomal protein L36-A	protein	99	32% helix, 1% strand	P05745
j	60S ribosomal protein L37-A	protein	87	13% helix, 7% strand	P49166
k	60S ribosomal protein L38	protein	77	19% helix, 16% strand	P49167
l	60S ribosomal protein L39	protein	50	8% helix, 0% strand	P04650
m	Ubiquitin-60S ribosomal protein L40	protein	52	15% helix, 13% strand	P0CH08
n	60S ribosomal protein L41-B	protein	25	48% helix, 0% strand	P0CX87
o	60S ribosomal protein L42-A	protein	105	4% helix, 8% strand	P0CX27
p	60S ribosomal protein L43-A	protein	91	25% helix, 13% strand	P0CX25
2	18S ribosomal RNA	rna	1776	—	—
q	40S ribosomal protein S0-A	protein	206	23% helix, 12% strand	P32905
r	40S ribosomal protein S1-A	protein	214	14% helix, 16% strand	P33442
s	40S ribosomal protein S2	protein	217	21% helix, 18% strand	P25443
t	40S ribosomal protein S3	protein	223	19% helix, 6% strand	P05750
u	40S ribosomal protein S4-A	protein	260	10% helix, 17% strand	P0CX35
v	40S ribosomal protein S5	protein	206	26% helix, 1% strand	P26783
w	40S ribosomal protein S6-A	protein	223	21% helix, 12% strand	P0CX37
x	40S ribosomal protein S7-A	protein	184	22% helix, 14% strand	P26786
y	40S ribosomal protein S8-A	protein	188	18% helix, 13% strand	P0CX39
z	40S ribosomal protein S9-A	protein	185	35% helix, 1% strand	O13516
AA	40S ribosomal protein S10-A	protein	96	21% helix, 4% strand	Q08745
AB	40S ribosomal protein S11-A	protein	153	3% helix, 22% strand	P0CX47
AC	40S ribosomal protein S12	protein	124	12% helix, 0% strand	P48589
AD	40S ribosomal protein S13	protein	150	38% helix, 0% strand	P05756
AE	40S ribosomal protein S14-B	protein	127	18% helix, 20% strand	P39516
AF	40S ribosomal protein S15	protein	124	11% helix, 6% strand	Q01855
AG	40S ribosomal protein S16-A	protein	141	7% helix, 6% strand	P0CX51
AH	40S ribosomal protein S17-B	protein	120	18% helix, 5% strand	P14127
AI	40S ribosomal protein S18-A	protein	145	15% helix, 6% strand	P0CX55
AJ	40S ribosomal protein S19-A	protein	143	21% helix, 3% strand	P07280
AK	40S ribosomal protein S20	protein	107	11% helix, 20% strand	P38701
AL	40S ribosomal protein S21-A	protein	87	15% helix, 7% strand	P0C0V8
AM	40S ribosomal protein S22-A	protein	129	23% helix, 19% strand	P0C0W1
AN	40S ribosomal protein S23-A	protein	144	14% helix, 17% strand	P0CX29
AO	40S ribosomal protein S24-A	protein	134	14% helix, 23% strand	P0CX31
AP	40S ribosomal protein S25-A	protein	70	17% helix, 9% strand	Q3E792
AQ	40S ribosomal protein S26-B	protein	97	7% helix, 12% strand	P39939
AR	40S ribosomal protein S27-A	protein	81	0% helix, 15% strand	P35997
AS	40S ribosomal protein S28-A	protein	63	0% helix, 19% strand	Q3E7X9
AT	40S ribosomal protein S29-A	protein	53	6% helix, 8% strand	P41057
AU	40S ribosomal protein S30-A	protein	60	22% helix, 3% strand	P0CX33
AV	Guanine nucleotide-binding protein subunit beta-like protein	protein	318	0% helix, 15% strand	P38011
AW	Ubiquitin-40S ribosomal protein S31	protein	37	0% helix, 5% strand	P05759
AX	Transfer RNA - Phe	rna	76	—	—
AY	Messenger RNA	rna	7	—	—
BA	60S ribosomal protein L1-A	protein	204	10% helix, 4% strand	P0CX43
AZ	Elongation factor 2	protein	840	20% helix, 11% strand	P32324

Ligands and binding sites

SO1 · [1R-(1.alpha.,3a.beta.,4.beta.,4a.beta.,7.beta.,7a.alpha.,8a.beta.)]8a-[(6-deoxy-4-O-methyl-beta-D-altropyranosyloxy)methyl]-4-formyl-4,4A,5,6,7,7A,8,8A-octahydro-7-methyl-3-(1-methylethyl)-1,4-methano-S-indacene-3A(1H)-carboxylic acid · ligand · chains AZ
GDP · Guanosine-5'-diphosphate · ligand · chains 1, AZ
ALF · Tetrafluoroaluminate ion · ligand · chains AZ
ZN · Zinc ion · metal · 8 copies · chains j, m, o, p, AE, AQ, AR, AT, 2, AW

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	939	0.90	0.93	117	empty
2	1091	0.88	0.90	102	empty
3	874	0.88	0.91	91	empty
4	1152	0.87	0.90	102	empty
5	731	0.87	0.92	75	empty

Interfaces

261 interfaces between chains.

1–B · 9203 Å² buried · 188 hydrogen bonds · protein-nucleic
1–C · 8337 Å² buried · 163 hydrogen bonds · protein-nucleic
1–N · 7514 Å² buried · 140 hydrogen bonds · protein-nucleic
1–A · 7286 Å² buried · 149 hydrogen bonds · protein-nucleic
1–4 · 5082 Å² buried · 264 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 5 disulfide, 1 modified (disulfide, nonstandard).

Compared structures

P14126 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L3 (P14126) · a predicted model of the same protein · chain B against A, TM-score 0.98
P0CX45 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L2-a (P0CX45) · a predicted model of the same protein · chain A against A, TM-score 0.97
P05748 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L15-a (P05748) · a predicted model of the same protein · chain N against A, TM-score 0.97
P05737 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L7-a (P05737) · a predicted model of the same protein · chain F against A, TM-score 0.97
P25443 · AlphaFold monomer V2.0 prediction for 40S ribosomal protein S2 (P25443) · a predicted model of the same protein · chain s against A, TM-score 0.97
P41805 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L10 (P41805) · a predicted model of the same protein · chain I against A, TM-score 0.96
P05743 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L26-a (P05743) · a predicted model of the same protein · chain Y against A, TM-score 0.96
P0C0W1 · AlphaFold monomer V2.0 prediction for 40S ribosomal protein S22-a (P0C0W1) · a predicted model of the same protein · chain AM against A, TM-score 0.96
P26784 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L16-a (P26784) · a predicted model of the same protein · chain O against A, TM-score 0.96
P0CX49 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L18-a (P0CX49) · a predicted model of the same protein · chain Q against A, TM-score 0.96
O13516 · AlphaFold monomer V2.0 prediction for 40S ribosomal protein S9-a (O13516) · a predicted model of the same protein · chain z against A, TM-score 0.96
P0C2H6 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L27-a (P0C2H6) · a predicted model of the same protein · chain Z against A, TM-score 0.96

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