MolNFT v1 · #88800 · protein + RNA

Cryo-EM structures of ribosomal 80S complexes with termination factors and cricket paralysis virus ires reveal the ires in the translocated state

4D61 · 18S rRNA: “Cryo-EM structures of ribosomal 80S complexes with termination factors and cricket paralysis virus ires…”. Electron microscopy, 20 pockets (best druggability 0.88). MolNFT v1 #88800 on GenesisL1: 3D structure, binding…

PDB: 4D61
Type: protein + RNA
Length: 7,584 residues
Chains: 37
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 18S rRNA; 40S ribosomal protein sa; 40S ribosomal protein S3A; 40S ribosomal protein S2…
UniProt: P62495, P15170
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · 37 distinct chains · 31% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
1	18S rRNA	rna	1742	—	—
A	40S ribosomal protein sa	protein	218	39% helix, 14% strand	—
B	40S ribosomal protein S3A	protein	213	28% helix, 27% strand	—
C	40S ribosomal protein S2	protein	222	34% helix, 25% strand	—
D	40S ribosomal protein S3	protein	212	34% helix, 27% strand	—
E	40S ribosomal protein S4, Y isoform 1	protein	257	14% helix, 34% strand	—
F	40S ribosomal protein S5	protein	188	47% helix, 7% strand	—
G	40S ribosomal protein S6	protein	232	30% helix, 22% strand	—
H	40S ribosomal protein S7	protein	191	39% helix, 23% strand	—
I	40S ribosomal protein S8	protein	207	29% helix, 21% strand	—
J	40S ribosomal protein S9	protein	179	54% helix, 4% strand	—
K	40S ribosomal protein S10	protein	94	41% helix, 20% strand	—
L	40S ribosomal protein S11	protein	146	10% helix, 35% strand	—
M	40S ribosomal protein S12	protein	120	42% helix, 19% strand	—
N	40S ribosomal protein S13	protein	150	59% helix, 0% strand	—
O	40S ribosomal protein S14	protein	137	27% helix, 25% strand	—
P	40S ribosomal protein S15	protein	118	36% helix, 13% strand	—
Q	40S ribosomal protein S16	protein	139	40% helix, 21% strand	—
R	40S ribosomal protein S17	protein	109	59% helix, 2% strand	—
S	40S ribosomal protein S18	protein	142	43% helix, 6% strand	—
T	40S ribosomal protein S19	protein	143	53% helix, 8% strand	—
U	40S ribosomal protein S20	protein	101	25% helix, 47% strand	—
V	40S ribosomal protein S21	protein	83	20% helix, 29% strand	—
W	40S ribosomal protein S15A	protein	129	36% helix, 26% strand	—
X	40S ribosomal protein S23	protein	134	24% helix, 30% strand	—
Y	40S ribosomal protein S24	protein	122	36% helix, 30% strand	—
Z	40S ribosomal protein S25	protein	76	39% helix, 21% strand	—
a	40S ribosomal protein S26	protein	96	14% helix, 17% strand	—
b	40S ribosomal protein S27	protein	80	11% helix, 26% strand	—
c	40S ribosomal protein S28	protein	62	0% helix, 53% strand	—
d	40S ribosomal protein S29	protein	53	26% helix, 4% strand	—
e	40S ribosomal protein S30	protein	51	29% helix, 0% strand	—
f	Ubiquitin-40S ribosomal protein S27A	protein	61	0% helix, 26% strand	—
g	Guanine nucleotide-binding protein subunit beta-2-like 1	protein	314	0% helix, 54% strand	—
h	Eukaryotic peptide chain release factor subunit 1	protein	436	40% helix, 19% strand	P62495
i	Eukaryotic peptide chain release factor GTP-binding subunit ERF3A	protein	426	20% helix, 35% strand	P15170
j	Cricket paralysis virus ires RNA	rna	201	—	—

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	1184	0.88	0.91	101	empty
2	1044	0.88	0.91	100	empty
3	1013	0.88	0.89	145	empty
4	663	0.88	0.93	90	empty
5	1007	0.88	0.90	98	empty

Interfaces

104 interfaces between chains.

1–G · 5521 Å² buried · 118 hydrogen bonds · protein-nucleic
1–I · 4419 Å² buried · 90 hydrogen bonds · protein-nucleic
1–E · 3936 Å² buried · 87 hydrogen bonds · protein-nucleic
1–J · 3469 Å² buried · 73 hydrogen bonds · protein-nucleic
1–N · 3137 Å² buried · 75 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

4D61 · Cryo-EM structures of ribosomal 80S complexes with termination factors and cricket… · the same entry in another collection · chain J against J, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P62495
Every structure of UniProt P15170
Elsewhere: RCSB PDB 4D61 · PDBe 4D61 · UniProt P62495 · UniProt P15170

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