MolNFT v1 · #88788 · protein + RNA

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

4D5L · 18S rRNA 2: “Cryo-EM structures of ribosomal 80S complexes with termination factors and cricket paralysis virus ires…”. Electron microscopy, 20 pockets (best druggability 0.90). MolNFT v1 #88788 on GenesisL1: 3D structure, binding…

PDB: 4D5L
Type: protein + RNA
Length: 6,521 residues
Chains: 34
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 18S rRNA 2; 40S ribosomal protein ES26; 40S ribosomal protein ES27; 40S ribosomal protein…
UniProt: G1SS70, G1TFM5, G1TM55, G1SVB0, B7NZS8, G1TPV3, G1TRM4, G1SFR8, G1SP51, G1SGX4, G1TPG3, G1SIZ2, G1TG89, G1SZ47, G1TDB3, G1TZ76, G1TIB4, G1U7M4, G1SK22, G1SJB4
Pockets: 20 · best druggability 0.90

Structure

electron microscopy · 34 distinct chains · 31% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
1	18S rRNA 2	rna	1742	—	—
A	40S ribosomal protein ES26	protein	218	39% helix, 14% strand	—
B	40S ribosomal protein ES27	protein	213	28% helix, 27% strand	G1SS70
C	40S ribosomal protein ES28	protein	222	34% helix, 25% strand	—
D	40S ribosomal protein US14	protein	212	34% helix, 27% strand	—
E	40S ribosomal protein ES30	protein	257	14% helix, 34% strand	—
F	40S ribosomal protein ES31	protein	188	47% helix, 7% strand	G1TFM5
G	40S ribosomal protein RACK1	protein	232	30% helix, 22% strand	G1TM55
H	40S ribosomal protein ES7	protein	191	39% helix, 23% strand	G1SVB0
I	40S ribosomal protein ES8	protein	207	29% helix, 21% strand	—
J	40S ribosomal protein US4	protein	179	54% helix, 4% strand	B7NZS8
K	40S ribosomal protein ES10	protein	94	41% helix, 20% strand	G1TPV3
L	40S ribosomal protein US17	protein	146	10% helix, 35% strand	G1TRM4
M	40S ribosomal protein ES12	protein	120	42% helix, 19% strand	G1SFR8
N	40S ribosomal protein US15	protein	150	59% helix, 0% strand	G1SP51
O	40S ribosomal protein US11	protein	137	27% helix, 25% strand	—
P	40S ribosomal protein US19	protein	118	36% helix, 13% strand	—
Q	40S ribosomal protein US9	protein	139	40% helix, 21% strand	G1SGX4
R	40S ribosomal protein ES17	protein	109	59% helix, 2% strand	—
S	40S ribosomal protein US13	protein	142	43% helix, 6% strand	G1TPG3
T	40S ribosomal protein ES19	protein	143	53% helix, 8% strand	—
U	40S ribosomal protein US10	protein	101	25% helix, 47% strand	G1SIZ2
V	40S ribosomal protein ES21	protein	83	20% helix, 29% strand	—
W	40S ribosomal protein US8	protein	129	36% helix, 26% strand	G1TG89
X	40S ribosomal protein US12	protein	134	24% helix, 30% strand	G1SZ47
Y	40S ribosomal protein ES24	protein	122	36% helix, 30% strand	—
Z	40S ribosomal protein ES25	protein	76	39% helix, 21% strand	G1TDB3
a	40S ribosomal protein US2	protein	96	14% helix, 17% strand	—
b	40S ribosomal protein ES1	protein	80	11% helix, 26% strand	G1TZ76
c	40S ribosomal protein US5	protein	62	0% helix, 53% strand	G1TIB4
d	40S ribosomal protein US3	protein	53	26% helix, 4% strand	G1U7M4
e	40S ribosomal protein ES4	protein	51	29% helix, 0% strand	—
f	40S ribosomal protein US7	protein	61	0% helix, 26% strand	G1SK22
g	40S ribosomal protein ES6	protein	314	0% helix, 54% strand	G1SJB4

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	906	0.90	0.93	123	empty
2	1041	0.88	0.90	84	empty
3	1187	0.88	0.90	107	empty
4	1097	0.87	0.89	96	empty
5	771	0.86	0.90	79	empty

Interfaces

87 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: 4 disulfide (disulfide).

Compared structures

4D5L · Cryo-EM structures of ribosomal 80S complexes with termination factors and cricket… · the same entry in another collection · chain A against A, 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 G1SS70
Every structure of UniProt G1TFM5
Every structure of UniProt G1TM55
Every structure of UniProt G1SVB0
Every structure of UniProt B7NZS8
Every structure of UniProt G1TPV3
Every structure of UniProt G1TRM4
Every structure of UniProt G1SFR8
Every structure of UniProt G1SP51
Every structure of UniProt G1SGX4
Every structure of UniProt G1TPG3
Every structure of UniProt G1SIZ2
Every structure of UniProt G1TG89
Every structure of UniProt G1SZ47
Every structure of UniProt G1TDB3
Every structure of UniProt G1TZ76
Every structure of UniProt G1TIB4
Every structure of UniProt G1U7M4
Every structure of UniProt G1SK22
Every structure of UniProt G1SJB4
Elsewhere: RCSB PDB 4D5L · PDBe 4D5L · UniProt G1SS70 · UniProt G1TFM5 · UniProt G1TM55 · UniProt G1SVB0 · UniProt B7NZS8 · UniProt G1TPV3 · UniProt G1TRM4 · UniProt G1SFR8 · UniProt G1SP51 · UniProt G1SGX4 · UniProt G1TPG3 · UniProt G1SIZ2 · UniProt G1TG89 · UniProt G1SZ47 · UniProt G1TDB3 · UniProt G1TZ76 · UniProt G1TIB4 · UniProt G1U7M4 · UniProt G1SK22 · UniProt G1SJB4

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