SMTL ID : 8ip9.1

Wheat 40S ribosome in complex with a tRNAi

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-mer

Ligands

1 x A- U- G: mRNA(Non-functional Binders)

A-U-G.1: 9 residues within 4Å: Chain 7: C.33, A.34, U.35, A.36 Chain A: C.1645, G.1646, C.1647, C.1648, U.1771 Protein-ligand interaction information (PLIP) not available

84 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.2: 1 residues within 4Å: Ligands: MG.64 No protein-ligand interaction detected (PLIP) MG.3: 1 residues within 4Å: Chain A: A.752 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain A: G.387, G.388 No protein-ligand interaction detected (PLIP) MG.5: 5 residues within 4Å: Chain A: C.100, A.101, U.102, U.103, C.365 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain A: C.428, G.430 No protein-ligand interaction detected (PLIP) MG.7: 2 residues within 4Å: Chain A: C.49, A.429 No protein-ligand interaction detected (PLIP) MG.8: 1 residues within 4Å: Chain A: A.101 No protein-ligand interaction detected (PLIP) MG.9: 2 residues within 4Å: Chain A: A.391, C.406 No protein-ligand interaction detected (PLIP) MG.10: 1 residues within 4Å: Chain A: A.405 No protein-ligand interaction detected (PLIP) MG.11: 4 residues within 4Å: Chain A: G.1637, U.1638, G.1803, A.1804 No protein-ligand interaction detected (PLIP) MG.12: 2 residues within 4Å: Chain 0: G.16 Chain A: G.947 No protein-ligand interaction detected (PLIP) MG.13: 4 residues within 4Å: Chain A: C.631, A.972, U.973 Chain N: M.4 No protein-ligand interaction detected (PLIP) MG.14: 4 residues within 4Å: Chain A: A.627, G.628, C.629, C.1033 No protein-ligand interaction detected (PLIP) MG.15: 1 residues within 4Å: Chain A: A.1030 No protein-ligand interaction detected (PLIP) MG.16: 1 residues within 4Å: Chain A: A.627 No protein-ligand interaction detected (PLIP) MG.17: 4 residues within 4Å: Chain A: U.622, A.623, A.624, A.625 No protein-ligand interaction detected (PLIP) MG.18: 1 residues within 4Å: Chain A: A.623 No protein-ligand interaction detected (PLIP) MG.19: 1 residues within 4Å: Chain A: A.1639 No protein-ligand interaction detected (PLIP) MG.20: 1 residues within 4Å: Chain A: A.1641 No protein-ligand interaction detected (PLIP) MG.21: 2 residues within 4Å: Chain A: A.1144, G.1145 No protein-ligand interaction detected (PLIP) MG.22: 2 residues within 4Å: Chain A: G.1114, G.1115 No protein-ligand interaction detected (PLIP) MG.23: 3 residues within 4Å: Chain A: C.17, G.1113, G.1114 No protein-ligand interaction detected (PLIP) MG.24: 1 residues within 4Å: Chain A: G.16 No protein-ligand interaction detected (PLIP) MG.25: 1 residues within 4Å: Chain A: G.1646 No protein-ligand interaction detected (PLIP) MG.26: 4 residues within 4Å: Chain A: C.1774, A.1775, U.1780, U.1781 No protein-ligand interaction detected (PLIP) MG.27: 4 residues within 4Å: Chain A: G.1637, A.1775, A.1776, A.1804 No protein-ligand interaction detected (PLIP) MG.28: 1 residues within 4Å: Chain A: C.1167 No protein-ligand interaction detected (PLIP) MG.29: 5 residues within 4Å: Chain A: C.1164, A.1165, G.1587, C.1588 Chain J: Y.148 No protein-ligand interaction detected (PLIP) MG.30: 4 residues within 4Å: Chain A: G.900, G.919, A.920, U.922 No protein-ligand interaction detected (PLIP) MG.31: 2 residues within 4Å: Chain A: G.340, G.341 No protein-ligand interaction detected (PLIP) MG.32: 2 residues within 4Å: Chain A: U.331, G.341 No protein-ligand interaction detected (PLIP) MG.33: 1 residues within 4Å: Chain A: U.940 No protein-ligand interaction detected (PLIP) MG.34: 2 residues within 4Å: Chain A: G.933, A.934 No protein-ligand interaction detected (PLIP) MG.35: 1 residues within 4Å: Chain A: G.1040 No protein-ligand interaction detected (PLIP) MG.36: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.37: 1 residues within 4Å: Chain A: G.1052 No protein-ligand interaction detected (PLIP) MG.38: 2 residues within 4Å: Chain A: G.1078, G.1079 No protein-ligand interaction detected (PLIP) MG.39: 2 residues within 4Å: Chain A: U.551, G.552 No protein-ligand interaction detected (PLIP) MG.40: 2 residues within 4Å: Chain A: A.554, C.587 No protein-ligand interaction detected (PLIP) MG.41: 1 residues within 4Å: Chain A: A.554 No protein-ligand interaction detected (PLIP) MG.42: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.43: 3 residues within 4Å: Chain A: G.556, A.559, A.560 No protein-ligand interaction detected (PLIP) MG.44: 1 residues within 4Å: Chain A: A.19 No protein-ligand interaction detected (PLIP) MG.45: 3 residues within 4Å: Chain A: G.375, A.609, G.611 No protein-ligand interaction detected (PLIP) MG.46: 2 residues within 4Å: Chain A: A.634, G.635 No protein-ligand interaction detected (PLIP) MG.47: 3 residues within 4Å: Chain A: A.867, A.868, G.871 No protein-ligand interaction detected (PLIP) MG.48: 1 residues within 4Å: Chain A: G.96 No protein-ligand interaction detected (PLIP) MG.49: 2 residues within 4Å: Chain A: A.432, G.433 No protein-ligand interaction detected (PLIP) MG.50: 3 residues within 4Å: Chain A: A.1212, G.1454, U.1455 No protein-ligand interaction detected (PLIP) MG.51: 3 residues within 4Å: Chain A: C.1209, U.1458, G.1459 No protein-ligand interaction detected (PLIP) MG.52: 3 residues within 4Å: Chain A: A.1206, A.1207, C.1607 No protein-ligand interaction detected (PLIP) MG.53: 2 residues within 4Å: Chain A: G.1205, A.1608 No protein-ligand interaction detected (PLIP) MG.54: 5 residues within 4Å: Chain A: A.1208, C.1209, U.1210, G.1461, C.1462 No protein-ligand interaction detected (PLIP) MG.55: 1 residues within 4Å: Chain A: C.1463 No protein-ligand interaction detected (PLIP) MG.56: 3 residues within 4Å: Chain A: G.1172, U.1173, A.1475 No protein-ligand interaction detected (PLIP) MG.57: 1 residues within 4Å: Chain A: C.1201 No protein-ligand interaction detected (PLIP) MG.58: 1 residues within 4Å: Chain A: U.1603 No protein-ligand interaction detected (PLIP) MG.59: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.60: 2 residues within 4Å: Chain A: G.1548, G.1549 No protein-ligand interaction detected (PLIP) MG.61: 3 residues within 4Å: Chain A: U.1474, C.1597, G.1598 No protein-ligand interaction detected (PLIP) MG.62: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.63: 1 residues within 4Å: Chain A: G.1301 No protein-ligand interaction detected (PLIP) MG.64: 5 residues within 4Å: Chain A: U.1297, G.1298, U.1307, G.1308 Ligands: MG.2 No protein-ligand interaction detected (PLIP) MG.65: 4 residues within 4Å: Chain A: A.1162, C.1163, G.1624, U.1625 No protein-ligand interaction detected (PLIP) MG.66: 3 residues within 4Å: Chain A: U.1286, U.1287, U.1289 No protein-ligand interaction detected (PLIP) MG.67: 5 residues within 4Å: Chain A: G.1277, G.1282, C.1283, G.1435, U.1436 No protein-ligand interaction detected (PLIP) MG.68: 4 residues within 4Å: Chain A: G.1277, C.1278, G.1434, U.1436 No protein-ligand interaction detected (PLIP) MG.69: 4 residues within 4Å: Chain A: G.1277, G.1281, U.1440, A.1442 No protein-ligand interaction detected (PLIP) MG.70: 1 residues within 4Å: Chain A: U.9 No protein-ligand interaction detected (PLIP) MG.71: 3 residues within 4Å: Chain A: G.1770, U.1771 Ligands: MG.85 No protein-ligand interaction detected (PLIP) MG.72: 1 residues within 4Å: Chain A: A.1000 No protein-ligand interaction detected (PLIP) MG.73: 3 residues within 4Å: Chain A: A.998, A.1010, C.1794 No protein-ligand interaction detected (PLIP) MG.74: 5 residues within 4Å: Chain A: A.1772, A.1773, U.1781, C.1794 Ligands: MG.75 No protein-ligand interaction detected (PLIP) MG.75: 6 residues within 4Å: Chain A: A.1773, G.1778, U.1779, U.1780, U.1781 Ligands: MG.74 No protein-ligand interaction detected (PLIP) MG.76: 5 residues within 4Å: Chain A: U.1771, A.1772, A.1773, G.1777, G.1778 No protein-ligand interaction detected (PLIP) MG.77: 3 residues within 4Å: Chain A: C.577, G.578, A.1143 No protein-ligand interaction detected (PLIP) MG.78: 5 residues within 4Å: Chain A: C.1478, U.1479 Chain I: A.158, N.161, K.163 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:A.158, I:N.161 MG.79: 2 residues within 4Å: Chain A: C.18 Chain E: D.24 No protein-ligand interaction detected (PLIP) MG.80: 1 residues within 4Å: Chain A: G.575 No protein-ligand interaction detected (PLIP) MG.81: 4 residues within 4Å: Chain A: G.556, G.557, C.558, A.560 No protein-ligand interaction detected (PLIP) MG.82: 4 residues within 4Å: Chain A: C.453 Chain H: P.29, K.30, T.81 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:K.30 MG.85: 1 residues within 4Å: Ligands: MG.71 No protein-ligand interaction detected (PLIP) MG.86: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.87: 2 residues within 4Å: Chain 7: A.36, C.38 No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION(Non-covalent)

ZN.83: 4 residues within 4Å: Chain U: C.21, C.24, C.39, C.42 4 PLIP interactions: 4 interactions with chain U Metal complexes: U:C.21, U:C.24, U:C.39, U:C.42 ZN.84: 4 residues within 4Å: Chain 0: C.23, C.26, C.74, C.77 4 PLIP interactions: 4 interactions with chain 0 Metal complexes: 0:C.23, 0:C.26, 0:C.74, 0:C.77

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tanaka, M. et al., Boric acid intercepts 80S ribosome migration from AUG-stop by stabilizing eRF1. Nat.Chem.Biol. (2024)

Release Date

2024-02-21

Peptides

40S ribosomal protein eS24: B
40S ribosomal protein eS8: C
40S ribosomal protein eS10: D
40S ribosomal protein S23: E
RACK1: F
40S ribosomal protein uS3: G
40S ribosomal protein eS4: H
40S ribosomal protein uS7: I
40S ribosomal protein uS9: J
40S ribosomal protein uS10: K
40S ribosomal protein uS11: L
40S ribosomal protein uS13: M
40S ribosomal protein uS15: N
40S ribosomal protein eS17: O
40S ribosomal protein eS19: P
40S ribosomal protein uS19: Q
40S ribosomal protein eS25: R
40S ribosomal protein eS28: S
40S ribosomal protein uS8: T
40S ribosomal protein uS14: U
40S ribosomal protein eS27: V
40S ribosomal protein eS30: W
40S ribosomal protein uS2: X
40S ribosomal protein eS1: Y
40S ribosomal protein eS21: Z
40S ribosomal protein eS26: 0
40S ribosomal protein uS4: 1
40S ribosomal protein uS5: 2
40S ribosomal protein eS6: 3
40S ribosomal protein eS7: 4
40S ribosomal protein uS17: 5
60S ribosomal protein eL41: 6

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
ba

C
ca

D
da

E
ga

F
ha

G
ia

H
ja

I
ka

J
la

K
ma

L
na

M
oa

N
pa

O
qa

P
ra

Q
sa

R
ta

S
ua

T
va

U
wa

V
xa

W
ya

X
za

Y
bb

Z
cb

0
db

1
eb

2
fb

3
gb

4
hb

5
ib

6
IB

40S ribosomal protein eS24

40S ribosomal protein eS8

40S ribosomal protein eS10

40S ribosomal protein S23

RACK1

40S ribosomal protein uS3

40S ribosomal protein eS4

40S ribosomal protein uS7

40S ribosomal protein uS9

40S ribosomal protein uS10

40S ribosomal protein uS11

40S ribosomal protein uS13

40S ribosomal protein uS15

40S ribosomal protein eS17

40S ribosomal protein eS19

40S ribosomal protein uS19

40S ribosomal protein eS25

40S ribosomal protein eS28

40S ribosomal protein uS8

40S ribosomal protein uS14

40S ribosomal protein eS27

40S ribosomal protein eS30

40S ribosomal protein uS2

40S ribosomal protein eS1

40S ribosomal protein eS21

40S ribosomal protein eS26

40S ribosomal protein uS4

40S ribosomal protein uS5

40S ribosomal protein eS6

40S ribosomal protein eS7

40S ribosomal protein uS17

60S ribosomal protein eL41

Related Entries With Identical Sequence