SMTL ID : 8auv.1

Cryo-EM structure of the plant 40S subunit

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

MG.1: 3 residues within 4Å: Chain C: A.94, G.96, G.407 No protein-ligand interaction detected (PLIP) MG.2: 4 residues within 4Å: Chain C: G.555, C.557, A.558, A.559 No protein-ligand interaction detected (PLIP) MG.3: 4 residues within 4Å: Chain C: A.865, A.866, A.868, A.966 No protein-ligand interaction detected (PLIP) MG.4: 3 residues within 4Å: Chain C: C.100, A.101, C.365 No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Chain C: A.973, A.974 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain C: G.627, A.1028, A.1030 No protein-ligand interaction detected (PLIP) MG.7: 1 residues within 4Å: Chain C: A.588 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain C: G.48, C.49, G.392 No protein-ligand interaction detected (PLIP) MG.9: 3 residues within 4Å: Chain C: A.1332, G.1333, A.1334 No protein-ligand interaction detected (PLIP) MG.10: 2 residues within 4Å: Chain C: U.9, A.11 No protein-ligand interaction detected (PLIP) MG.11: 3 residues within 4Å: Chain C: A.932, A.933, C.934 No protein-ligand interaction detected (PLIP) MG.12: 7 residues within 4Å: Chain C: A.1771, G.1775, G.1776, U.1777, U.1778, U.1779 Ligands: K.89 4 PLIP interactions: 3 Ligand-Water interactions, 1 interactions with chain C Metal complexes: H2O.1, H2O.4, H2O.24, C:A.1771 MG.13: 2 residues within 4Å: Chain C: A.55, C.428 No protein-ligand interaction detected (PLIP) MG.14: 1 residues within 4Å: Chain C: A.405 No protein-ligand interaction detected (PLIP) MG.15: 4 residues within 4Å: Chain C: G.16, U.611, A.623, G.1110 No protein-ligand interaction detected (PLIP) MG.16: 3 residues within 4Å: Chain C: G.1276, C.1277, G.1433 No protein-ligand interaction detected (PLIP) MG.17: 2 residues within 4Å: Chain C: A.28, A.441 No protein-ligand interaction detected (PLIP) MG.18: 2 residues within 4Å: Chain C: G.375, A.608 No protein-ligand interaction detected (PLIP) MG.19: 5 residues within 4Å: Chain C: U.1769, A.1770, A.1771, G.1775, G.1776 4 PLIP interactions: 3 Ligand-Water interactions, 1 interactions with chain C Metal complexes: H2O.9, H2O.34, H2O.67, C:A.1771 MG.20: 2 residues within 4Å: Chain C: A.43, U.99 No protein-ligand interaction detected (PLIP) MG.21: 4 residues within 4Å: Chain C: U.621, A.622, A.623, A.624 No protein-ligand interaction detected (PLIP) MG.22: 4 residues within 4Å: Chain C: U.1382, U.1383, C.1384, U.1385 No protein-ligand interaction detected (PLIP) MG.23: 2 residues within 4Å: Chain C: A.622, A.1033 No protein-ligand interaction detected (PLIP) MG.24: 1 residues within 4Å: Chain Y: I.11 No protein-ligand interaction detected (PLIP) MG.25: 2 residues within 4Å: Chain C: U.1305, U.1306 No protein-ligand interaction detected (PLIP) MG.26: 3 residues within 4Å: Chain C: G.638, A.639, A.810 No protein-ligand interaction detected (PLIP) MG.27: 2 residues within 4Å: Chain C: G.1331, G.1333 No protein-ligand interaction detected (PLIP) MG.28: 2 residues within 4Å: Chain C: A.626, G.627 No protein-ligand interaction detected (PLIP) MG.29: 4 residues within 4Å: Chain C: A.101, U.102, A.364, C.365 No protein-ligand interaction detected (PLIP) MG.30: 3 residues within 4Å: Chain C: U.480, C.547, A.548 No protein-ligand interaction detected (PLIP) MG.31: 3 residues within 4Å: Chain C: A.970, U.971 Chain Y: R.124 No protein-ligand interaction detected (PLIP) MG.32: 3 residues within 4Å: Chain C: G.1111, G.1112, G.1113 No protein-ligand interaction detected (PLIP) MG.33: 4 residues within 4Å: Chain C: G.1297, G.1298, A.1299 Ligands: K.83 No protein-ligand interaction detected (PLIP) MG.34: 2 residues within 4Å: Chain C: U.95, G.96 No protein-ligand interaction detected (PLIP) MG.35: 3 residues within 4Å: Chain C: G.1635, U.1636, G.1801 No protein-ligand interaction detected (PLIP) MG.36: 2 residues within 4Å: Chain C: U.1285, U.1286 No protein-ligand interaction detected (PLIP) MG.37: 5 residues within 4Å: Chain 8: U.1 Chain C: A.1774, U.1778, A.1802 Chain U: L.150 5 PLIP interactions: 1 interactions with chain U, 4 Ligand-Water interactions Metal complexes: U:L.150, H2O.6, H2O.31, H2O.69, H2O.91 MG.38: 2 residues within 4Å: Chain C: G.334, G.340 No protein-ligand interaction detected (PLIP) MG.39: 2 residues within 4Å: Chain C: A.1068 Chain H: Q.160 No protein-ligand interaction detected (PLIP) MG.40: 5 residues within 4Å: Chain 7: Y.146 Chain C: C.1162, A.1163, U.1585, C.1586 No protein-ligand interaction detected (PLIP) MG.41: 3 residues within 4Å: Chain C: G.1172, G.1173, A.1174 No protein-ligand interaction detected (PLIP) MG.42: 3 residues within 4Å: Chain C: G.1203, G.1204, A.1606 No protein-ligand interaction detected (PLIP) MG.43: 5 residues within 4Å: Chain C: G.1276, C.1277, A.1432, G.1433, G.1434 No protein-ligand interaction detected (PLIP) MG.44: 4 residues within 4Å: Chain C: U.1272, G.1273, G.1453, U.1454 No protein-ligand interaction detected (PLIP) MG.45: 4 residues within 4Å: Chain C: G.1203, A.1205, C.1461, C.1462 No protein-ligand interaction detected (PLIP) MG.46: 5 residues within 4Å: Chain C: U.1544, G.1545, G.1546, G.1547, G.1548 No protein-ligand interaction detected (PLIP) MG.47: 2 residues within 4Å: Chain C: G.1546, G.1547 No protein-ligand interaction detected (PLIP) MG.48: 2 residues within 4Å: Chain C: G.565, A.583 No protein-ligand interaction detected (PLIP) MG.49: 2 residues within 4Å: Chain C: C.993, C.1014 No protein-ligand interaction detected (PLIP) MG.50: 4 residues within 4Å: Chain 8: U.5, U.6 Chain C: G.1768, U.1769 No protein-ligand interaction detected (PLIP) MG.51: 6 residues within 4Å: Chain C: A.1207, C.1208, U.1209, U.1210, G.1460, C.1461 No protein-ligand interaction detected (PLIP) MG.52: 2 residues within 4Å: Chain C: C.1200, C.1470 No protein-ligand interaction detected (PLIP) MG.53: 2 residues within 4Å: Chain C: C.1208, G.1458 No protein-ligand interaction detected (PLIP) MG.54: 3 residues within 4Å: Chain C: G.879, A.936, A.947 No protein-ligand interaction detected (PLIP) MG.55: 1 residues within 4Å: Chain C: C.386 No protein-ligand interaction detected (PLIP) MG.56: 2 residues within 4Å: Chain C: C.1164, C.1165 No protein-ligand interaction detected (PLIP) MG.57: 4 residues within 4Å: Chain C: G.392, G.393, G.394, C.406 No protein-ligand interaction detected (PLIP) MG.58: 2 residues within 4Å: Chain C: C.1487, A.1488 No protein-ligand interaction detected (PLIP) MG.59: 2 residues within 4Å: Chain C: G.1017, U.1018 No protein-ligand interaction detected (PLIP) MG.60: 2 residues within 4Å: Chain C: A.382, U.383 No protein-ligand interaction detected (PLIP) MG.61: 2 residues within 4Å: Chain C: G.1776, U.1777 No protein-ligand interaction detected (PLIP) MG.62: 1 residues within 4Å: Chain C: U.1535 No protein-ligand interaction detected (PLIP) MG.63: 3 residues within 4Å: Chain C: A.1205, A.1206, C.1605 No protein-ligand interaction detected (PLIP) MG.64: 5 residues within 4Å: Chain C: G.120, U.121, U.122, U.300, U.301 No protein-ligand interaction detected (PLIP) MG.65: 1 residues within 4Å: Chain C: U.923 No protein-ligand interaction detected (PLIP) MG.66: 2 residues within 4Å: Chain C: G.987, G.988 No protein-ligand interaction detected (PLIP) MG.67: 3 residues within 4Å: Chain C: G.1049, G.1050, C.1051 No protein-ligand interaction detected (PLIP) MG.68: 1 residues within 4Å: Chain C: A.475 No protein-ligand interaction detected (PLIP) MG.69: 4 residues within 4Å: Chain C: G.390, A.391, A.405, C.406 No protein-ligand interaction detected (PLIP) MG.70: 1 residues within 4Å: Chain W: K.137 No protein-ligand interaction detected (PLIP) MG.71: 5 residues within 4Å: Chain C: G.904, G.905 Chain U: D.64, E.67 Ligands: K.122 5 PLIP interactions: 2 interactions with chain U, 3 Ligand-Water interactions Metal complexes: U:E.67, U:E.67, H2O.10, H2O.24, H2O.83 MG.72: 2 residues within 4Å: Chain C: U.310, G.311 No protein-ligand interaction detected (PLIP) MG.73: 5 residues within 4Å: Chain C: A.210, G.211, C.253, A.254, U.255 No protein-ligand interaction detected (PLIP) MG.119: 4 residues within 4Å: Chain C: A.944, G.945 Chain L: G.16, H.17 No protein-ligand interaction detected (PLIP) MG.124: 7 residues within 4Å: Chain C: U.1573, C.1574 Chain W: T.31, S.32, I.33, K.34, I.36 3 PLIP interactions: 3 interactions with chain W Metal complexes: W:T.31, W:I.33, W:I.36 MG.130: 4 residues within 4Å: Chain 8: U.3, U.4 Chain C: G.1776, U.1777 No protein-ligand interaction detected (PLIP)

47 x K: POTASSIUM ION(Non-covalent)(Non-functional Binders)

K.74: 5 residues within 4Å: Chain C: C.568, C.578, G.579 Chain V: P.61, N.62 Ligand excluded by PLIP K.75: 5 residues within 4Å: Chain 8: U.10 Chain C: C.568, G.580, A.1763 Chain V: P.61 Ligand excluded by PLIP K.76: 4 residues within 4Å: Chain 8: U.4 Chain C: C.1003, A.1004, G.1005 Ligand excluded by PLIP K.77: 4 residues within 4Å: Chain C: U.1171, G.1172, G.1173, G.1580 Ligand excluded by PLIP K.78: 6 residues within 4Å: Chain C: G.1274, U.1275, C.1436, U.1442, G.1443, C.1444 Ligand excluded by PLIP K.79: 2 residues within 4Å: Chain C: U.1007, G.1788 Ligand excluded by PLIP K.80: 4 residues within 4Å: Chain C: U.566, G.567, A.582, A.583 Ligand excluded by PLIP K.81: 2 residues within 4Å: Chain C: G.567, U.581 Ligand excluded by PLIP K.82: 4 residues within 4Å: Chain C: C.1772, A.1773, U.1778, U.1779 Ligand excluded by PLIP K.83: 6 residues within 4Å: Chain C: U.1296, G.1297, U.1306, G.1307, A.1325 Ligands: MG.33 Ligand excluded by PLIP K.84: 5 residues within 4Å: Chain C: G.990, U.992, C.993, G.1017, U.1018 Ligand excluded by PLIP K.85: 5 residues within 4Å: Chain C: A.1046, U.1047, C.1048, G.1076, G.1077 Ligand excluded by PLIP K.86: 3 residues within 4Å: Chain C: A.109, G.110, U.111 Ligand excluded by PLIP K.87: 4 residues within 4Å: Chain C: G.92, G.400, A.401, G.402 Ligand excluded by PLIP K.88: 4 residues within 4Å: Chain C: G.92, A.93, A.94, G.402 Ligand excluded by PLIP K.89: 5 residues within 4Å: Chain C: A.1770, A.1771, U.1779, C.1792 Ligands: MG.12 Ligand excluded by PLIP K.90: 5 residues within 4Å: Chain C: G.57, U.58, U.89, G.90, C.91 Ligand excluded by PLIP K.91: 5 residues within 4Å: Chain C: C.448, U.451, C.452, G.462, A.464 Ligand excluded by PLIP K.92: 2 residues within 4Å: Chain C: C.1151, U.1633 Ligand excluded by PLIP K.93: 5 residues within 4Å: Chain C: G.1276, G.1281, C.1282, G.1434, U.1435 Ligand excluded by PLIP K.94: 6 residues within 4Å: Chain C: U.103, A.106, U.107, C.365, G.387, G.388 Ligand excluded by PLIP K.95: 6 residues within 4Å: Chain C: C.1031, G.1032, A.1033, A.1798, A.1799, G.1800 Ligand excluded by PLIP K.96: 4 residues within 4Å: Chain C: C.1198, A.1199, C.1200 Chain T: N.78 Ligand excluded by PLIP K.97: 4 residues within 4Å: Chain C: C.428, C.431, A.432, G.433 Ligand excluded by PLIP K.98: 3 residues within 4Å: Chain C: A.553, G.554, U.585 Ligand excluded by PLIP K.99: 4 residues within 4Å: Chain C: G.555, G.556, C.557, A.559 Ligand excluded by PLIP K.100: 5 residues within 4Å: Chain C: C.1159, A.1160, C.1624, U.1627, G.1628 Ligand excluded by PLIP K.101: 6 residues within 4Å: Chain C: G.994, A.995, A.996, G.997, C.1014, U.1015 Ligand excluded by PLIP K.102: 4 residues within 4Å: Chain C: U.959, G.960, U.961 Chain Y: S.12 Ligand excluded by PLIP K.103: 3 residues within 4Å: Chain C: U.331, A.332, G.341 Ligand excluded by PLIP K.104: 6 residues within 4Å: Chain C: U.1148, G.1149, A.1150, U.1636, C.1638, A.1639 Ligand excluded by PLIP K.105: 3 residues within 4Å: Chain C: A.212, U.213, G.246 Ligand excluded by PLIP K.106: 4 residues within 4Å: Chain B: K.179, Q.181, R.182 Chain C: C.271 Ligand excluded by PLIP K.107: 5 residues within 4Å: Chain C: A.335, U.336, G.338, U.339, G.340 Ligand excluded by PLIP K.108: 5 residues within 4Å: Chain C: U.1803, A.1805 Chain L: G.9, K.34, I.36 Ligand excluded by PLIP K.109: 5 residues within 4Å: Chain C: A.105, U.107, C.108, G.311, C.312 Ligand excluded by PLIP K.110: 4 residues within 4Å: Chain C: A.40, A.41, U.383, U.384 Ligand excluded by PLIP K.111: 4 residues within 4Å: Chain C: A.981, A.982, C.1025, A.1128 Ligand excluded by PLIP K.112: 5 residues within 4Å: Chain C: G.1635, U.1636, A.1773, A.1774, A.1802 Ligand excluded by PLIP K.113: 3 residues within 4Å: Chain C: G.1157, A.1290, C.1630 Ligand excluded by PLIP K.114: 4 residues within 4Å: Chain C: A.1033, A.1799, G.1800 Chain L: F.3 Ligand excluded by PLIP K.122: 6 residues within 4Å: Chain C: G.905, U.906 Chain U: N.37, D.64, E.67 Ligands: MG.71 Ligand excluded by PLIP K.123: 7 residues within 4Å: Chain C: A.1763 Chain V: E.57, A.58, K.59, Q.60, N.62, S.63 Ligand excluded by PLIP K.125: 5 residues within 4Å: Chain C: C.1464 Chain W: T.136, T.139, G.140, R.141 Ligand excluded by PLIP K.127: 6 residues within 4Å: Chain C: G.1438 Chain X: N.26, H.28, A.29, C.39, Q.41 Ligand excluded by PLIP K.128: 4 residues within 4Å: Chain Y: R.3, M.4, H.5, S.6 Ligand excluded by PLIP K.129: 6 residues within 4Å: Chain 5: A.168, N.171, K.173, T.174 Chain C: C.1477, U.1478 Ligand excluded by PLIP

1 x SPD: SPERMIDINE(Non-covalent)

SPD.115: 12 residues within 4Å: Chain 7: C.128, E.129, P.130, K.131, G.137 Chain C: A.1592, A.1593, G.1594, C.1595, C.1612, G.1613, U.1614 No protein-ligand interaction detected (PLIP)

3 x SPM: SPERMINE(Non-covalent)(Non-functional Binders)

SPM.116: 14 residues within 4Å: Chain C: C.17, U.378, U.607, A.608, A.609, G.610, U.611, U.612, G.616, G.1111, G.1112 Chain V: D.24, K.25, S.26 No protein-ligand interaction detected (PLIP) SPM.117: 11 residues within 4Å: Chain C: A.625, A.626, G.627, C.628, U.629, C.630, G.631, C.972, C.1031, U.1034, G.1035 No protein-ligand interaction detected (PLIP) SPM.118: 13 residues within 4Å: Chain C: A.995, A.996, G.997, A.998, U.1007, A.1008, C.1009, G.1785, G.1786, U.1787, C.1792, U.1793, G.1794 No protein-ligand interaction detected (PLIP)

3 x ZN: ZINC ION(Non-covalent)

ZN.120: 6 residues within 4Å: Chain L: C.23, N.25, C.26, K.28, C.74, C.77 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.23, L:C.26, L:C.74, L:C.77 ZN.121: 6 residues within 4Å: Chain P: C.121, N.123, C.126, C.141, K.143, C.144 4 PLIP interactions: 4 interactions with chain P Metal complexes: P:C.121, P:C.126, P:C.141, P:C.144 ZN.126: 6 residues within 4Å: Chain C: G.1438 Chain X: C.21, V.23, C.24, C.39, C.42 4 PLIP interactions: 4 interactions with chain X Metal complexes: X:C.21, X:C.24, X:C.39, X:C.42

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Smirnova, J. et al., Structure of the actively translating plant 80S ribosome at 2.2 angstrom resolution. Nat.Plants (2023)

Release Date

2023-06-07

Peptides

eS4 (40S ribosomal protein S4): A
eS6 (40S ribosomal protein S6): B
eS10 (40S ribosomal protein S10): D
eS12 (40S ribosomal protein S12): E
eS17 (40S ribosomal protein S17): F
eS19 (40S ribosomal protein S19): G
eS1 (40S ribosomal protein S3a): H
eS21 (40S ribosomal protein S21): I
eS24 (40S ribosomal protein S24): J
eS25 (40S ribosomal protein S25): K
eS26 (40S ribosomal protein S26): L
eS27 (40S ribosomal protein S27): M
eS28 (40S ribosomal protein S28): N
eS30 (40S ribosomal protein S30): O
eS31 (ubiquitin-40S ribosomal protein S27a): P
eS7 (40S ribosomal protein S7): Q
eS8 (40S ribosomal protein S8): R
RACK1 (guanine nucleotide-binding protein subunit beta-like protein): S
uS10 (40S ribosomal protein S20): T
uS11 (40S ribosomal protein S14): U
uS12 (40S ribosomal protein S23): V
uS13 (40S ribosomal protein S18): W
uS14 (40S ribosomal protein S29): X
uS15 (40S ribosomal protein S13): Y
uS17 (40S ribosomal protein S11): Z
uS19 (40S ribosomal protein S15): 0
uS2 (40S ribosomal protein SA): 1
uS3 (40S ribosomal protein S3): 2
uS4 (40S ribosomal protein S9): 3
uS5 (40S ribosomal protein S2): 4
uS7 (40S ribosomal protein S5): 5
uS8 (40S ribosomal protein S15a): 6
uS9 (40S ribosomal protein S16): 7

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
k

D
l

E
C

F
D

G
E

H
F

I
G

J
H

K
I

L
J

M
K

N
L

O
M

P
N

Q
O

R
P

S
Q

T
R

U
S

V
T

W
U

X
V

Y
W

Z
X

0
Y

1
Z

2
a

3
b

4
c

5
d

6
e

7
f

eS4 (40S ribosomal protein S4)

eS6 (40S ribosomal protein S6)

eS10 (40S ribosomal protein S10)

eS12 (40S ribosomal protein S12)

eS17 (40S ribosomal protein S17)

eS19 (40S ribosomal protein S19)

eS1 (40S ribosomal protein S3a)

eS21 (40S ribosomal protein S21)

eS24 (40S ribosomal protein S24)

eS25 (40S ribosomal protein S25)

eS26 (40S ribosomal protein S26)

eS27 (40S ribosomal protein S27)

eS28 (40S ribosomal protein S28)

eS30 (40S ribosomal protein S30)

eS31 (ubiquitin-40S ribosomal protein S27a)

eS7 (40S ribosomal protein S7)

eS8 (40S ribosomal protein S8)

RACK1 (guanine nucleotide-binding protein subunit beta-like protein)

uS10 (40S ribosomal protein S20)

uS11 (40S ribosomal protein S14)

uS12 (40S ribosomal protein S23)

uS13 (40S ribosomal protein S18)

uS14 (40S ribosomal protein S29)

uS15 (40S ribosomal protein S13)

uS17 (40S ribosomal protein S11)

uS19 (40S ribosomal protein S15)

uS2 (40S ribosomal protein SA)

uS3 (40S ribosomal protein S3)

uS4 (40S ribosomal protein S9)

uS5 (40S ribosomal protein S2)

uS7 (40S ribosomal protein S5)

uS8 (40S ribosomal protein S15a)

uS9 (40S ribosomal protein S16)

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