SMTL ID : 8jiw.1

Atomic structure of wheat ribosome reveals unique features of the plant ribosomes

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

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

K.1: 5 residues within 4Å: Chain 0: T.139, G.140, R.141 Chain A: C.1466, C.1468 Ligand excluded by PLIP K.3: 3 residues within 4Å: Chain A: C.1200, A.1201, C.1202 Ligand excluded by PLIP K.4: 4 residues within 4Å: Chain A: G.1278, G.1283, G.1436, U.1437 Ligand excluded by PLIP K.5: 4 residues within 4Å: Chain A: U.1173, G.1174, G.1175, G.1583 Ligand excluded by PLIP K.6: 5 residues within 4Å: Chain A: G.1278, G.1282, G.1283, U.1437, U.1441 Ligand excluded by PLIP K.7: 3 residues within 4Å: Chain A: U.1277, C.1438, U.1444 Ligand excluded by PLIP K.8: 3 residues within 4Å: Chain A: C.1360, G.1361, G.1362 Ligand excluded by PLIP K.9: 4 residues within 4Å: Chain A: G.1551, A.1552, U.1553, C.1577 Ligand excluded by PLIP K.78: 5 residues within 4Å: Chain A: U.1806, A.1808 Chain R: G.9, D.33, K.34 Ligand excluded by PLIP K.79: 4 residues within 4Å: Chain A: A.335, U.336, G.339, G.340 Ligand excluded by PLIP K.80: 3 residues within 4Å: Chain A: A.109, G.110, U.111 Ligand excluded by PLIP K.81: 4 residues within 4Å: Chain A: G.92, G.400, A.401, G.402 Ligand excluded by PLIP K.82: 4 residues within 4Å: Chain A: G.92, A.93, A.94, G.402 Ligand excluded by PLIP K.83: 4 residues within 4Å: Chain A: U.1298, G.1299, U.1308 Ligands: MG.70 Ligand excluded by PLIP K.85: 3 residues within 4Å: Chain 1: I.91, Y.92, G.93 Ligand excluded by PLIP K.86: 4 residues within 4Å: Chain 4: N.26, H.28, C.39, Q.41 Ligand excluded by PLIP

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

MG.2: 5 residues within 4Å: Chain 0: T.31, V.36, G.37 Chain A: U.1575, U.1576 1 PLIP interactions: 1 interactions with chain 0 Metal complexes: 0:V.36 MG.10: 4 residues within 4Å: Chain A: C.1163, C.1164, C.1589, C.1590 No protein-ligand interaction detected (PLIP) MG.11: 3 residues within 4Å: Chain A: C.1167, A.1168, G.1169 No protein-ligand interaction detected (PLIP) MG.12: 2 residues within 4Å: Chain A: G.1172, U.1173 No protein-ligand interaction detected (PLIP) MG.13: 3 residues within 4Å: Chain A: G.1174, G.1175, G.1471 No protein-ligand interaction detected (PLIP) MG.14: 3 residues within 4Å: Chain A: U.1287, U.1288, U.1290 No protein-ligand interaction detected (PLIP) MG.15: 3 residues within 4Å: Chain A: A.1201, G.1206, A.1609 No protein-ligand interaction detected (PLIP) MG.16: 2 residues within 4Å: Chain A: A.1207, A.1208 No protein-ligand interaction detected (PLIP) MG.17: 3 residues within 4Å: Chain A: A.1207, U.1211, U.1212 No protein-ligand interaction detected (PLIP) MG.18: 2 residues within 4Å: Chain A: A.1209, C.1210 No protein-ligand interaction detected (PLIP) MG.19: 2 residues within 4Å: Chain A: U.1441, G.1442 No protein-ligand interaction detected (PLIP) MG.20: 6 residues within 4Å: Chain A: G.1278, C.1279, A.1434, G.1435, G.1436 Ligands: MG.21 No protein-ligand interaction detected (PLIP) MG.21: 6 residues within 4Å: Chain A: G.1278, C.1279, A.1434, G.1435, G.1436 Ligands: MG.20 No protein-ligand interaction detected (PLIP) MG.22: 4 residues within 4Å: Chain A: U.1288, C.1289, A.1429, U.1430 No protein-ligand interaction detected (PLIP) MG.23: 2 residues within 4Å: Chain A: G.1335, A.1336 No protein-ligand interaction detected (PLIP) MG.24: 4 residues within 4Å: Chain A: G.1333, G.1335 Chain V: I.158, D.206 No protein-ligand interaction detected (PLIP) MG.25: 2 residues within 4Å: Chain A: G.1455, U.1456 No protein-ligand interaction detected (PLIP) MG.26: 2 residues within 4Å: Chain A: G.1181, C.1182 No protein-ligand interaction detected (PLIP) MG.27: 2 residues within 4Å: Chain A: G.1550, G.1551 No protein-ligand interaction detected (PLIP) MG.28: 2 residues within 4Å: Chain A: G.1549, G.1550 No protein-ligand interaction detected (PLIP) MG.29: 4 residues within 4Å: Chain A: U.1384, U.1385, C.1386, U.1387 No protein-ligand interaction detected (PLIP) MG.30: 1 residues within 4Å: Chain A: G.1484 No protein-ligand interaction detected (PLIP) MG.31: 3 residues within 4Å: Chain A: C.1489, A.1490 Chain Z: G.78 No protein-ligand interaction detected (PLIP) MG.32: 3 residues within 4Å: Chain A: A.1162, C.1163, C.1164 No protein-ligand interaction detected (PLIP) MG.33: 2 residues within 4Å: Chain A: G.1175, C.1470 No protein-ligand interaction detected (PLIP) MG.34: 3 residues within 4Å: Chain A: C.1202, U.1612 Chain Z: F.144 No protein-ligand interaction detected (PLIP) MG.35: 1 residues within 4Å: Chain A: G.1394 No protein-ligand interaction detected (PLIP) MG.36: 4 residues within 4Å: Chain A: G.211, C.253, A.254, U.255 No protein-ligand interaction detected (PLIP) MG.37: 4 residues within 4Å: Chain A: A.627, G.628, C.629, C.1033 No protein-ligand interaction detected (PLIP) MG.38: 2 residues within 4Å: Chain A: A.976, G.977 No protein-ligand interaction detected (PLIP) MG.39: 1 residues within 4Å: Chain A: A.1030 No protein-ligand interaction detected (PLIP) MG.40: 4 residues within 4Å: Chain A: U.622, A.623, A.624, A.625 No protein-ligand interaction detected (PLIP) MG.41: 2 residues within 4Å: Chain A: A.623, A.624 No protein-ligand interaction detected (PLIP) MG.42: 4 residues within 4Å: Chain A: G.1638, U.1639, G.1804, A.1805 No protein-ligand interaction detected (PLIP) MG.43: 2 residues within 4Å: Chain A: G.947 Chain R: G.16 No protein-ligand interaction detected (PLIP) MG.44: 2 residues within 4Å: Chain A: G.16, C.618 No protein-ligand interaction detected (PLIP) MG.45: 2 residues within 4Å: Chain A: C.49, A.429 No protein-ligand interaction detected (PLIP) MG.46: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.47: 1 residues within 4Å: Chain A: G.96 No protein-ligand interaction detected (PLIP) MG.48: 2 residues within 4Å: Chain A: G.387, G.388 No protein-ligand interaction detected (PLIP) MG.49: 2 residues within 4Å: Chain A: G.390, C.406 No protein-ligand interaction detected (PLIP) MG.50: 1 residues within 4Å: Chain A: A.405 No protein-ligand interaction detected (PLIP) MG.51: 3 residues within 4Å: Chain A: A.101, U.102, C.365 No protein-ligand interaction detected (PLIP) MG.52: 2 residues within 4Å: Chain A: G.326, A.345 No protein-ligand interaction detected (PLIP) MG.53: 2 residues within 4Å: Chain A: G.334, G.340 No protein-ligand interaction detected (PLIP) MG.54: 3 residues within 4Å: Chain A: G.366, A.382, U.383 No protein-ligand interaction detected (PLIP) MG.55: 3 residues within 4Å: Chain A: G.96, C.406, G.407 No protein-ligand interaction detected (PLIP) MG.56: 1 residues within 4Å: Chain A: C.428 No protein-ligand interaction detected (PLIP) MG.57: 1 residues within 4Å: Chain A: A.519 No protein-ligand interaction detected (PLIP) MG.58: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.59: 4 residues within 4Å: Chain A: G.556, C.558, A.559, A.560 No protein-ligand interaction detected (PLIP) MG.60: 3 residues within 4Å: Chain A: G.639, A.640, A.812 No protein-ligand interaction detected (PLIP) MG.61: 2 residues within 4Å: Chain A: G.933, A.934 No protein-ligand interaction detected (PLIP) MG.62: 2 residues within 4Å: Chain A: G.1114, G.1115 No protein-ligand interaction detected (PLIP) MG.63: 5 residues within 4Å: Chain A: A.1774, G.1778, G.1779, U.1781, U.1782 No protein-ligand interaction detected (PLIP) MG.64: 5 residues within 4Å: Chain A: U.1772, A.1773, A.1774, G.1778, G.1779 No protein-ligand interaction detected (PLIP) MG.65: 2 residues within 4Å: Chain A: U.1781 Chain L: L.151 No protein-ligand interaction detected (PLIP) MG.66: 1 residues within 4Å: Chain A: U.99 No protein-ligand interaction detected (PLIP) MG.67: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.68: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.69: 3 residues within 4Å: Chain A: G.881, U.940, G.941 No protein-ligand interaction detected (PLIP) MG.70: 1 residues within 4Å: Ligands: K.83 No protein-ligand interaction detected (PLIP) MG.71: 1 residues within 4Å: Chain A: A.28 No protein-ligand interaction detected (PLIP) MG.72: 2 residues within 4Å: Chain A: G.361, U.362 No protein-ligand interaction detected (PLIP) MG.73: 2 residues within 4Å: Chain A: G.566, A.584 No protein-ligand interaction detected (PLIP) MG.74: 1 residues within 4Å: Chain A: A.1070 No protein-ligand interaction detected (PLIP) MG.75: 1 residues within 4Å: Chain A: G.20 No protein-ligand interaction detected (PLIP) MG.76: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.77: 1 residues within 4Å: Chain A: G.1052 No protein-ligand interaction detected (PLIP) MG.84: 5 residues within 4Å: Chain 0: Q.134, H.135, T.136 Chain A: C.1464, G.1465 1 PLIP interactions: 1 interactions with chain 0 Metal complexes: 0:Q.134

1 x ZN: ZINC ION(Non-covalent)

ZN.87: 4 residues within 4Å: Chain 4: C.21, C.24, C.39, C.42 4 PLIP interactions: 4 interactions with chain 4 Metal complexes: 4:C.21, 4:C.24, 4:C.39, 4:C.42

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mishra, R.K. et al., Cryo-EM structure of wheat ribosome reveals unique features of the plant ribosomes. Structure (2024)

Release Date

2024-03-27

Peptides

40S ribosomal protein SA: B
40S ribosomal protein S3a: C
S5 DRBM domain-containing protein: D
40S ribosomal protein S4: E
40S ribosomal protein S6: F
40S ribosomal protein S7: G
40S ribosomal protein S8: H
30S ribosomal protein S4, chloroplastic: I
40S ribosomal protein S11 N-terminal domain-containing protein: J
Ribosomal protein S13/S15 N-terminal domain-containing protein: K
40S ribosomal protein S14: L
40S ribosomal protein S17: M
40S ribosomal protein S21: N
30S ribosomal protein S8, chloroplastic: O
40S ribosomal protein S23: P
40S ribosomal protein S24: Q
40S ribosomal protein S26: R
40S ribosomal protein S27: S
40S ribosomal protein S30: T
60S ribosomal protein L41: U
KH type-2 domain-containing protein: V
Ribosomal protein S7 domain-containing protein: W
Plectin/S10 N-terminal domain-containing protein: X
40S ribosomal protein S15: Y
40S ribosomal protein S16: Z
40S ribosomal protein S18: 0
40S ribosomal protein S19: 1
Ribosomal protein S10 domain-containing protein: 2
40S ribosomal protein S28: 3
40S ribosomal protein S29: 4
Mitogen-activated protein kinase: 5
40S ribosomal protein S25: 6

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
BA

C
BB

D
BC

E
BE

F
BG

G
BH

H
BI

I
BJ

J
BL

K
BN

L
BO

M
BR

N
BV

O
BW

P
BX

Q
BY

R
Ba

S
Bb

T
Be

U
Cn

V
BD

W
BF

X
BK

Y
BP

Z
BQ

0
BS

1
BT

2
BU

3
Bc

4
Bd

5
Bg

6
BZ

40S ribosomal protein SA

40S ribosomal protein S3a

S5 DRBM domain-containing protein

40S ribosomal protein S4

40S ribosomal protein S6

40S ribosomal protein S7

40S ribosomal protein S8

30S ribosomal protein S4, chloroplastic

40S ribosomal protein S11 N-terminal domain-containing protein

Ribosomal protein S13/S15 N-terminal domain-containing protein

40S ribosomal protein S14

40S ribosomal protein S17

40S ribosomal protein S21

30S ribosomal protein S8, chloroplastic

40S ribosomal protein S23

40S ribosomal protein S24

40S ribosomal protein S26

40S ribosomal protein S27

40S ribosomal protein S30

60S ribosomal protein L41

KH type-2 domain-containing protein

Ribosomal protein S7 domain-containing protein

Plectin/S10 N-terminal domain-containing protein

40S ribosomal protein S15

40S ribosomal protein S16

40S ribosomal protein S18

40S ribosomal protein S19

Ribosomal protein S10 domain-containing protein

40S ribosomal protein S28

40S ribosomal protein S29

Mitogen-activated protein kinase

40S ribosomal protein S25

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