SMTL ID : 7qiy.1

Specific features and methylation sites of a plant ribosome. 40S head ribosomal subunit.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

A-U-C.1: 7 residues within 4Å: Chain A: G.1152, C.1642, G.1643 Chain O: G.6, A.7, U.8, A.9 Protein-ligand interaction information (PLIP) not available

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

K.2: 4 residues within 4Å: Chain A: C.1197, A.1198, C.1199 Chain J: N.79 No protein-ligand interaction detected (PLIP) K.3: 5 residues within 4Å: Chain A: G.1275, G.1280, C.1281, G.1433, U.1434 No protein-ligand interaction detected (PLIP) K.4: 4 residues within 4Å: Chain A: U.1170, G.1171, G.1172, G.1579 No protein-ligand interaction detected (PLIP) K.5: 7 residues within 4Å: Chain A: G.1275, G.1279, G.1280, U.1434, C.1435, U.1438, A.1440 No protein-ligand interaction detected (PLIP) K.6: 6 residues within 4Å: Chain A: G.1273, U.1274, C.1435, U.1441, G.1442, C.1443 No protein-ligand interaction detected (PLIP) K.7: 5 residues within 4Å: Chain A: G.1358, G.1359, A.1360, U.1370, C.1371 No protein-ligand interaction detected (PLIP) K.8: 5 residues within 4Å: Chain A: G.1547, A.1548, U.1549, A.1550, U.1572 No protein-ligand interaction detected (PLIP) K.38: 5 residues within 4Å: Chain A: C.1463 Chain H: T.136, T.139, G.140, R.141 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:T.136, H:T.139 K.40: 6 residues within 4Å: Chain A: U.1484, U.1485, A.1530 Chain I: I.79, Y.80, G.81 3 PLIP interactions: 2 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:I.79, I:G.81, H2O.5 K.41: 6 residues within 4Å: Chain A: G.1437 Chain L: N.26, H.28, A.29, C.39, Q.41 2 PLIP interactions: 1 interactions with chain L, 1 Ligand-Water interactions Metal complexes: L:H.28, H2O.3

1 x PUT: 1,4-DIAMINOBUTANE(Non-functional Binders)

PUT.9: 9 residues within 4Å: Chain A: A.1591, A.1592, G.1593, C.1594, C.1611, G.1612, U.1613 Chain F: R.136, G.137 No protein-ligand interaction detected (PLIP)

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

MG.10: 4 residues within 4Å: Chain A: C.1161, A.1162, U.1584, C.1585 No protein-ligand interaction detected (PLIP) MG.11: 3 residues within 4Å: Chain A: C.1164, A.1165, G.1166 No protein-ligand interaction detected (PLIP) MG.12: 4 residues within 4Å: Chain A: G.1169, U.1170, U.1472, A.1473 No protein-ligand interaction detected (PLIP) MG.13: 2 residues within 4Å: Chain A: G.1171, G.1172 No protein-ligand interaction detected (PLIP) MG.14: 3 residues within 4Å: Chain A: A.1195, U.1284, U.1285 No protein-ligand interaction detected (PLIP) MG.15: 4 residues within 4Å: Chain A: G.1202, G.1203, A.1605, C.1607 No protein-ligand interaction detected (PLIP) MG.16: 3 residues within 4Å: Chain A: A.1204, A.1205, C.1604 No protein-ligand interaction detected (PLIP) MG.17: 5 residues within 4Å: Chain A: A.1206, C.1207, U.1208, G.1459, C.1460 No protein-ligand interaction detected (PLIP) MG.18: 1 residues within 4Å: Chain A: C.1207 No protein-ligand interaction detected (PLIP) MG.19: 2 residues within 4Å: Chain A: U.1271, U.1436 No protein-ligand interaction detected (PLIP) MG.20: 3 residues within 4Å: Chain A: G.1275, C.1276, G.1432 No protein-ligand interaction detected (PLIP) MG.21: 4 residues within 4Å: Chain A: C.1276, A.1431, G.1432, G.1433 No protein-ligand interaction detected (PLIP) MG.22: 2 residues within 4Å: Chain A: C.1286, A.1426 No protein-ligand interaction detected (PLIP) MG.23: 2 residues within 4Å: Chain A: G.1332, A.1333 No protein-ligand interaction detected (PLIP) MG.24: 3 residues within 4Å: Chain A: G.1330, A.1331, G.1332 No protein-ligand interaction detected (PLIP) MG.25: 3 residues within 4Å: Chain A: U.1271, G.1452, U.1453 No protein-ligand interaction detected (PLIP) MG.26: 4 residues within 4Å: Chain A: G.1202, A.1204, C.1460, C.1461 No protein-ligand interaction detected (PLIP) MG.27: 4 residues within 4Å: Chain A: U.1543, G.1544, G.1546, G.1547 No protein-ligand interaction detected (PLIP) MG.28: 2 residues within 4Å: Chain A: G.1545, G.1546 No protein-ligand interaction detected (PLIP) MG.29: 3 residues within 4Å: Chain A: U.1381, U.1382, C.1383 No protein-ligand interaction detected (PLIP) MG.30: 2 residues within 4Å: Chain A: U.1482, U.1534 No protein-ligand interaction detected (PLIP) MG.31: 4 residues within 4Å: Chain A: C.1486, A.1487, G.1528, A.1529 No protein-ligand interaction detected (PLIP) MG.32: 3 residues within 4Å: Chain A: C.1160, A.1162, G.1621 No protein-ligand interaction detected (PLIP) MG.33: 1 residues within 4Å: Chain A: G.1172 No protein-ligand interaction detected (PLIP) MG.34: 3 residues within 4Å: Chain A: A.1198, C.1199, C.1469 No protein-ligand interaction detected (PLIP) MG.35: 3 residues within 4Å: Chain A: G.1389, G.1390, G.1391 No protein-ligand interaction detected (PLIP) MG.36: 4 residues within 4Å: Chain A: C.1461, G.1564 Chain H: G.133, H.135 3 PLIP interactions: 1 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:G.133, H2O.3, H2O.8 MG.39: 6 residues within 4Å: Chain A: U.1572 Chain H: T.31, I.33, K.34, G.35, I.36 4 PLIP interactions: 3 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:T.31, H:I.33, H:I.36, H2O.3

1 x BGC: beta-D-glucopyranose(Post Translational Modification)

BGC.37: 9 residues within 4Å: Chain B: S.38, R.54, V.94, L.99, C.100, A.101, I.102, A.103, D.172 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.54, B:A.101, B:I.102, B:D.172, B:D.172

1 x ZN: ZINC ION(Non-covalent)

ZN.42: 5 residues within 4Å: Chain L: C.21, V.23, C.24, C.39, C.42 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.21, L:C.24, L:C.39, L:C.42

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cottilli, P. et al., Cryo-EM structure and rRNA modification sites of a plant ribosome. Plant Commun. (2022)

Release Date

2022-06-15

Peptides

KH type-2 domain-containing protein: B
Ribosomal_S7 domain-containing protein: C
S10_plectin domain-containing protein: D
40S head ribosomal protein uS19: E
40S head ribosomal protein uS9: F
40S ribosomal protein S17: G
40S head ribosomal protein uS13: H
40S head ribosomal protein eS19: I
Ribosomal_S10 domain-containing protein: J
40S head ribosomal protein eS28: K
40S ribosomal protein S29: L
Mitogen-activated protein kinase: M
40S ribosomal protein S25: N

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
D

C
E

D
F

E
G

F
H

G
I

H
J

I
K

J
L

K
M

L
N

M
O

N
P

KH type-2 domain-containing protein

Ribosomal_S7 domain-containing protein

S10_plectin domain-containing protein

40S head ribosomal protein uS19

40S head ribosomal protein uS9

40S ribosomal protein S17

40S head ribosomal protein uS13

40S head ribosomal protein eS19

Ribosomal_S10 domain-containing protein

40S head ribosomal protein eS28

40S ribosomal protein S29

Mitogen-activated protein kinase

40S ribosomal protein S25

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