SMTL ID : 7qix.1

Specific features and methylation sites of a plant ribosome. 40S body ribosomal 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-mer

Ligands

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

K.1: 3 residues within 4Å: Chain A: A.304, A.305 Chain E: A.2 Ligand excluded by PLIP K.2: 6 residues within 4Å: Chain A: U.1802, A.1804 Chain L: G.9, R.10, K.34, I.36 Ligand excluded by PLIP K.3: 4 residues within 4Å: Chain A: A.335, U.336, U.339, G.340 Ligand excluded by PLIP K.4: 3 residues within 4Å: Chain A: A.109, G.110, U.111 Ligand excluded by PLIP K.5: 4 residues within 4Å: Chain A: G.92, G.400, A.401, G.402 Ligand excluded by PLIP K.6: 4 residues within 4Å: Chain A: G.92, A.93, A.94, G.402 Ligand excluded by PLIP K.7: 2 residues within 4Å: Chain A: G.1296 Ligands: MG.62 Ligand excluded by PLIP K.8: 4 residues within 4Å: Chain A: U.454, G.455, C.459, G.460 Ligand excluded by PLIP K.9: 5 residues within 4Å: Chain A: A.997, A.1009, G.1784, C.1791, U.1792 Ligand excluded by PLIP K.10: 5 residues within 4Å: Chain A: A.1769, A.1770, U.1778, C.1791 Ligands: MG.53 Ligand excluded by PLIP K.11: 3 residues within 4Å: Chain A: U.331, A.332, G.341 Ligand excluded by PLIP K.12: 5 residues within 4Å: Chain A: A.1047, U.1048, C.1049, G.1077, G.1078 Ligand excluded by PLIP K.13: 4 residues within 4Å: Chain A: U.960, G.961, U.962 Chain P: S.12 Ligand excluded by PLIP K.14: 6 residues within 4Å: Chain A: C.448, A.450, U.451, C.452, G.462, A.464 Ligand excluded by PLIP K.15: 5 residues within 4Å: Chain A: A.105, U.107, C.108, G.311, C.312 Ligand excluded by PLIP K.16: 4 residues within 4Å: Chain A: G.375, G.611, G.617, U.1103 Ligand excluded by PLIP K.17: 5 residues within 4Å: Chain A: G.614, U.615 Chain H: K.97, Y.98 Chain K: R.17 Ligand excluded by PLIP K.18: 3 residues within 4Å: Chain A: C.979, G.980, A.1027 Ligand excluded by PLIP K.19: 3 residues within 4Å: Chain A: C.1771, U.1777, U.1778 Ligand excluded by PLIP

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

MG.20: 5 residues within 4Å: Chain A: A.210, G.211, C.253, A.254, U.255 No protein-ligand interaction detected (PLIP) MG.21: 3 residues within 4Å: Chain A: G.628, C.629, G.1036 No protein-ligand interaction detected (PLIP) MG.22: 3 residues within 4Å: Chain A: A.627, A.974, A.975 No protein-ligand interaction detected (PLIP) MG.23: 2 residues within 4Å: Chain A: A.627, C.1032 No protein-ligand interaction detected (PLIP) MG.24: 2 residues within 4Å: Chain A: A.1029, A.1031 No protein-ligand interaction detected (PLIP) MG.25: 3 residues within 4Å: Chain A: A.623, A.624, A.625 No protein-ligand interaction detected (PLIP) MG.26: 2 residues within 4Å: Chain A: A.623, A.1034 No protein-ligand interaction detected (PLIP) MG.27: 2 residues within 4Å: Chain A: G.1800, A.1801 No protein-ligand interaction detected (PLIP) MG.28: 2 residues within 4Å: Chain A: A.945, G.946 No protein-ligand interaction detected (PLIP) MG.29: 3 residues within 4Å: Chain A: G.375, A.609, G.611 No protein-ligand interaction detected (PLIP) MG.30: 2 residues within 4Å: Chain A: U.8, U.9 No protein-ligand interaction detected (PLIP) MG.31: 3 residues within 4Å: Chain A: G.16, A.624, G.1111 No protein-ligand interaction detected (PLIP) MG.32: 4 residues within 4Å: Chain A: G.48, C.49, G.392, A.429 No protein-ligand interaction detected (PLIP) MG.33: 1 residues within 4Å: Chain A: U.89 No protein-ligand interaction detected (PLIP) MG.34: 1 residues within 4Å: Chain A: G.96 No protein-ligand interaction detected (PLIP) MG.35: 1 residues within 4Å: Chain A: C.386 No protein-ligand interaction detected (PLIP) MG.36: 3 residues within 4Å: Chain A: A.405, C.406 Chain E: R.3 No protein-ligand interaction detected (PLIP) MG.37: 1 residues within 4Å: Chain A: A.405 No protein-ligand interaction detected (PLIP) MG.38: 3 residues within 4Å: Chain A: C.100, A.101, C.365 No protein-ligand interaction detected (PLIP) MG.39: 4 residues within 4Å: Chain A: A.101, U.102, A.364, C.365 No protein-ligand interaction detected (PLIP) MG.40: 2 residues within 4Å: Chain A: A.345, C.346 No protein-ligand interaction detected (PLIP) MG.41: 3 residues within 4Å: Chain A: G.333, G.341, C.342 No protein-ligand interaction detected (PLIP) MG.42: 3 residues within 4Å: Chain A: G.381, A.382, U.383 No protein-ligand interaction detected (PLIP) MG.43: 4 residues within 4Å: Chain A: G.96, C.406, G.407 Chain E: R.3 No protein-ligand interaction detected (PLIP) MG.44: 3 residues within 4Å: Chain A: A.55, G.407, C.428 No protein-ligand interaction detected (PLIP) MG.45: 1 residues within 4Å: Chain A: A.518 No protein-ligand interaction detected (PLIP) MG.46: 2 residues within 4Å: Chain A: C.547, A.548 No protein-ligand interaction detected (PLIP) MG.47: 1 residues within 4Å: Chain A: A.588 No protein-ligand interaction detected (PLIP) MG.48: 4 residues within 4Å: Chain A: G.555, C.557, A.558, A.559 No protein-ligand interaction detected (PLIP) MG.49: 3 residues within 4Å: Chain A: G.639, A.640, A.811 No protein-ligand interaction detected (PLIP) MG.50: 5 residues within 4Å: Chain A: G.932, A.933, A.934, C.935, U.949 No protein-ligand interaction detected (PLIP) MG.51: 2 residues within 4Å: Chain A: A.971, U.972 No protein-ligand interaction detected (PLIP) MG.52: 3 residues within 4Å: Chain A: G.1112, G.1113, G.1114 No protein-ligand interaction detected (PLIP) MG.53: 6 residues within 4Å: Chain A: A.1770, G.1774, G.1775, U.1777, U.1778 Ligands: K.10 4 PLIP interactions: 3 Ligand-Water interactions, 1 interactions with chain A Metal complexes: H2O.5, H2O.7, H2O.12, A:A.1770 MG.54: 5 residues within 4Å: Chain A: U.1768, A.1769, A.1770, G.1774, G.1775 4 PLIP interactions: 3 Ligand-Water interactions, 1 interactions with chain A Metal complexes: H2O.3, H2O.12, H2O.17, A:A.1770 MG.55: 4 residues within 4Å: Chain A: A.1773, U.1777, A.1801 Chain Q: L.150 No protein-ligand interaction detected (PLIP) MG.56: 3 residues within 4Å: Chain A: G.42, A.43, U.99 No protein-ligand interaction detected (PLIP) MG.57: 2 residues within 4Å: Chain A: G.1039 Chain P: I.11 No protein-ligand interaction detected (PLIP) MG.58: 1 residues within 4Å: Chain A: C.1079 No protein-ligand interaction detected (PLIP) MG.59: 3 residues within 4Å: Chain A: A.981, C.1026, A.1027 No protein-ligand interaction detected (PLIP) MG.60: 2 residues within 4Å: Chain A: A.105, U.310 No protein-ligand interaction detected (PLIP) MG.61: 4 residues within 4Å: Chain A: G.880, A.937, U.939, G.940 No protein-ligand interaction detected (PLIP) MG.62: 4 residues within 4Å: Chain A: G.1296, G.1297, A.1298 Ligands: K.7 No protein-ligand interaction detected (PLIP) MG.63: 2 residues within 4Å: Chain A: C.973, G.1036 No protein-ligand interaction detected (PLIP) MG.64: 1 residues within 4Å: Chain A: A.28 No protein-ligand interaction detected (PLIP) MG.65: 3 residues within 4Å: Chain A: A.104, G.361, U.362 No protein-ligand interaction detected (PLIP) MG.66: 2 residues within 4Å: Chain A: A.364, G.366 No protein-ligand interaction detected (PLIP) MG.67: 2 residues within 4Å: Chain A: A.553, G.554 No protein-ligand interaction detected (PLIP) MG.68: 3 residues within 4Å: Chain A: G.564, G.565, A.583 No protein-ligand interaction detected (PLIP) MG.69: 2 residues within 4Å: Chain A: A.866, A.867 No protein-ligand interaction detected (PLIP) MG.70: 3 residues within 4Å: Chain A: A.1069 Chain D: Q.157, Q.160 No protein-ligand interaction detected (PLIP) MG.71: 2 residues within 4Å: Chain A: U.1083, U.1084 No protein-ligand interaction detected (PLIP) MG.72: 5 residues within 4Å: Chain A: G.617, C.618, U.1100, U.1103, G.1104 No protein-ligand interaction detected (PLIP) MG.73: 1 residues within 4Å: Chain A: G.1105 No protein-ligand interaction detected (PLIP) MG.74: 2 residues within 4Å: Chain A: C.17, U.612 No protein-ligand interaction detected (PLIP) MG.75: 1 residues within 4Å: Chain A: A.609 No protein-ligand interaction detected (PLIP) MG.76: 2 residues within 4Å: Chain A: G.1775, U.1776 No protein-ligand interaction detected (PLIP) MG.77: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.78: 1 residues within 4Å: Chain A: G.1051 No protein-ligand interaction detected (PLIP) MG.80: 4 residues within 4Å: Chain A: U.270, C.271 Chain N: Q.181, R.182 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.79: 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

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

60S ribosomal protein L41: B
40S ribosomal protein SA: C
40S ribosomal protein S3a: D
40S body ribosomal protein eS4: E
40S ribosomal protein S7: F
40S ribosomal protein S8: G
Ribosomal_S17_N domain-containing protein: H
40S ribosomal protein S17: I
40S ribosomal protein S21: J
40S body ribosomal protein uS12: K
40S ribosomal protein S26: L
S5 DRBM domain-containing protein: M
40S ribosomal protein S6: N
40S body ribosomal protein uS4: O
30S ribosomal protein S15, chloroplastic: P
Ribosomal protein S14: Q
40S ribosomal protein S24: R
40S ribosomal protein S27: S
40S ribosomal protein S30: T
40S ribosomal protein S15a-1: U
Ribosomal protein L19: V

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

O
Q

P
R

Q
S

R
U

S
V

T
W

U
T

V
X

60S ribosomal protein L41

40S ribosomal protein SA

40S ribosomal protein S3a

40S body ribosomal protein eS4

40S ribosomal protein S7

40S ribosomal protein S8

Ribosomal_S17_N domain-containing protein

40S ribosomal protein S17

40S ribosomal protein S21

40S body ribosomal protein uS12

40S ribosomal protein S26

S5 DRBM domain-containing protein

40S ribosomal protein S6

40S body ribosomal protein uS4

30S ribosomal protein S15, chloroplastic

Ribosomal protein S14

40S ribosomal protein S24

40S ribosomal protein S27

40S ribosomal protein S30

40S ribosomal protein S15a-1

Ribosomal protein L19

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