SMTL ID : 8r6f.1

CryoEM structure of wheat 40S ribosomal subunit, body domain

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-mer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain K: C.23, C.26, C.74, C.77 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.23, K:C.26, K:C.74, K:C.77

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

MG.2: 3 residues within 4Å: Chain N: Q.181 Chain U: U.270, C.271 No protein-ligand interaction detected (PLIP) MG.17: 3 residues within 4Å: Chain U: G.407, C.428, G.430 No protein-ligand interaction detected (PLIP) MG.18: 3 residues within 4Å: Chain U: G.1298, G.1299 Ligands: K.9 No protein-ligand interaction detected (PLIP) MG.19: 7 residues within 4Å: Chain U: A.1773, G.1777, G.1778, U.1779, U.1780, U.1781 Ligands: K.11 4 PLIP interactions: 3 Ligand-Water interactions, 1 interactions with chain U Metal complexes: H2O.10, H2O.13, H2O.29, U:A.1773 MG.20: 3 residues within 4Å: Chain U: C.253, A.254, U.255 No protein-ligand interaction detected (PLIP) MG.21: 2 residues within 4Å: Chain U: G.628, C.629 No protein-ligand interaction detected (PLIP) MG.22: 1 residues within 4Å: Chain U: A.627 No protein-ligand interaction detected (PLIP) MG.23: 1 residues within 4Å: Chain U: A.1030 No protein-ligand interaction detected (PLIP) MG.24: 4 residues within 4Å: Chain U: U.622, A.623, A.624, A.625 No protein-ligand interaction detected (PLIP) MG.25: 1 residues within 4Å: Chain U: A.623 No protein-ligand interaction detected (PLIP) MG.26: 4 residues within 4Å: Chain U: G.1637, U.1638, G.1803, A.1804 No protein-ligand interaction detected (PLIP) MG.27: 1 residues within 4Å: Chain U: G.947 No protein-ligand interaction detected (PLIP) MG.28: 3 residues within 4Å: Chain U: G.375, A.609, G.611 No protein-ligand interaction detected (PLIP) MG.29: 1 residues within 4Å: Chain U: G.16 No protein-ligand interaction detected (PLIP) MG.30: 2 residues within 4Å: Chain U: C.49, A.429 No protein-ligand interaction detected (PLIP) MG.31: 1 residues within 4Å: Chain U: G.96 No protein-ligand interaction detected (PLIP) MG.32: 3 residues within 4Å: Chain U: G.96, C.406, G.407 No protein-ligand interaction detected (PLIP) MG.33: 1 residues within 4Å: Chain U: U.384 No protein-ligand interaction detected (PLIP) MG.34: 1 residues within 4Å: Chain U: C.406 No protein-ligand interaction detected (PLIP) MG.35: 1 residues within 4Å: Chain U: A.405 No protein-ligand interaction detected (PLIP) MG.36: 2 residues within 4Å: Chain U: A.101, C.365 No protein-ligand interaction detected (PLIP) MG.37: 3 residues within 4Å: Chain U: A.101, U.102, C.365 No protein-ligand interaction detected (PLIP) MG.38: 1 residues within 4Å: Chain U: G.333 No protein-ligand interaction detected (PLIP) MG.39: 4 residues within 4Å: Chain U: G.367, G.381, A.382, U.383 No protein-ligand interaction detected (PLIP) MG.40: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.41: 2 residues within 4Å: Chain U: G.1114, G.1115 No protein-ligand interaction detected (PLIP) MG.42: 5 residues within 4Å: Chain U: U.1771, A.1772, A.1773, G.1777, G.1778 4 PLIP interactions: 3 Ligand-Water interactions, 1 interactions with chain U Metal complexes: H2O.10, H2O.19, H2O.38, U:A.1773 MG.43: 2 residues within 4Å: Chain U: G.42, U.99 No protein-ligand interaction detected (PLIP) MG.44: 3 residues within 4Å: Chain U: C.618, C.1101, G.1105 No protein-ligand interaction detected (PLIP) MG.45: 3 residues within 4Å: Chain U: G.639, A.640, A.812 No protein-ligand interaction detected (PLIP) MG.46: 3 residues within 4Å: Chain U: G.556, A.559, A.560 No protein-ligand interaction detected (PLIP) MG.47: 2 residues within 4Å: Chain U: C.548, A.549 No protein-ligand interaction detected (PLIP)

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

K.3: 3 residues within 4Å: Chain C: A.2 Chain U: A.304, A.305 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:A.2, H2O.6, H2O.38 K.4: 5 residues within 4Å: Chain U: G.92, A.93, A.94, G.402 Ligands: K.5 No protein-ligand interaction detected (PLIP) K.5: 5 residues within 4Å: Chain U: G.92, G.400, A.401, G.402 Ligands: K.4 No protein-ligand interaction detected (PLIP) K.6: 3 residues within 4Å: Chain K: K.34 Chain U: U.1805, A.1807 3 PLIP interactions: 1 interactions with chain K, 2 Ligand-Water interactions Metal complexes: K:K.34, H2O.3, H2O.3 K.7: 4 residues within 4Å: Chain U: A.335, U.336, G.339, G.340 No protein-ligand interaction detected (PLIP) K.8: 3 residues within 4Å: Chain U: A.109, G.110, U.111 No protein-ligand interaction detected (PLIP) K.9: 5 residues within 4Å: Chain U: U.1297, G.1298, U.1307, G.1308 Ligands: MG.18 No protein-ligand interaction detected (PLIP) K.10: 5 residues within 4Å: Chain C: Q.62 Chain U: U.454, G.455, C.459, G.460 No protein-ligand interaction detected (PLIP) K.11: 5 residues within 4Å: Chain U: A.1772, A.1773, U.1781, C.1794 Ligands: MG.19 No protein-ligand interaction detected (PLIP) K.12: 3 residues within 4Å: Chain U: U.331, A.332, G.341 No protein-ligand interaction detected (PLIP) K.13: 4 residues within 4Å: Chain U: U.1049, C.1050, G.1078, G.1079 No protein-ligand interaction detected (PLIP) K.14: 4 residues within 4Å: Chain R: S.12 Chain U: U.961, G.962, U.963 No protein-ligand interaction detected (PLIP) K.15: 5 residues within 4Å: Chain U: C.448, A.450, U.451, C.452, G.462 No protein-ligand interaction detected (PLIP) K.16: 4 residues within 4Å: Chain U: C.1774, G.1777, U.1780, U.1781 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kravchenko, O.V. et al., High-Resolution Structure and Internal Mobility of a Plant 40S Ribosomal Subunit. Int J Mol Sci (2023)

Release Date

2023-12-27

Peptides

40S ribosomal protein S24: A
40S ribosomal protein S23: B
40S ribosomal protein S4: C
30S ribosomal protein S11, chloroplastic: D
Small ribosomal subunit protein uS8c: E
40S ribosomal protein S27: F
40S ribosomal protein S30: G
Small ribosomal subunit protein uS2: H
Small ribosomal subunit protein eS1: I
Genome assembly, chromosome: II: J
40S ribosomal protein S26: K
30S ribosomal protein S4, chloroplastic: L
S5 DRBM domain-containing protein: M
40S ribosomal protein S6: N
40S ribosomal protein S7: O
40S ribosomal protein S17: P
Small ribosomal subunit protein uS17 N-terminal domain-containing protein: Q
Small ribosomal subunit protein uS15 N-terminal domain-containing protein: R
Large ribosomal subunit protein eL41z/eL41y/eL41x/eL41w/eL41v: S
40S ribosomal protein S8: T

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
Y

B
X

C
E

D
O

E
W

F
b

G
e

H
k

I
B

J
V

K
a

L
J

M
C

N
G

O
H

P
h

Q
L

R
N

S
n

T
I

40S ribosomal protein S24

40S ribosomal protein S23

40S ribosomal protein S4

30S ribosomal protein S11, chloroplastic

Small ribosomal subunit protein uS8c

40S ribosomal protein S27

40S ribosomal protein S30

Small ribosomal subunit protein uS2

Small ribosomal subunit protein eS1

Genome assembly, chromosome: II

40S ribosomal protein S26

30S ribosomal protein S4, chloroplastic

S5 DRBM domain-containing protein

40S ribosomal protein S6

40S ribosomal protein S7

40S ribosomal protein S17

Small ribosomal subunit protein uS17 N-terminal domain-containing protein

Small ribosomal subunit protein uS15 N-terminal domain-containing protein

Large ribosomal subunit protein eL41z/eL41y/eL41x/eL41w/eL41v

40S ribosomal protein S8

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