SMTL ID : 8r57.1

CryoEM structure of wheat 40S ribosomal subunit, head domain

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

MG.1: 5 residues within 4Å: Chain D: A.158, N.161, K.163 Chain O: C.1478, U.1479 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:A.158, D:N.161, D:K.163 MG.9: 2 residues within 4Å: Chain O: U.1474, C.1597 No protein-ligand interaction detected (PLIP) MG.10: 4 residues within 4Å: Chain E: Y.148 Chain O: C.1163, A.1164, G.1587 No protein-ligand interaction detected (PLIP) MG.11: 3 residues within 4Å: Chain O: G.1173, G.1174, A.1175 No protein-ligand interaction detected (PLIP) MG.12: 2 residues within 4Å: Chain O: C.1166, G.1168 No protein-ligand interaction detected (PLIP) MG.13: 3 residues within 4Å: Chain O: A.1206, A.1207, C.1607 No protein-ligand interaction detected (PLIP) MG.14: 6 residues within 4Å: Chain O: A.1208, C.1209, U.1210, U.1211, G.1461, C.1462 No protein-ligand interaction detected (PLIP) MG.15: 3 residues within 4Å: Chain O: C.1209, U.1458, G.1459 No protein-ligand interaction detected (PLIP) MG.16: 3 residues within 4Å: Chain O: G.1277, C.1278, G.1434 No protein-ligand interaction detected (PLIP) MG.17: 4 residues within 4Å: Chain O: C.1278, A.1433, G.1434, G.1435 No protein-ligand interaction detected (PLIP) MG.18: 1 residues within 4Å: Chain O: G.1334 No protein-ligand interaction detected (PLIP) MG.19: 3 residues within 4Å: Chain O: G.1274, G.1454, U.1455 No protein-ligand interaction detected (PLIP) MG.20: 2 residues within 4Å: Chain O: G.1180, C.1463 No protein-ligand interaction detected (PLIP) MG.21: 3 residues within 4Å: Chain O: G.1547, G.1548, G.1549 No protein-ligand interaction detected (PLIP) MG.22: 2 residues within 4Å: Chain O: G.1548, G.1549 No protein-ligand interaction detected (PLIP) MG.23: 2 residues within 4Å: Chain O: U.1384, C.1385 No protein-ligand interaction detected (PLIP) MG.24: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.25: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.26: 1 residues within 4Å: Chain O: U.1603 No protein-ligand interaction detected (PLIP) MG.27: 2 residues within 4Å: Chain O: U.1273, U.1438 No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain J: C.21, C.24, C.39, C.42 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.21, J:C.24, J:C.39, J:C.42 ZN.28: 5 residues within 4Å: Chain P: C.122, N.124, C.127, C.142, C.145 3 PLIP interactions: 3 interactions with chain P Metal complexes: P:C.127, P:C.142, P:C.145

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

K.3: 5 residues within 4Å: Chain J: N.26, H.28, C.39, Q.41 Chain O: G.1439 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:H.28 K.4: 4 residues within 4Å: Chain O: U.1172, G.1173, G.1174, G.1582 No protein-ligand interaction detected (PLIP) K.5: 4 residues within 4Å: Chain F: N.83 Chain O: C.1199, A.1200, C.1201 No protein-ligand interaction detected (PLIP) K.6: 6 residues within 4Å: Chain O: G.1277, G.1281, U.1436, C.1437, U.1440, A.1442 No protein-ligand interaction detected (PLIP) K.7: 4 residues within 4Å: Chain O: G.1282, C.1283, G.1435, U.1436 No protein-ligand interaction detected (PLIP) K.8: 6 residues within 4Å: Chain O: G.1275, U.1276, C.1437, U.1443, G.1444, C.1445 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

Plectin/eS10 N-terminal domain-containing protein: A
40S ribosomal protein S12: B
40S ribosomal protein S3: C
Small ribosomal subunit protein uS7c: D
40S ribosomal protein S16: E
Ribosomal protein S20: F
40S ribosomal protein S19: G
40S ribosomal protein S25: H
40S ribosomal protein S28: I
Small ribosomal subunit protein uS14: J
Ribosomal protein RACK1 subfamily. WD repeat G protein beta family: K
Putative ribosomal protein S18: L
40S ribosomal protein S15: M
40S ribosomal protein S17: N
Ubiquitin-like domain-containing protein: P

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
K

B
M

C
F

D
P

E
Q

F
U

G
T

H
Z

I
c

J
d

K
g

L
S

M
R

N
h

P
f

Plectin/eS10 N-terminal domain-containing protein

40S ribosomal protein S12

40S ribosomal protein S3

Small ribosomal subunit protein uS7c

40S ribosomal protein S16

Ribosomal protein S20

40S ribosomal protein S19

40S ribosomal protein S25

40S ribosomal protein S28

Small ribosomal subunit protein uS14

Ribosomal protein RACK1 subfamily. WD repeat G protein beta family

Putative ribosomal protein S18

40S ribosomal protein S15

40S ribosomal protein S17

Ubiquitin-like domain-containing protein

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