SMTL ID : 9frk.1

Cryo-EM structure of Saccharolobus solfataricus 30S initiation complex bound to SD mRNA

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-mer

Ligands

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

MG.1: 3 residues within 4Å: Chain A: A.532, A.533, A.534 No protein-ligand interaction detected (PLIP) MG.2: 2 residues within 4Å: Chain A: A.568, A.569 No protein-ligand interaction detected (PLIP) MG.3: 2 residues within 4Å: Chain A: A.719, G.720 No protein-ligand interaction detected (PLIP) MG.4: 6 residues within 4Å: Chain A: A.1458, G.1462, G.1463, A.1465, G.1466 Ligands: SPM.79 4 PLIP interactions: 3 Ligand-Water interactions, 1 interactions with chain A Metal complexes: H2O.1, H2O.1, H2O.3, A:A.1458 MG.5: 1 residues within 4Å: Chain A: G.691 No protein-ligand interaction detected (PLIP) MG.6: 5 residues within 4Å: Chain A: U.1456, A.1457, A.1458, G.1462, G.1463 4 PLIP interactions: 3 Ligand-Water interactions, 1 interactions with chain A Metal complexes: H2O.1, H2O.2, H2O.4, A:A.1458 MG.7: 4 residues within 4Å: Chain A: G.465, C.467, A.468, A.469 No protein-ligand interaction detected (PLIP) MG.8: 4 residues within 4Å: Chain A: G.96, A.97, G.98, G.295 No protein-ligand interaction detected (PLIP) MG.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.10: 5 residues within 4Å: Chain A: G.1011, C.1012, A.1160, G.1161, G.1162 No protein-ligand interaction detected (PLIP) MG.11: 5 residues within 4Å: Chain A: U.944, C.945, U.946, G.1186, C.1187 No protein-ligand interaction detected (PLIP) MG.12: 5 residues within 4Å: Chain A: G.257, U.258, G.272, C.274 Chain K: D.8 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:D.8 MG.13: 4 residues within 4Å: Chain A: A.555, A.556, G.557, U.558 No protein-ligand interaction detected (PLIP) MG.14: 1 residues within 4Å: Chain A: C.536 No protein-ligand interaction detected (PLIP) MG.15: 4 residues within 4Å: Chain A: U.939, G.940, A.1007 Chain Q: D.26 1 PLIP interactions: 1 interactions with chain Q Metal complexes: Q:D.26 MG.16: 3 residues within 4Å: Chain A: A.942, A.943, C.1327 No protein-ligand interaction detected (PLIP) MG.17: 2 residues within 4Å: Chain A: U.1020, C.1021 No protein-ligand interaction detected (PLIP) MG.18: 4 residues within 4Å: Chain A: G.1042, C.1044, C.1058, A.1060 No protein-ligand interaction detected (PLIP) MG.19: 3 residues within 4Å: Chain A: G.1066, A.1067, G.1068 No protein-ligand interaction detected (PLIP) MG.20: 3 residues within 4Å: Chain A: A.1067, G.1068, A.1069 No protein-ligand interaction detected (PLIP) MG.21: 4 residues within 4Å: Chain A: C.1187, C.1188, U.1286, C.1287 No protein-ligand interaction detected (PLIP) MG.22: 4 residues within 4Å: Chain A: U.1267, G.1269, G.1270, G.1296 No protein-ligand interaction detected (PLIP) MG.23: 3 residues within 4Å: Chain A: G.1268, G.1269 Chain V: R.48 No protein-ligand interaction detected (PLIP) MG.24: 1 residues within 4Å: Chain A: G.1335 No protein-ligand interaction detected (PLIP) MG.25: 3 residues within 4Å: Chain A: U.321, U.322, G.323 No protein-ligand interaction detected (PLIP) MG.26: 2 residues within 4Å: Chain A: G.17, U.521 No protein-ligand interaction detected (PLIP) MG.27: 2 residues within 4Å: Chain A: G.541, G.718 No protein-ligand interaction detected (PLIP) MG.28: 5 residues within 4Å: Chain A: U.612, A.613, G.614, G.615 Chain R: H.11 1 PLIP interactions: 1 interactions with chain R Metal complexes: R:H.11 MG.29: 1 residues within 4Å: Chain A: G.1294 No protein-ligand interaction detected (PLIP) MG.30: 2 residues within 4Å: Chain A: C.160, A.194 No protein-ligand interaction detected (PLIP) MG.31: 1 residues within 4Å: Chain A: A.728 No protein-ligand interaction detected (PLIP) MG.32: 3 residues within 4Å: Chain A: G.1008, C.1179, C.1180 No protein-ligand interaction detected (PLIP) MG.33: 3 residues within 4Å: Chain A: G.887, C.1353 Chain G: D.69 No protein-ligand interaction detected (PLIP) MG.34: 3 residues within 4Å: Chain A: U.531, A.532, A.779 No protein-ligand interaction detected (PLIP) MG.35: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.36: 2 residues within 4Å: Chain A: C.518, U.519 No protein-ligand interaction detected (PLIP) MG.37: 3 residues within 4Å: Chain A: U.10, G.11, A.12 No protein-ligand interaction detected (PLIP) MG.38: 2 residues within 4Å: Chain A: G.89, A.90 No protein-ligand interaction detected (PLIP) MG.39: 2 residues within 4Å: Chain A: G.92, G.93 No protein-ligand interaction detected (PLIP) MG.40: 2 residues within 4Å: Chain A: G.93, C.94 No protein-ligand interaction detected (PLIP) MG.41: 2 residues within 4Å: Chain A: A.133 Ligands: SPM.78 No protein-ligand interaction detected (PLIP) MG.42: 1 residues within 4Å: Chain A: C.181 No protein-ligand interaction detected (PLIP) MG.43: 1 residues within 4Å: Chain A: G.177 No protein-ligand interaction detected (PLIP) MG.44: 3 residues within 4Å: Chain A: G.88, G.330, A.331 No protein-ligand interaction detected (PLIP) MG.45: 2 residues within 4Å: Chain A: G.463, G.464 No protein-ligand interaction detected (PLIP) MG.46: 3 residues within 4Å: Chain A: G.537, C.538, G.781 No protein-ligand interaction detected (PLIP) MG.47: 2 residues within 4Å: Chain A: G.716, U.717 No protein-ligand interaction detected (PLIP) MG.48: 1 residues within 4Å: Chain A: G.594 No protein-ligand interaction detected (PLIP) MG.49: 3 residues within 4Å: Chain A: G.614, G.615 Chain R: G.8 No protein-ligand interaction detected (PLIP) MG.50: 4 residues within 4Å: Chain A: C.821, G.822, C.832, G.833 No protein-ligand interaction detected (PLIP) MG.51: 2 residues within 4Å: Chain A: G.851, G.852 No protein-ligand interaction detected (PLIP) MG.52: 1 residues within 4Å: Chain A: U.1356 No protein-ligand interaction detected (PLIP) MG.53: 3 residues within 4Å: Chain A: C.917, C.1187, C.1188 No protein-ligand interaction detected (PLIP) MG.54: 2 residues within 4Å: Chain A: A.929, G.930 No protein-ligand interaction detected (PLIP) MG.55: 2 residues within 4Å: Chain A: C.1021, G.1157 No protein-ligand interaction detected (PLIP) MG.56: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.96: 3 residues within 4Å: Chain A: C.1362 Chain G: Q.67, E.72 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:E.72 MG.99: 3 residues within 4Å: Chain A: G.261, G.272 Chain S: L.101 1 PLIP interactions: 1 interactions with chain S Metal complexes: S:L.101 MG.103: 1 residues within 4Å: Chain 7: G.20 No protein-ligand interaction detected (PLIP)

36 x SPM: SPERMINE(Non-covalent)(Non-functional Binders)

SPM.57: 10 residues within 4Å: Chain A: A.3, U.4, C.5, U.16, G.17, U.519 Chain G: T.180, G.182, E.183, T.184 Ligand excluded by PLIP SPM.58: 9 residues within 4Å: Chain A: G.21, G.462, G.463, G.466, G.484, G.511, U.512 Chain O: G.109 Ligands: SPM.85 Ligand excluded by PLIP SPM.59: 7 residues within 4Å: Chain A: G.245, A.294, G.295, G.296, G.297, G.311, A.312 Ligand excluded by PLIP SPM.60: 7 residues within 4Å: Chain A: G.92, G.93, C.94, U.95, C.314, C.316, C.317 Ligand excluded by PLIP SPM.61: 10 residues within 4Å: Chain A: A.90, C.91, G.92, G.93, G.320, U.321, C.334, A.335, A.336 Chain K: D.22 Ligand excluded by PLIP SPM.62: 9 residues within 4Å: Chain A: A.2, U.4, C.23, G.303, A.304, G.305, A.517, C.518 Chain E: E.12 Ligand excluded by PLIP SPM.63: 11 residues within 4Å: Chain A: G.43, G.44, U.95, G.96, G.295, G.296, G.297, A.312, G.313, C.315 Chain E: G.2 Ligand excluded by PLIP SPM.64: 11 residues within 4Å: Chain A: G.41, G.42, G.313, C.314, C.361, A.362, G.394, A.395, G.396, G.397, G.398 Ligand excluded by PLIP SPM.65: 11 residues within 4Å: Chain A: U.321, G.324, G.325, C.326, A.335, A.336, G.337, G.338, G.339, C.340 Chain K: D.22 Ligand excluded by PLIP SPM.66: 7 residues within 4Å: Chain A: U.566, A.567, A.568, G.588, G.589 Chain F: W.11, N.100 Ligand excluded by PLIP SPM.67: 9 residues within 4Å: Chain A: G.624, A.625, G.626, G.627, C.692, G.693, G.694, U.700, A.701 Ligand excluded by PLIP SPM.68: 13 residues within 4Å: Chain A: A.740, A.741, A.742, A.743, A.754, C.755, C.758, U.759, G.760, G.1472, G.1473, N.1479, U.1480 Ligand excluded by PLIP SPM.69: 7 residues within 4Å: Chain A: G.826, G.827, A.829, G.830, G.1035, U.1036, G.1037 Ligand excluded by PLIP SPM.70: 7 residues within 4Å: Chain A: C.945, A.948, C.949, U.950, U.1183, G.1184, G.1185 Ligand excluded by PLIP SPM.71: 11 residues within 4Å: Chain 0: I.132, S.134, Y.144, E.180 Chain A: G.1011, G.1015, G.1016, C.1017, G.1161, G.1162, U.1163 Ligand excluded by PLIP SPM.72: 9 residues within 4Å: Chain A: C.1317, G.1318, U.1332, G.1333, C.1334 Chain L: E.121, K.122, R.125, Y.126 Ligand excluded by PLIP SPM.73: 7 residues within 4Å: Chain A: C.378, A.379, U.381, G.382, C.391, G.392, U.393 Ligand excluded by PLIP SPM.74: 8 residues within 4Å: Chain A: U.431, C.432, U.438, C.439, A.444, A.445, G.446, G.447 Ligand excluded by PLIP SPM.75: 7 residues within 4Å: Chain A: G.244, G.245, C.247, A.287 Chain S: Y.60, R.73, R.74 Ligand excluded by PLIP SPM.76: 8 residues within 4Å: Chain A: G.37, G.38, G.39, U.40, G.398, C.399 Chain F: K.18, Q.19 Ligand excluded by PLIP SPM.77: 4 residues within 4Å: Chain A: G.126, G.127, G.197, G.198 Ligand excluded by PLIP SPM.78: 8 residues within 4Å: Chain A: G.139, G.140, G.141, U.146, G.147, G.148 Chain H: Y.184 Ligands: MG.41 Ligand excluded by PLIP SPM.79: 11 residues within 4Å: Chain A: A.1457, A.1458, G.1466, N.1467, N.1468, G.1469, U.1470, N.1479, U.1480 Chain N: R.128 Ligands: MG.4 Ligand excluded by PLIP SPM.80: 9 residues within 4Å: Chain A: G.621, G.622, C.794, A.795, C.796, A.797, G.808, C.809, C.810 Ligand excluded by PLIP SPM.81: 11 residues within 4Å: Chain A: G.918, U.925, U.926, G.927, G.928, A.929, C.1187, C.1188, G.1189, C.1190 Chain P: R.133 Ligand excluded by PLIP SPM.82: 9 residues within 4Å: Chain A: G.906, G.907, U.908, G.1197, U.1198, C.1316, U.1330, C.1331 Chain L: Y.126 Ligand excluded by PLIP SPM.83: 6 residues within 4Å: Chain A: G.7, G.8, C.15, U.16 Chain G: E.183, T.187 Ligand excluded by PLIP SPM.84: 7 residues within 4Å: Chain A: G.8, U.9, U.10, C.486, G.487, A.878, A.879 Ligand excluded by PLIP SPM.85: 8 residues within 4Å: Chain A: G.21, A.22, C.23, C.24, G.510 Chain E: P.17, W.18 Ligands: SPM.58 Ligand excluded by PLIP SPM.86: 6 residues within 4Å: Chain A: A.131, U.132, A.133, G.150, A.151, U.152 Ligand excluded by PLIP SPM.87: 8 residues within 4Å: Chain A: U.110, U.115, A.234, U.235, G.236, G.237, G.238, G.239 Ligand excluded by PLIP SPM.88: 5 residues within 4Å: Chain A: G.548, C.549, C.603, U.604, G.605 Ligand excluded by PLIP SPM.89: 8 residues within 4Å: Chain A: C.575, G.576, G.577, C.578, C.580, A.581, A.582, C.583 Ligand excluded by PLIP SPM.90: 6 residues within 4Å: Chain A: U.926, G.927, G.1009, U.1010, C.1164, A.1165 Ligand excluded by PLIP SPM.91: 13 residues within 4Å: Chain A: G.895, C.896, C.1024, A.1025, G.1047, U.1048, U.1049, A.1050, A.1051, G.1052, U.1053, C.1054, U.1352 Ligand excluded by PLIP SPM.92: 7 residues within 4Å: Chain 3: R.101 Chain A: G.1206, C.1207, G.1209, G.1210, A.1254, C.1255 Ligand excluded by PLIP

8 x ZN: ZINC ION(Non-covalent)

ZN.93: 6 residues within 4Å: Chain D: C.34, C.37, G.38, C.57, N.59, C.60 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.34, D:C.37, D:C.57, D:C.60 ZN.94: 5 residues within 4Å: Chain D: C.16, S.18, C.19, D.45, C.48 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.16, D:C.19, D:D.45, D:C.48 ZN.95: 5 residues within 4Å: Chain G: C.121, C.126, C.128, G.129, H.132 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.121, G:C.126, G:C.128, G:H.132 ZN.97: 5 residues within 4Å: Chain Q: C.19, C.22, L.36, C.37, C.40 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:C.19, Q:C.22, Q:C.37, Q:C.40 ZN.98: 4 residues within 4Å: Chain S: C.23, C.28, H.31, C.84 4 PLIP interactions: 4 interactions with chain S Metal complexes: S:C.23, S:C.28, S:H.31, S:C.84 ZN.100: 6 residues within 4Å: Chain X: C.21, C.24, G.25, C.40, S.42, C.43 4 PLIP interactions: 4 interactions with chain X Metal complexes: X:C.21, X:C.24, X:C.40, X:C.43 ZN.101: 5 residues within 4Å: Chain 2: C.38, K.40, C.41, C.61, C.64 4 PLIP interactions: 4 interactions with chain 2 Metal complexes: 2:C.38, 2:C.41, 2:C.61, 2:C.64 ZN.102: 5 residues within 4Å: Chain 2: C.21, C.24, N.25, C.50, D.53 3 PLIP interactions: 3 interactions with chain 2 Metal complexes: 2:C.21, 2:C.24, 2:D.53

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bourgeois, G. et al., Structures of Saccharolobus solfataricus initiation complexes with leaderless mRNAs highlight archaeal features and eukaryotic proximity. Nat Commun (2025)

Release Date

2025-01-15

Peptides

Small ribosomal subunit protein eS1: B
Small ribosomal subunit protein uS2: C
Small zinc finger protein HVO-2753-like zinc-binding pocket domain-containing protein: D
Small ribosomal subunit protein uS4: E
Small ribosomal subunit protein eS4: F
Small ribosomal subunit protein uS5: G
Small ribosomal subunit protein eS6: H
Small ribosomal subunit protein uS7: I
Small ribosomal subunit protein uS8: J
Small ribosomal subunit protein eS8: K
Small ribosomal subunit protein uS9: L
Small ribosomal subunit protein uS10: M
Small ribosomal subunit protein uS11: N
Small ribosomal subunit protein uS12: O
Small ribosomal subunit protein uS13: P
Small ribosomal subunit protein uS14: Q
Small ribosomal subunit protein uS15: R
Small ribosomal subunit protein uS17: S
Small ribosomal subunit protein eS17: T
Small ribosomal subunit protein uS19: U
Small ribosomal subunit protein eS19: V
Small ribosomal subunit protein eS24: W
Small ribosomal subunit protein eS27: X
Small ribosomal subunit protein eS28: Y
Small ribosomal subunit protein eS31: Z
Small ribosomal subunit protein uS3: 0
Large ribosomal subunit protein eL8: 1
aS34: 2
Small ribosomal subunit protein eS25: 3
VapB-type antitoxin: 4
LSU ribosomal protein S30E (Rps30E): 5

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
A

C
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

T
S

U
T

V
U

W
V

X
W

Y
X

Z
Y

0
Z

1
3

2
a

3
c

4
d

5
e

Small ribosomal subunit protein eS1

Small ribosomal subunit protein uS2

Small zinc finger protein HVO-2753-like zinc-binding pocket domain-containing protein

Small ribosomal subunit protein uS4

Small ribosomal subunit protein eS4

Small ribosomal subunit protein uS5

Small ribosomal subunit protein eS6

Small ribosomal subunit protein uS7

Small ribosomal subunit protein uS8

Small ribosomal subunit protein eS8

Small ribosomal subunit protein uS9

Small ribosomal subunit protein uS10

Small ribosomal subunit protein uS11

Small ribosomal subunit protein uS12

Small ribosomal subunit protein uS13

Small ribosomal subunit protein uS14

Small ribosomal subunit protein uS15

Small ribosomal subunit protein uS17

Small ribosomal subunit protein eS17

Small ribosomal subunit protein uS19

Small ribosomal subunit protein eS19

Small ribosomal subunit protein eS24

Small ribosomal subunit protein eS27

Small ribosomal subunit protein eS28

Small ribosomal subunit protein eS31

Small ribosomal subunit protein uS3

Large ribosomal subunit protein eL8

aS34

Small ribosomal subunit protein eS25

VapB-type antitoxin

LSU ribosomal protein S30E (Rps30E)

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