SMTL ID : 9nta.1

Methanosarcina acetivorans 50S subunit obtained from methanol-grown cells

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-mer

Ligands

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

MG.1: 3 residues within 4Å: Chain A: G.2247, A.2250, G.2251 No protein-ligand interaction detected (PLIP) MG.2: 3 residues within 4Å: Chain A: G.185, C.427, U.428 No protein-ligand interaction detected (PLIP) MG.3: 5 residues within 4Å: Chain A: U.872, A.873, A.874, U.875, A.1816 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain A: G.816, G.846 No protein-ligand interaction detected (PLIP) MG.5: 4 residues within 4Å: Chain A: C.1810, G.1812, C.1824, A.1825 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain A: A.449, G.450, A.453 No protein-ligand interaction detected (PLIP) MG.7: 7 residues within 4Å: Chain A: A.835, A.836, A.874, G.1670, A.1671, C.1672, C.1674 No protein-ligand interaction detected (PLIP) MG.8: 4 residues within 4Å: Chain A: G.903, U.1277, A.1278, G.1279 No protein-ligand interaction detected (PLIP) MG.9: 4 residues within 4Å: Chain A: U.869, C.2451, G.2599, A.2600 No protein-ligand interaction detected (PLIP) MG.10: 4 residues within 4Å: Chain A: U.157, A.164, G.2251, U.2252 No protein-ligand interaction detected (PLIP) MG.11: 3 residues within 4Å: Chain A: A.160, A.162, C.163 No protein-ligand interaction detected (PLIP) MG.12: 2 residues within 4Å: Chain A: G.948, A.949 No protein-ligand interaction detected (PLIP) MG.13: 1 residues within 4Å: Chain A: C.1416 No protein-ligand interaction detected (PLIP) MG.14: 3 residues within 4Å: Chain A: G.1732, C.2007, U.2562 No protein-ligand interaction detected (PLIP) MG.15: 5 residues within 4Å: Chain A: C.1058, C.1059, G.1060, A.1062, G.1077 No protein-ligand interaction detected (PLIP) MG.16: 5 residues within 4Å: Chain A: G.2073, G.2074, U.2586, G.2587, A.2588 No protein-ligand interaction detected (PLIP) MG.17: 3 residues within 4Å: Chain A: A.1431, G.1658, U.1659 No protein-ligand interaction detected (PLIP) MG.18: 5 residues within 4Å: Chain A: U.1870, G.1871, C.1872, A.1990, A.1991 No protein-ligand interaction detected (PLIP) MG.19: 3 residues within 4Å: Chain A: C.2087, C.2257, U.2258 No protein-ligand interaction detected (PLIP) MG.20: 3 residues within 4Å: Chain A: U.1440, C.1466, G.1467 No protein-ligand interaction detected (PLIP) MG.21: 2 residues within 4Å: Chain A: A.1823, C.1824 No protein-ligand interaction detected (PLIP) MG.22: 3 residues within 4Å: Chain A: C.914, G.2088, U.2089 No protein-ligand interaction detected (PLIP) MG.23: 2 residues within 4Å: Chain A: C.1387, G.1388 No protein-ligand interaction detected (PLIP) MG.24: 3 residues within 4Å: Chain A: G.633, G.634, A.1339 No protein-ligand interaction detected (PLIP) MG.25: 4 residues within 4Å: Chain A: U.2095, U.2096, G.2247, G.2248 No protein-ligand interaction detected (PLIP) MG.26: 1 residues within 4Å: Chain A: U.1452 No protein-ligand interaction detected (PLIP) MG.27: 2 residues within 4Å: Chain A: A.726, C.727 No protein-ligand interaction detected (PLIP) MG.28: 4 residues within 4Å: Chain A: G.634, A.1339, A.1340, A.1341 No protein-ligand interaction detected (PLIP) MG.29: 4 residues within 4Å: Chain A: U.1057, C.1058, C.1073, C.1074 No protein-ligand interaction detected (PLIP) MG.30: 4 residues within 4Å: Chain A: A.183, A.184, G.185, A.429 No protein-ligand interaction detected (PLIP) MG.31: 2 residues within 4Å: Chain A: G.2033 Chain S: I.25 No protein-ligand interaction detected (PLIP) MG.32: 2 residues within 4Å: Chain A: C.917, C.1032 No protein-ligand interaction detected (PLIP) MG.33: 6 residues within 4Å: Chain A: A.299, A.323, G.324, G.334, U.339, U.340 No protein-ligand interaction detected (PLIP) MG.34: 4 residues within 4Å: Chain A: G.450, C.451, G.452, A.453 No protein-ligand interaction detected (PLIP) MG.35: 3 residues within 4Å: Chain A: G.883, G.884, C.885 No protein-ligand interaction detected (PLIP) MG.36: 3 residues within 4Å: Chain A: G.787, U.807, G.808 No protein-ligand interaction detected (PLIP) MG.37: 5 residues within 4Å: Chain A: A.169, G.170, U.218, U.386, G.387 No protein-ligand interaction detected (PLIP) MG.38: 2 residues within 4Å: Chain A: G.143, G.144 No protein-ligand interaction detected (PLIP) MG.39: 1 residues within 4Å: Chain A: G.620 No protein-ligand interaction detected (PLIP) MG.40: 2 residues within 4Å: Chain A: A.1063, G.1064 No protein-ligand interaction detected (PLIP) MG.41: 3 residues within 4Å: Chain A: G.1708, G.1709, A.1710 No protein-ligand interaction detected (PLIP) MG.42: 3 residues within 4Å: Chain A: A.2083, C.2454, G.2455 No protein-ligand interaction detected (PLIP) MG.56: 2 residues within 4Å: Chain 2: C.54, K.55 No protein-ligand interaction detected (PLIP)

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

K.43: 6 residues within 4Å: Chain A: C.951, C.953, U.954, G.955, C.994, A.995 No protein-ligand interaction detected (PLIP) K.44: 7 residues within 4Å: Chain A: U.302, G.328, U.329, A.333, C.336 Chain U: S.99, N.100 No protein-ligand interaction detected (PLIP) K.45: 4 residues within 4Å: Chain A: G.1828, A.1865, A.1866, G.1993 No protein-ligand interaction detected (PLIP) K.46: 5 residues within 4Å: Chain A: A.162, C.163, G.2090, G.2091, U.2253 No protein-ligand interaction detected (PLIP) K.47: 3 residues within 4Å: Chain A: A.160, A.161, A.162 No protein-ligand interaction detected (PLIP) K.48: 5 residues within 4Å: Chain A: U.2525, U.2526, A.2580, G.2581, A.2582 No protein-ligand interaction detected (PLIP) K.49: 4 residues within 4Å: Chain A: G.2259, G.2260, U.2507, A.2508 No protein-ligand interaction detected (PLIP) K.50: 6 residues within 4Å: Chain A: A.1825, U.1826, G.1864 Chain C: R.189, V.190, S.191 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:R.189 K.51: 4 residues within 4Å: Chain A: U.329, C.332, A.333 Chain E: K.188 No protein-ligand interaction detected (PLIP) K.52: 3 residues within 4Å: Chain A: A.1486, A.1660, C.1661 No protein-ligand interaction detected (PLIP) K.53: 4 residues within 4Å: Chain A: G.865, A.867 Chain C: R.4, N.9 No protein-ligand interaction detected (PLIP)

5 x ZN: ZINC ION(Non-covalent)

ZN.54: 4 residues within 4Å: Chain V: C.6, C.9, C.32, C.36 4 PLIP interactions: 4 interactions with chain V Metal complexes: V:C.6, V:C.9, V:C.32, V:C.36 ZN.55: 4 residues within 4Å: Chain 1: C.43, C.46, C.61, C.64 4 PLIP interactions: 4 interactions with chain 1 Metal complexes: 1:C.43, 1:C.46, 1:C.61, 1:C.64 ZN.57: 4 residues within 4Å: Chain 2: C.19, C.22, C.34, C.37 4 PLIP interactions: 4 interactions with chain 2 Metal complexes: 2:C.19, 2:C.22, 2:C.34, 2:C.37 ZN.58: 4 residues within 4Å: Chain 4: C.20, C.23, C.34, C.37 4 PLIP interactions: 4 interactions with chain 4 Metal complexes: 4:C.20, 4:C.23, 4:C.34, 4:C.37 ZN.59: 4 residues within 4Å: Chain 5: C.11, C.14, C.71, C.74 4 PLIP interactions: 4 interactions with chain 5 Metal complexes: 5:C.11, 5:C.14, 5:C.71, 5:C.74

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fordjour, G.N.R. et al., Cryo-EM Study and In Vivo Chemical Mapping of the Methanosarcina acetivorans Ribosome and Its Dimerization via a Repurposed Enzyme and Translation Factor. J.Biol.Chem. (2025)

Release Date

2025-09-24

Peptides

Large ribosomal subunit protein uL2: C
Large ribosomal subunit protein uL3: D
Large ribosomal subunit protein uL4: E
Large ribosomal subunit protein uL5: F
Large ribosomal subunit protein uL6: G
Large ribosomal subunit protein eL8: H
Large ribosomal subunit protein uL16: I
Large ribosomal subunit protein uL13: J
Large ribosomal subunit protein uL14: K
Large ribosomal subunit protein uL15: L
Large ribosomal subunit protein eL15: M
Large ribosomal subunit protein uL18: N
Large ribosomal subunit protein eL18: O
Large ribosomal subunit protein eL19: P
Large ribosomal subunit protein eL20: Q
Large ribosomal subunit protein eL21: R
Large ribosomal subunit protein uL22: S
Large ribosomal subunit protein uL23: T
Large ribosomal subunit protein uL24: U
Large ribosomal subunit protein eL24: V
Large ribosomal subunit protein uL29: W
Large ribosomal subunit protein uL30: X
Large ribosomal subunit protein eL30: Y
Large ribosomal subunit protein eL31: Z
Large ribosomal subunit protein eL32: 0
Large ribosomal subunit protein eL43: 1
Large ribosomal subunit protein eL37: 2
Large ribosomal subunit protein eL39: 3
Large ribosomal subunit protein eL40: 4
Large ribosomal subunit protein eL42: 5

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
BC

D
BD

E
BE

F
BF

G
BG

H
BH

I
BI

J
BJ

K
BK

L
BL

M
BM

N
BN

O
BO

P
BP

Q
BQ

R
BR

S
BS

T
BT

U
BU

V
BV

W
BW

X
BX

Y
BY

Z
BZ

0
Ba

1
Bb

2
Bc

3
Bd

4
Be

5
Bf

Large ribosomal subunit protein uL2

Large ribosomal subunit protein uL3

Large ribosomal subunit protein uL4

Large ribosomal subunit protein uL5

Large ribosomal subunit protein uL6

Large ribosomal subunit protein eL8

Large ribosomal subunit protein uL16

Large ribosomal subunit protein uL13

Large ribosomal subunit protein uL14

Large ribosomal subunit protein uL15

Large ribosomal subunit protein eL15

Large ribosomal subunit protein uL18

Large ribosomal subunit protein eL18

Large ribosomal subunit protein eL19

Large ribosomal subunit protein eL20

Large ribosomal subunit protein eL21

Large ribosomal subunit protein uL22

Large ribosomal subunit protein uL23

Large ribosomal subunit protein uL24

Large ribosomal subunit protein eL24

Large ribosomal subunit protein uL29

Large ribosomal subunit protein uL30

Large ribosomal subunit protein eL30

Large ribosomal subunit protein eL31

Large ribosomal subunit protein eL32

Large ribosomal subunit protein eL43

Large ribosomal subunit protein eL37

Large ribosomal subunit protein eL39

Large ribosomal subunit protein eL40

Large ribosomal subunit protein eL42

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