› 5o60

Electron Microscopy
3.2Å resolution

Structure of the 50S large ribosomal subunit from Mycobacterium smegmatis

Released:
DOI: 10.2210/pdb5o60/pdb
PDB entry 5o60 coloured by chain, front view.
PDB entry 5o60 coloured by chain, side view.
PDB entry 5o60 coloured by chain, top view.
Source organism: Mycolicibacterium smegmatis MC2 155
Primary publication:
The Complete Structure of the Mycobacterium smegmatis 70S Ribosome.
Hentschel J, Burnside C, Mignot I, Leibundgut M, Boehringer D, Ban N
Cell Rep 20 149-160 (2017)
PMID: 28683309
Related structures: EMD-3750

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 35-mer (preferred)
PDBe Complex ID:
PDB-CPX-106278 (preferred)
Entry contents:
32 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (35 distinct):
50S ribosomal protein bL37 Chain: 3
Molecule details ›
Chain: 3
Length: 24 amino acids
Theoretical weight: 2.84 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QTP4 (Residues: 1-24; Coverage: 100%)
Gene name: MSMEG_1916
Large ribosomal subunit protein uL2 Chain: C
Molecule details ›
Chain: C
Length: 278 amino acids
Theoretical weight: 30.43 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSD4 (Residues: 1-278; Coverage: 100%)
Gene names: MSMEG_1439, MSMEI_1403, rplB
Sequence domains:
Structure domains:
Large ribosomal subunit protein uL3 Chain: D
Molecule details ›
Chain: D
Length: 217 amino acids
Theoretical weight: 23.01 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSD1 (Residues: 1-217; Coverage: 100%)
Gene names: MSMEG_1436, MSMEI_1400, rplC
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL4 Chain: E
Molecule details ›
Chain: E
Length: 215 amino acids
Theoretical weight: 22.92 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSD2 (Residues: 1-215; Coverage: 100%)
Gene names: MSMEG_1437, MSMEI_1401, rplD
Sequence domains: Ribosomal protein L4/L1 family
Large ribosomal subunit protein uL5 Chain: F
Molecule details ›
Chain: F
Length: 187 amino acids
Theoretical weight: 21.15 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSG1 (Residues: 1-187; Coverage: 100%)
Gene names: MSMEG_1467, MSMEI_1431, rplE
Sequence domains:
Large ribosomal subunit protein uL6 Chain: G
Molecule details ›
Chain: G
Length: 179 amino acids
Theoretical weight: 19.48 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSG4 (Residues: 1-179; Coverage: 100%)
Gene names: MSMEG_1470, MSMEI_1434, rplF
Sequence domains: Ribosomal protein L6
Large ribosomal subunit protein bL9 Chain: H
Molecule details ›
Chain: H
Length: 151 amino acids
Theoretical weight: 15.95 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0R7F6 (Residues: 1-151; Coverage: 100%)
Gene names: MSMEG_6894, MSMEI_6710, rplI
Sequence domains:
Large ribosomal subunit protein uL10 Chain: I
Molecule details ›
Chain: I
Length: 175 amino acids
Theoretical weight: 18.04 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QS62 (Residues: 1-175; Coverage: 100%)
Gene names: MSMEG_1364, MSMEI_1325, rplJ
Sequence domains: Ribosomal protein L10
Structure domains: Alpha-Beta Plaits
Large ribosomal subunit protein uL11 Chain: J
Molecule details ›
Chain: J
Length: 142 amino acids
Theoretical weight: 15.02 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QS45 (Residues: 1-142; Coverage: 100%)
Gene names: MSMEG_1346, MSMEI_1308, rplK
Sequence domains:
Structure domains:
Large ribosomal subunit protein uL13 Chain: K
Molecule details ›
Chain: K
Length: 147 amino acids
Theoretical weight: 16.15 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSP8 (Residues: 1-147; Coverage: 100%)
Gene names: MSMEG_1556, MSMEI_1519, rplM
Sequence domains: Ribosomal protein L13
Large ribosomal subunit protein uL14 Chain: L
Molecule details ›
Chain: L
Length: 122 amino acids
Theoretical weight: 13.4 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSF9 (Residues: 1-122; Coverage: 100%)
Gene names: MSMEG_1465, MSMEI_1429, rplN
Sequence domains: Ribosomal protein L14p/L23e
Structure domains: Ribosomal protein L14
Large ribosomal subunit protein uL15 Chain: M
Molecule details ›
Chain: M
Length: 147 amino acids
Theoretical weight: 15.6 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSG8 (Residues: 1-147; Coverage: 100%)
Gene names: MSMEG_1474, rplO
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
Large ribosomal subunit protein uL16 Chain: N
Molecule details ›
Chain: N
Length: 138 amino acids
Theoretical weight: 15.77 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSD8 (Residues: 1-138; Coverage: 100%)
Gene names: MSMEG_1443, MSMEI_1407, rplP
Sequence domains: Ribosomal protein L16p/L10e
Structure domains: Ribosomal protein L10e/L16
Large ribosomal subunit protein bL17 Chain: O
Molecule details ›
Chain: O
Length: 199 amino acids
Theoretical weight: 21.89 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSL9 (Residues: 1-199; Coverage: 100%)
Gene names: MSMEG_1525, MSMEI_1489, rplQ
Sequence domains: Ribosomal protein L17
Large ribosomal subunit protein uL18 Chain: P
Molecule details ›
Chain: P
Length: 127 amino acids
Theoretical weight: 13.71 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSG5 (Residues: 1-127; Coverage: 100%)
Gene names: MSMEG_1471, rplR
Sequence domains: Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
Structure domains: Nucleotidyltransferase; domain 5
Large ribosomal subunit protein bL19 Chain: Q
Molecule details ›
Chain: Q
Length: 113 amino acids
Theoretical weight: 12.89 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QV42 (Residues: 1-113; Coverage: 100%)
Gene names: MSMEG_2440, MSMEI_2379, rplS
Sequence domains: Ribosomal protein L19
Large ribosomal subunit protein bL20 Chain: R
Molecule details ›
Chain: R
Length: 129 amino acids
Theoretical weight: 14.49 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QYU6 (Residues: 1-129; Coverage: 100%)
Gene names: MSMEG_3791, MSMEI_3703, rplT
Sequence domains: Ribosomal protein L20
Large ribosomal subunit protein bL21 Chain: S
Molecule details ›
Chain: S
Length: 103 amino acids
Theoretical weight: 11.06 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0R151 (Residues: 1-103; Coverage: 100%)
Gene names: MSMEG_4625, MSMEI_4508, rplU
Sequence domains: Ribosomal prokaryotic L21 protein
Large ribosomal subunit protein uL22 Chain: T
Molecule details ›
Chain: T
Length: 153 amino acids
Theoretical weight: 16.35 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSD6 (Residues: 1-153; Coverage: 100%)
Gene names: MSMEG_1441, MSMEI_1405, rplV
Sequence domains: Ribosomal protein L22p/L17e
Structure domains: Ribosomal protein L22/L17
Large ribosomal subunit protein uL23 Chain: U
Molecule details ›
Chain: U
Length: 100 amino acids
Theoretical weight: 11.05 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSD3 (Residues: 1-100; Coverage: 100%)
Gene names: MSMEG_1438, MSMEI_1402, rplW
Sequence domains: Ribosomal protein L23
Structure domains: Alpha-Beta Plaits
Large ribosomal subunit protein uL24 Chain: V
Molecule details ›
Chain: V
Length: 105 amino acids
Theoretical weight: 11.23 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSG0 (Residues: 1-105; Coverage: 100%)
Gene names: MSMEG_1466, MSMEI_1430, rplX
Sequence domains:
Large ribosomal subunit protein bL25 Chain: W
Molecule details ›
Chain: W
Length: 215 amino acids
Theoretical weight: 22.57 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0R3D2 (Residues: 1-215; Coverage: 100%)
Gene names: MSMEG_5431, ctc, rplY
Sequence domains:
Large ribosomal subunit protein bL27 Chain: X
Molecule details ›
Chain: X
Length: 88 amino acids
Theoretical weight: 9.25 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0R150 (Residues: 1-88; Coverage: 100%)
Gene names: MSMEG_4624, MSMEI_4507, rpmA
Sequence domains: Ribosomal L27 protein
Large ribosomal subunit protein bL28 Chain: Y
Molecule details ›
Chain: Y
Length: 64 amino acids
Theoretical weight: 6.89 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QV03 (Residues: 1-64; Coverage: 100%)
Gene names: MSMEG_2400, rpmB
Sequence domains: Ribosomal L28 family
Large ribosomal subunit protein uL29 Chain: Z
Molecule details ›
Chain: Z
Length: 77 amino acids
Theoretical weight: 8.79 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSD9 (Residues: 1-77; Coverage: 100%)
Gene names: MSMEG_1444, MSMEI_1408, rpmC
Sequence domains: Ribosomal L29 protein
Large ribosomal subunit protein uL30 Chain: a
Molecule details ›
Chain: a
Length: 61 amino acids
Theoretical weight: 7.02 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSG7 (Residues: 1-61; Coverage: 100%)
Gene names: MSMEG_1473, MSMEI_1437, rpmD
Sequence domains: Ribosomal protein L30p/L7e
Structure domains: Ribosomal protein L30, ferredoxin-like fold domain
Large ribosomal subunit protein bL32 Chain: b
Molecule details ›
Chain: b
Length: 57 amino acids
Theoretical weight: 6.47 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0R3I9 (Residues: 1-57; Coverage: 100%)
Gene names: MSMEG_5489, MSMEI_5337, rpmF
Sequence domains: Ribosomal L32p protein family
Large ribosomal subunit protein bL33A Chain: c
Molecule details ›
Chain: c
Length: 55 amino acids
Theoretical weight: 6.47 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QS39 (Residues: 1-55; Coverage: 100%)
Gene names: MSMEG_1339, MSMEI_1301, rpmG1, rpmG2
Sequence domains: Ribosomal protein L33
Structure domains: Ribosomal protein L33
Large ribosomal subunit protein bL34 Chain: d
Molecule details ›
Chain: d
Length: 47 amino acids
Theoretical weight: 5.52 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0R7K0 (Residues: 1-47; Coverage: 100%)
Gene names: MSMEG_6946, MSMEI_6752, rpmH
Sequence domains: Ribosomal protein L34
Structure domains: Helix Hairpins
Large ribosomal subunit protein bL35 Chain: e
Molecule details ›
Chain: e
Length: 64 amino acids
Theoretical weight: 7.3 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QYU7 (Residues: 1-64; Coverage: 100%)
Gene names: MSMEG_3792, MSMEI_3704, rpmI
Sequence domains: Ribosomal protein L35
Large ribosomal subunit protein bL36 Chain: f
Molecule details ›
Chain: f
Length: 37 amino acids
Theoretical weight: 4.34 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSL4 (Residues: 1-37; Coverage: 100%)
Gene names: MSMEG_1520, MSMEI_1484, rpmJ
Sequence domains: Ribosomal protein L36
Large ribosomal subunit protein bL31 Chain: g
Molecule details ›
Chain: g
Length: 75 amino acids
Theoretical weight: 8.31 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0R215 (Residues: 1-75; Coverage: 100%)
Gene names: MSMEG_4951, MSMEI_4823, rpmE
Sequence domains: Ribosomal protein L31
23S ribosomal RNA Chain: A
Molecule details ›
Chain: A
Length: 3120 nucleotides
Theoretical weight: 1012.14 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
5S ribosomal RNA Chain: B
Molecule details ›
Chain: B
Length: 118 nucleotides
Theoretical weight: 38.06 KDa
Sequence domains: 5S ribosomal RNA
tRNA CCA-end acetylated (Phe) Chain: 2
Molecule details ›
Chain: 2
Length: 3 nucleotides
Theoretical weight: 895 Da

Ligands and Environments

3 bound ligands:
Ligand MG 408 x MG
Ligand ZN 4 x ZN
Ligand PHE 1 x PHE
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.203Å
Relevant EMDB volumes: EMD-3750

Quick links

Citations

4 review citations

Advanced Methods for Studying Structure and Interactions of Macrolide Antibiotics.
Jednačak et al. (2020)
3 more

2 mentions without citation

Recent Insights into the Structure and Function of Mycobacterial Membrane Proteins Facilitated by Cryo-EM.
Bendre et al. (2021)
1 more