› 5o61

Electron Microscopy
3.31Å resolution

The complete structure of the Mycobacterium smegmatis 70S ribosome

Released:
DOI: 10.2210/pdb5o61/pdb
PDB entry 5o61 coloured by chain, front view.
PDB entry 5o61 coloured by chain, side view.
PDB entry 5o61 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-3751

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 57-mer (preferred)
PDBe Complex ID:
PDB-CPX-106260 (preferred)
Entry contents:
52 distinct polypeptide molecules
5 distinct RNA molecules
Macromolecules (57 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:
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
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:
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
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
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
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
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
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
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
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
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
Ribosomal protein mS38 C-terminal domain-containing protein Chain: BB
Molecule details ›
Chain: BB
Length: 33 amino acids
Theoretical weight: 4.16 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QR10 (Residues: 1-33; Coverage: 100%)
Gene name: MSMEG_0945
Sequence domains: Mitochondrial mRNA-processing protein COX24, C-terminal
Small ribosomal subunit protein uS3 Chain: BC
Molecule details ›
Chain: BC
Length: 275 amino acids
Theoretical weight: 30.19 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSD7 (Residues: 1-275; Coverage: 100%)
Gene names: MSMEG_1442, MSMEI_1406, rpsC
Sequence domains:
Small ribosomal subunit protein uS4 Chain: BD
Molecule details ›
Chain: BD
Length: 201 amino acids
Theoretical weight: 23.42 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSL7 (Residues: 1-201; Coverage: 100%)
Gene names: MSMEG_1523, MSMEI_1487, rpsD
Sequence domains:
Small ribosomal subunit protein uS5 Chain: BE
Molecule details ›
Chain: BE
Length: 214 amino acids
Theoretical weight: 21.95 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSG6 (Residues: 1-214; Coverage: 100%)
Gene names: MSMEG_1472, MSMEI_1436, rpsE
Sequence domains:
30S ribosomal protein S6 Chain: BF
Molecule details ›
Chain: BF
Length: 96 amino acids
Theoretical weight: 10.99 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
Small ribosomal subunit protein uS7 Chain: BG
Molecule details ›
Chain: BG
Length: 156 amino acids
Theoretical weight: 17.66 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QS97 (Residues: 1-156; Coverage: 100%)
Gene names: MSMEG_1399, MSMEI_1361, rpsG
Sequence domains: Ribosomal protein S7p/S5e
Small ribosomal subunit protein uS8 Chain: BH
Molecule details ›
Chain: BH
Length: 132 amino acids
Theoretical weight: 14.49 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSG3 (Residues: 1-132; Coverage: 100%)
Gene names: MSMEG_1469, MSMEI_1433, rpsH
Sequence domains: Ribosomal protein S8
Small ribosomal subunit protein uS9 Chain: BI
Molecule details ›
Chain: BI
Length: 150 amino acids
Theoretical weight: 16.79 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSP9 (Residues: 1-150; Coverage: 100%)
Gene names: MSMEG_1557, MSMEI_1520, rpsI
Sequence domains: Ribosomal protein S9/S16
Small ribosomal subunit protein uS10 Chain: BJ
Molecule details ›
Chain: BJ
Length: 101 amino acids
Theoretical weight: 11.45 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSD0 (Residues: 1-101; Coverage: 100%)
Gene names: MSMEG_1435, MSMEI_1399, rpsJ
Sequence domains: Ribosomal protein S10p/S20e
Small ribosomal subunit protein uS11 Chain: BK
Molecule details ›
Chain: BK
Length: 138 amino acids
Theoretical weight: 14.67 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSL6 (Residues: 1-138; Coverage: 100%)
Gene names: MSMEG_1522, MSMEI_1486, rpsK
Sequence domains: Ribosomal protein S11
Small ribosomal subunit protein uS12 Chain: BL
Molecule details ›
Chain: BL
Length: 124 amino acids
Theoretical weight: 13.9 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QS96 (Residues: 1-124; Coverage: 100%)
Gene names: MSMEG_1398, MSMEI_1360, rpsL
Sequence domains: Ribosomal protein S12/S23
Small ribosomal subunit protein uS13 Chain: BM
Molecule details ›
Chain: BM
Length: 124 amino acids
Theoretical weight: 14.25 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSL5 (Residues: 1-124; Coverage: 100%)
Gene names: MSMEG_1521, MSMEI_1485, rpsM
Sequence domains: Ribosomal protein S13/S18
Small ribosomal subunit protein uS14B Chain: BN
Molecule details ›
Chain: BN
Length: 61 amino acids
Theoretical weight: 6.98 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSG2 (Residues: 1-61; Coverage: 100%)
Gene names: MSMEG_1468, MSMEI_1432, rpsN, rpsZ
Sequence domains: Ribosomal protein S14p/S29e
Small ribosomal subunit protein uS15 Chain: BO
Molecule details ›
Chain: BO
Length: 89 amino acids
Theoretical weight: 10.37 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QVQ3 (Residues: 1-89; Coverage: 100%)
Gene names: MSMEG_2654, MSMEI_2591, rpsO
Sequence domains: Ribosomal protein S15
Small ribosomal subunit protein bS16 Chain: BP
Molecule details ›
Chain: BP
Length: 156 amino acids
Theoretical weight: 16.8 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QV37 (Residues: 1-156; Coverage: 100%)
Gene names: MSMEG_2435, MSMEI_2374, rpsP
Sequence domains: Ribosomal protein S16
Small ribosomal subunit protein uS17 Chain: BQ
Molecule details ›
Chain: BQ
Length: 98 amino acids
Theoretical weight: 11.13 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSE0 (Residues: 1-98; Coverage: 100%)
Gene names: MSMEG_1445, MSMEI_1409, rpsQ
Sequence domains: Ribosomal protein S17
Small ribosomal subunit protein bS18B Chain: BR
Molecule details ›
Chain: BR
Length: 84 amino acids
Theoretical weight: 9.52 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0R7F7 (Residues: 1-84; Coverage: 100%)
Gene names: MSMEG_6895, MSMEI_6711, rpsR1, rpsR2
Sequence domains: Ribosomal protein S18
Small ribosomal subunit protein uS19 Chain: BS
Molecule details ›
Chain: BS
Length: 93 amino acids
Theoretical weight: 10.8 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSD5 (Residues: 1-93; Coverage: 100%)
Gene names: MSMEG_1440, MSMEI_1404, rpsS
Sequence domains: Ribosomal protein S19
Small ribosomal subunit protein bS20 Chain: BT
Molecule details ›
Chain: BT
Length: 86 amino acids
Theoretical weight: 9.56 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0R102 (Residues: 1-86; Coverage: 100%)
Gene names: MSMEG_4571, MSMEI_4459, rpsT
Sequence domains: Ribosomal protein S20
Small ribosomal subunit protein uS2 Chain: BV
Molecule details ›
Chain: BV
Length: 277 amino acids
Theoretical weight: 30.15 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QVB8 (Residues: 1-277; Coverage: 100%)
Gene names: MSMEG_2519, MSMEI_2460, rpsB
Sequence domains: Ribosomal protein S2
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
16S ribosomal RNA Chain: BA
Molecule details ›
Chain: BA
Length: 1528 nucleotides
Theoretical weight: 495.37 KDa
Sequence domains: Bacterial small subunit ribosomal RNA
P/P-site Phe-tRNA(Phe) Chain: BW
Molecule details ›
Chain: BW
Length: 76 nucleotides
Theoretical weight: 24.49 KDa
Sequence domains: tRNA
Messenger RNA Chain: BX
Molecule details ›
Chain: BX
Length: 6 nucleotides
Theoretical weight: 1.79 KDa

Ligands and Environments

3 bound ligands:
Ligand MG 625 x MG
Ligand ZN 6 x ZN
Ligand PHE 1 x PHE
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.31Å
Relevant EMDB volumes: EMD-3751

Quick links

Citations

2 review citations

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

13 mentions without citation

Translational regulation in mycobacteria and its implications for pathogenicity.
Sawyer et al. (2018)
12 more