› 6dzp

Electron Microscopy
3.42Å resolution

Cryo-EM Structure of Mycobacterium smegmatis C(minus) 50S ribosomal subunit

Released:
DOI: 10.2210/pdb6dzp/pdb
PDB entry 6dzp coloured by chain, front view.
PDB entry 6dzp coloured by chain, side view.
PDB entry 6dzp coloured by chain, top view.
Source organism: Mycolicibacterium smegmatis MC2 155
Primary publication:
Zinc depletion induces ribosome hibernation in mycobacteria.
Li Y, Sharma MR, Koripella RK, Yang Y, Kaushal PS, Lin Q, Wade JT, Gray TA, Derbyshire KM, Agrawal RK, Ojha AK
Proc Natl Acad Sci U S A 115 8191-8196 (2018)
PMID: 30038002
Related structures: EMD-8937

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 34-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-106282 (preferred)
Entry contents:
32 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (34 distinct):
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: 214 amino acids
Theoretical weight: 22.79 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSD2 (Residues: 2-215; 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: 186 amino acids
Theoretical weight: 21.02 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSG1 (Residues: 2-187; 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: 146 amino acids
Theoretical weight: 16.02 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSP8 (Residues: 2-147; Coverage: 99%)
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: 126 amino acids
Theoretical weight: 13.58 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: I7FGD9 (Residues: 2-127; Coverage: 99%)
Gene names: MSMEI_1435, 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: 102 amino acids
Theoretical weight: 10.92 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0R151 (Residues: 2-103; Coverage: 99%)
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: 152 amino acids
Theoretical weight: 16.22 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSD6 (Residues: 2-153; Coverage: 99%)
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: 99 amino acids
Theoretical weight: 10.92 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSD3 (Residues: 2-100; Coverage: 99%)
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 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 bL33B Chain: c
Molecule details ›
Chain: c
Length: 54 amino acids
Theoretical weight: 6.62 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0R551 (Residues: 1-54; Coverage: 100%)
Gene names: MSMEG_6067, MSMEI_5907, 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
50S ribosomal protein L31 Chain: g
Molecule details ›
Chain: g
Length: 82 amino acids
Theoretical weight: 9.14 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0R554 (Residues: 1-82; Coverage: 100%)
Gene names: MSMEG_6070, rpmE
Sequence domains: Ribosomal protein L31
Large ribosomal subunit protein bL28 Chain: y
Molecule details ›
Chain: y
Length: 78 amino acids
Theoretical weight: 8.93 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0R552 (Residues: 1-77; Coverage: 99%)
Gene names: MSMEG_6068, rpmB
Sequence domains: Ribosomal L28 family
Uncharacterized protein Chain: 3
Molecule details ›
Chain: 3
Length: 23 amino acids
Theoretical weight: 2.71 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QTP4 (Residues: 2-24; Coverage: 96%)
Gene name: MSMEG_1916
23S ribosomal RNA Chain: A
Molecule details ›
Chain: A
Length: 3119 nucleotides
Theoretical weight: 1011.83 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

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.42Å
Relevant EMDB volumes: EMD-8937

Quick links

Citations

10 review citations

Ribosome Hibernation.
Prossliner et al. (2018)
9 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