› 6dzi

Electron Microscopy
3.46Å resolution

Cryo-EM Structure of Mycobacterium smegmatis 70S C(minus) ribosome 70S-MPY complex

Released:
DOI: 10.2210/pdb6dzi/pdb
PDB entry 6dzi coloured by chain, front view.
PDB entry 6dzi coloured by chain, side view.
PDB entry 6dzi coloured by chain, top view.
Source organisms:
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-8932

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 56-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-106281 (preferred)
Entry contents:
53 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (56 distinct):
CONSERVED PROTEIN DOMAIN Chain: j
Molecule details ›
Chain: j
Length: 32 amino acids
Theoretical weight: 4.03 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
Small ribosomal subunit protein uS3 Chain: k
Molecule details ›
Chain: k
Length: 208 amino acids
Theoretical weight: 23.62 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSD7 (Residues: 2-209; Coverage: 76%)
Gene names: MSMEG_1442, MSMEI_1406, rpsC
Sequence domains:
Small ribosomal subunit protein uS4 Chain: l
Molecule details ›
Chain: l
Length: 200 amino acids
Theoretical weight: 23.28 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSL7 (Residues: 2-201; Coverage: 100%)
Gene names: MSMEG_1523, MSMEI_1487, rpsD
Sequence domains:
Small ribosomal subunit protein uS5 Chain: m
Molecule details ›
Chain: m
Length: 180 amino acids
Theoretical weight: 18.48 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSG6 (Residues: 35-214; Coverage: 84%)
Gene names: MSMEG_1472, MSMEI_1436, rpsE
Sequence domains:
30S ribosomal protein S6 Chain: n
Molecule details ›
Chain: n
Length: 96 amino acids
Theoretical weight: 10.99 KDa
Source organism: Mycolicibacterium smegmatis
Small ribosomal subunit protein uS7 Chain: p
Molecule details ›
Chain: p
Length: 155 amino acids
Theoretical weight: 17.53 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QS97 (Residues: 2-156; Coverage: 99%)
Gene names: MSMEG_1399, MSMEI_1361, rpsG
Sequence domains: Ribosomal protein S7p/S5e
Small ribosomal subunit protein uS8 Chain: q
Molecule details ›
Chain: q
Length: 131 amino acids
Theoretical weight: 14.36 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSG3 (Residues: 2-132; Coverage: 99%)
Gene names: MSMEG_1469, MSMEI_1433, rpsH
Sequence domains: Ribosomal protein S8
Small ribosomal subunit protein uS9 Chain: 4
Molecule details ›
Chain: 4
Length: 126 amino acids
Theoretical weight: 14.09 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSP9 (Residues: 25-150; Coverage: 84%)
Gene names: MSMEG_1557, MSMEI_1520, rpsI
Sequence domains: Ribosomal protein S9/S16
Small ribosomal subunit protein uS10 Chain: s
Molecule details ›
Chain: s
Length: 99 amino acids
Theoretical weight: 11.25 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSD0 (Residues: 3-101; Coverage: 98%)
Gene names: MSMEG_1435, MSMEI_1399, rpsJ
Sequence domains: Ribosomal protein S10p/S20e
Small ribosomal subunit protein uS11 Chain: t
Molecule details ›
Chain: t
Length: 115 amino acids
Theoretical weight: 12.15 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSL6 (Residues: 23-137; Coverage: 83%)
Gene names: MSMEG_1522, MSMEI_1486, rpsK
Sequence domains: Ribosomal protein S11
Small ribosomal subunit protein uS12 Chain: u
Molecule details ›
Chain: u
Length: 122 amino acids
Theoretical weight: 13.68 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QS96 (Residues: 2-123; Coverage: 98%)
Gene names: MSMEG_1398, MSMEI_1360, rpsL
Sequence domains: Ribosomal protein S12/S23
Small ribosomal subunit protein uS13 Chain: v
Molecule details ›
Chain: v
Length: 116 amino acids
Theoretical weight: 13.37 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSL5 (Residues: 2-117; Coverage: 94%)
Gene names: MSMEG_1521, MSMEI_1485, rpsM
Sequence domains: Ribosomal protein S13/S18
Small ribosomal subunit protein uS15 Chain: x
Molecule details ›
Chain: x
Length: 88 amino acids
Theoretical weight: 10.24 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QVQ3 (Residues: 2-89; Coverage: 99%)
Gene names: MSMEG_2654, MSMEI_2591, rpsO
Sequence domains: Ribosomal protein S15
Small ribosomal subunit protein bS16 Chain: z
Molecule details ›
Chain: z
Length: 113 amino acids
Theoretical weight: 12.64 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QV37 (Residues: 2-114; Coverage: 72%)
Gene names: MSMEG_2435, MSMEI_2374, rpsP
Sequence domains: Ribosomal protein S16
Small ribosomal subunit protein uS17 Chain: 5
Molecule details ›
Chain: 5
Length: 94 amino acids
Theoretical weight: 10.68 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSE0 (Residues: 4-97; Coverage: 96%)
Gene names: MSMEG_1445, MSMEI_1409, rpsQ
Sequence domains: Ribosomal protein S17
Small ribosomal subunit protein uS19 Chain: 6
Molecule details ›
Chain: 6
Length: 82 amino acids
Theoretical weight: 9.38 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSD5 (Residues: 2-83; Coverage: 88%)
Gene names: MSMEG_1440, MSMEI_1404, rpsS
Sequence domains: Ribosomal protein S19
Small ribosomal subunit protein bS20 Chain: 7
Molecule details ›
Chain: 7
Length: 85 amino acids
Theoretical weight: 9.42 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0R102 (Residues: 2-86; Coverage: 99%)
Gene names: MSMEG_4571, MSMEI_4459, rpsT
Sequence domains: Ribosomal protein S20
Small ribosomal subunit protein uS2 Chain: 8
Molecule details ›
Chain: 8
Length: 228 amino acids
Theoretical weight: 25.58 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QVB8 (Residues: 1-228; Coverage: 82%)
Gene names: MSMEG_2519, MSMEI_2460, rpsB
Sequence domains: Ribosomal protein S2
Small ribosomal subunit protein bS18A Chain: r
Molecule details ›
Chain: r
Length: 84 amino acids
Theoretical weight: 9.45 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0R549 (Residues: 1-84; Coverage: 99%)
Gene names: MSMEG_6065, MSMEI_5905, rpsR1, rpsR2
Sequence domains: Ribosomal protein S18
Ribosome hibernation promoting factor Chain: Y
Molecule details ›
Chain: Y
Length: 103 amino acids
Theoretical weight: 12.24 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QTK6 (Residues: 27-129; Coverage: 45%)
Gene names: MSMEG_1878, hpf
Sequence domains: Sigma 54 modulation protein / S30EA ribosomal protein
Small ribosomal subunit protein uS14A Chain: 9
Molecule details ›
Chain: 9
Length: 100 amino acids
Theoretical weight: 11.66 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0R550 (Residues: 2-101; Coverage: 99%)
Gene names: MSMEG_6066, MSMEI_5906, rpsN
Sequence domains: Ribosomal protein S14p/S29e
Large ribosomal subunit protein uL2 Chain: C
Molecule details ›
Chain: C
Length: 275 amino acids
Theoretical weight: 30.01 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSD4 (Residues: 2-276; Coverage: 99%)
Gene names: MSMEG_1439, MSMEI_1403, rplB
Sequence domains:
Large ribosomal subunit protein uL3 Chain: D
Molecule details ›
Chain: D
Length: 214 amino acids
Theoretical weight: 22.62 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSD1 (Residues: 2-215; Coverage: 99%)
Gene names: MSMEG_1436, MSMEI_1400, rplC
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL4 Chain: E
Molecule details ›
Chain: E
Length: 209 amino acids
Theoretical weight: 22.35 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSD2 (Residues: 2-210; Coverage: 97%)
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: 182 amino acids
Theoretical weight: 20.59 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSG1 (Residues: 6-187; Coverage: 97%)
Gene names: MSMEG_1467, MSMEI_1431, rplE
Sequence domains:
Large ribosomal subunit protein uL6 Chain: G
Molecule details ›
Chain: G
Length: 176 amino acids
Theoretical weight: 19.17 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSG4 (Residues: 2-177; Coverage: 98%)
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: 126 amino acids
Theoretical weight: 13.1 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QS62 (Residues: 1-126; Coverage: 72%)
Gene names: MSMEG_1364, MSMEI_1325, rplJ
Sequence domains: Ribosomal protein L10
Large ribosomal subunit protein uL11 Chain: J
Molecule details ›
Chain: J
Length: 133 amino acids
Theoretical weight: 14.11 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QS45 (Residues: 10-142; Coverage: 94%)
Gene names: MSMEG_1346, MSMEI_1308, rplK
Sequence 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
Large ribosomal subunit protein uL15 Chain: M
Molecule details ›
Chain: M
Length: 145 amino acids
Theoretical weight: 15.38 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: I7G436 (Residues: 3-147; Coverage: 99%)
Gene names: MSMEI_1438, rplO
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
Large ribosomal subunit protein uL16 Chain: N
Molecule details ›
Chain: N
Length: 136 amino acids
Theoretical weight: 15.5 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSD8 (Residues: 1-136; Coverage: 99%)
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: 118 amino acids
Theoretical weight: 13.21 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSL9 (Residues: 2-119; Coverage: 59%)
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
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: 124 amino acids
Theoretical weight: 14.04 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QYU6 (Residues: 2-125; Coverage: 96%)
Gene names: MSMEG_3791, MSMEI_3703, rplT
Sequence domains: Ribosomal protein L20
Large ribosomal subunit protein bL21 Chain: S
Molecule details ›
Chain: S
Length: 100 amino acids
Theoretical weight: 10.72 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0R151 (Residues: 3-102; Coverage: 97%)
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: 114 amino acids
Theoretical weight: 12.41 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSD6 (Residues: 6-119; Coverage: 75%)
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: 97 amino acids
Theoretical weight: 10.75 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSD3 (Residues: 2-98; Coverage: 97%)
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: 192 amino acids
Theoretical weight: 20.33 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0R3D2 (Residues: 4-195; Coverage: 89%)
Gene names: MSMEG_5431, ctc, rplY
Sequence domains:
Large ribosomal subunit protein bL27 Chain: X
Molecule details ›
Chain: X
Length: 79 amino acids
Theoretical weight: 8.32 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0R150 (Residues: 8-86; Coverage: 90%)
Gene names: MSMEG_4624, MSMEI_4507, rpmA
Sequence domains: Ribosomal L27 protein
Large ribosomal subunit protein uL29 Chain: Z
Molecule details ›
Chain: Z
Length: 64 amino acids
Theoretical weight: 7.59 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSD9 (Residues: 4-67; Coverage: 83%)
Gene names: MSMEG_1444, MSMEI_1408, rpmC
Sequence domains: Ribosomal L29 protein
Large ribosomal subunit protein uL30 Chain: a
Molecule details ›
Chain: a
Length: 59 amino acids
Theoretical weight: 6.76 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSG7 (Residues: 2-60; Coverage: 97%)
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: 54 amino acids
Theoretical weight: 6.05 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0R3I9 (Residues: 2-55; Coverage: 95%)
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: 53 amino acids
Theoretical weight: 6.48 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0R551 (Residues: 2-54; Coverage: 98%)
Gene names: MSMEG_6067, MSMEI_5907, rpmG2
Sequence domains: Ribosomal protein L33
Large ribosomal subunit protein bL34 Chain: d
Molecule details ›
Chain: d
Length: 46 amino acids
Theoretical weight: 5.39 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0R7K0 (Residues: 2-47; Coverage: 98%)
Gene names: MSMEG_6946, MSMEI_6752, rpmH
Sequence domains: Ribosomal protein L34
Large ribosomal subunit protein bL35 Chain: e
Molecule details ›
Chain: e
Length: 63 amino acids
Theoretical weight: 7.17 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QYU7 (Residues: 2-64; Coverage: 98%)
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
50S ribosomal protein L28 Chain: y
Molecule details ›
Chain: y
Length: 77 amino acids
Theoretical weight: 8.79 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
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
16S ribosomal RNA Chain: h
Molecule details ›
Chain: h
Length: 1511 nucleotides
Theoretical weight: 490.11 KDa
Sequence domains: Bacterial small subunit ribosomal RNA
23 S rRNA (3119-MER) Chain: A
Molecule details ›
Chain: A
Length: 3119 nucleotides
Theoretical weight: 1011.83 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
5S RNA (118-MER) 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: 3.46Å
Relevant EMDB volumes: EMD-8932

Quick links

Citations

9 review citations

Ribosome Hibernation.
Prossliner et al. (2018)
8 more

8 mentions without citation

Ribosome hibernation: a new molecular framework for targeting nonreplicating persisters of mycobacteria.
Li et al. (2021)
7 more