› 5myj

Electron Microscopy
5.6Å resolution

Structure of 70S ribosome from Lactococcus lactis

Released:
DOI: 10.2210/pdb5myj/pdb
PDB entry 5myj coloured by chain, front view.
PDB entry 5myj coloured by chain, side view.
PDB entry 5myj coloured by chain, top view.
Source organism: Lactococcus cremoris subsp. cremoris MG1363
Primary publication:
A general mechanism of ribosome dimerization revealed by single-particle cryo-electron microscopy.
Franken LE, Oostergetel GT, Pijning T, Puri P, Arkhipova V, Boekema EJ, Poolman B, Guskov A
Nat Commun 8 722 (2017)
PMID: 28959045
Related structures: EMD-3581

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 51-mer (preferred)
PDBe Complex ID:
PDB-CPX-106934 (preferred)
Entry contents:
48 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (51 distinct):
Small ribosomal subunit protein uS2 Chain: AB
Molecule details ›
Chain: AB
Length: 255 amino acids
Theoretical weight: 28.59 KDa
Source organism: Lactococcus cremoris subsp. cremoris MG1363
UniProt:
  • Canonical: A2RNV0 (Residues: 1-255; Coverage: 100%)
Gene names: llmg_2430, rpsB
Sequence domains: Ribosomal protein S2
Small ribosomal subunit protein uS3 Chain: AC
Molecule details ›
Chain: AC
Length: 217 amino acids
Theoretical weight: 24.06 KDa
Source organism: Lactococcus cremoris subsp. cremoris MG1363
UniProt:
  • Canonical: A2RNP9 (Residues: 1-217; Coverage: 100%)
Gene names: llmg_2377, rpsC
Sequence domains:
Small ribosomal subunit protein uS4 Chain: AD
Molecule details ›
Chain: AD
Length: 203 amino acids
Theoretical weight: 23.23 KDa
Source organism: Lactococcus cremoris subsp. cremoris MG1363
UniProt:
  • Canonical: A2RI10 (Residues: 1-203; Coverage: 100%)
Gene names: llmg_0296, rpsD
Sequence domains:
Small ribosomal subunit protein uS5 Chain: AE
Molecule details ›
Chain: AE
Length: 168 amino acids
Theoretical weight: 17.61 KDa
Source organism: Lactococcus cremoris subsp. cremoris MG1363
UniProt:
  • Canonical: A2RNN6 (Residues: 1-168; Coverage: 100%)
Gene names: llmg_2364, rpsE
Sequence domains:
Small ribosomal subunit protein bS6 Chain: AF
Molecule details ›
Chain: AF
Length: 97 amino acids
Theoretical weight: 11.32 KDa
Source organism: Lactococcus cremoris subsp. cremoris MG1363
UniProt:
  • Canonical: A2RNZ4 (Residues: 1-97; Coverage: 100%)
Gene names: llmg_2475, rpsF
Sequence domains: Ribosomal protein S6
Small ribosomal subunit protein uS7 Chain: AG
Molecule details ›
Chain: AG
Length: 155 amino acids
Theoretical weight: 17.71 KDa
Source organism: Lactococcus cremoris subsp. cremoris MG1363
UniProt:
  • Canonical: A2RP73 (Residues: 1-155; Coverage: 100%)
Gene names: llmg_2557, rpsG
Sequence domains: Ribosomal protein S7p/S5e
Small ribosomal subunit protein uS8 Chain: AH
Molecule details ›
Chain: AH
Length: 132 amino acids
Theoretical weight: 14.69 KDa
Source organism: Lactococcus cremoris subsp. cremoris MG1363
UniProt:
  • Canonical: A2RNN9 (Residues: 1-132; Coverage: 100%)
Gene names: llmg_2367, rpsH
Sequence domains: Ribosomal protein S8
Small ribosomal subunit protein uS9 Chain: AI
Molecule details ›
Chain: AI
Length: 130 amino acids
Theoretical weight: 14.12 KDa
Source organism: Lactococcus cremoris subsp. cremoris MG1363
UniProt:
  • Canonical: A2RP61 (Residues: 1-130; Coverage: 100%)
Gene names: llmg_2545, rpsI
Sequence domains: Ribosomal protein S9/S16
Small ribosomal subunit protein uS10 Chain: AJ
Molecule details ›
Chain: AJ
Length: 102 amino acids
Theoretical weight: 11.76 KDa
Source organism: Lactococcus cremoris subsp. cremoris MG1363
UniProt:
  • Canonical: A2RNQ6 (Residues: 1-102; Coverage: 100%)
Gene names: llmg_2384, rpsJ
Sequence domains: Ribosomal protein S10p/S20e
Small ribosomal subunit protein uS11 Chain: AK
Molecule details ›
Chain: AK
Length: 127 amino acids
Theoretical weight: 13.31 KDa
Source organism: Lactococcus cremoris subsp. cremoris MG1363
UniProt:
  • Canonical: A2RNM8 (Residues: 1-127; Coverage: 100%)
Gene names: llmg_2355, rpsK
Sequence domains: Ribosomal protein S11
Small ribosomal subunit protein uS12 Chain: AL
Molecule details ›
Chain: AL
Length: 137 amino acids
Theoretical weight: 15.16 KDa
Source organism: Lactococcus cremoris subsp. cremoris MG1363
UniProt:
  • Canonical: A2RP74 (Residues: 1-137; Coverage: 100%)
Gene names: llmg_2558, rpsL
Sequence domains: Ribosomal protein S12/S23
Small ribosomal subunit protein uS13 Chain: AM
Molecule details ›
Chain: AM
Length: 121 amino acids
Theoretical weight: 13.52 KDa
Source organism: Lactococcus cremoris subsp. cremoris MG1363
UniProt:
  • Canonical: A2RNM9 (Residues: 1-121; Coverage: 100%)
Gene names: llmg_2356, rpsM
Sequence domains: Ribosomal protein S13/S18
Small ribosomal subunit protein uS14 Chain: AN
Molecule details ›
Chain: AN
Length: 61 amino acids
Theoretical weight: 7.15 KDa
Source organism: Lactococcus cremoris subsp. cremoris MG1363
UniProt:
  • Canonical: A2RNP2 (Residues: 1-61; Coverage: 100%)
Gene names: llmg_2370, rpsN, rpsZ
Sequence domains: Ribosomal protein S14p/S29e
Small ribosomal subunit protein uS15 Chain: AO
Molecule details ›
Chain: AO
Length: 89 amino acids
Theoretical weight: 10.37 KDa
Source organism: Lactococcus cremoris subsp. cremoris MG1363
UniProt:
  • Canonical: A2RMV9 (Residues: 1-89; Coverage: 100%)
Gene names: llmg_2078, rpsO
Sequence domains: Ribosomal protein S15
Small ribosomal subunit protein bS16 Chain: AP
Molecule details ›
Chain: AP
Length: 90 amino acids
Theoretical weight: 10.27 KDa
Source organism: Lactococcus cremoris subsp. cremoris MG1363
UniProt:
  • Canonical: A2RJS1 (Residues: 1-90; Coverage: 100%)
Gene names: llmg_0932, rpsP
Sequence domains: Ribosomal protein S16
Small ribosomal subunit protein uS17 Chain: AQ
Molecule details ›
Chain: AQ
Length: 86 amino acids
Theoretical weight: 10.17 KDa
Source organism: Lactococcus cremoris subsp. cremoris MG1363
UniProt:
  • Canonical: A2RNP6 (Residues: 1-86; Coverage: 100%)
Gene names: llmg_2374, rpsQ
Sequence domains: Ribosomal protein S17
Small ribosomal subunit protein bS18 Chain: AR
Molecule details ›
Chain: AR
Length: 81 amino acids
Theoretical weight: 9.39 KDa
Source organism: Lactococcus cremoris subsp. cremoris MG1363
UniProt:
  • Canonical: A2RNZ2 (Residues: 1-81; Coverage: 100%)
Gene names: llmg_2473, rpsR
Sequence domains: Ribosomal protein S18
Small ribosomal subunit protein uS19 Chain: AS
Molecule details ›
Chain: AS
Length: 92 amino acids
Theoretical weight: 10.6 KDa
Source organism: Lactococcus cremoris subsp. cremoris MG1363
UniProt:
  • Canonical: A2RNQ1 (Residues: 1-92; Coverage: 100%)
Gene names: llmg_2379, rpsS
Sequence domains: Ribosomal protein S19
Small ribosomal subunit protein bS20 Chain: AT
Molecule details ›
Chain: AT
Length: 77 amino acids
Theoretical weight: 8.38 KDa
Source organism: Lactococcus cremoris subsp. cremoris MG1363
UniProt:
  • Canonical: A2RMG0 (Residues: 1-77; Coverage: 100%)
Gene names: llmg_1921, rpsT
Sequence domains: Ribosomal protein S20
Small ribosomal subunit protein bS21 Chain: AU
Molecule details ›
Chain: AU
Length: 58 amino acids
Theoretical weight: 7.04 KDa
Source organism: Lactococcus cremoris subsp. cremoris MG1363
UniProt:
  • Canonical: A2RHW9 (Residues: 1-58; Coverage: 100%)
Gene names: llmg_0251, rpsU
Sequence domains: Ribosomal protein S21
Large ribosomal subunit protein bL28 Chain: B0
Molecule details ›
Chain: B0
Length: 64 amino acids
Theoretical weight: 7.19 KDa
Source organism: Lactococcus cremoris subsp. cremoris MG1363
UniProt:
  • Canonical: A2RHS3 (Residues: 1-64; Coverage: 100%)
Gene names: llmg_0204, rpmB
Sequence domains: Ribosomal L28 family
Large ribosomal subunit protein uL29 Chain: B1
Molecule details ›
Chain: B1
Length: 69 amino acids
Theoretical weight: 7.87 KDa
Source organism: Lactococcus cremoris subsp. cremoris MG1363
UniProt:
  • Canonical: A2RNP7 (Residues: 1-69; Coverage: 100%)
Gene names: llmg_2375, rpmC
Sequence domains: Ribosomal L29 protein
Large ribosomal subunit protein uL30 Chain: B2
Molecule details ›
Chain: B2
Length: 59 amino acids
Theoretical weight: 6.2 KDa
Source organism: Lactococcus cremoris subsp. cremoris MG1363
UniProt:
  • Canonical: A2RNN5 (Residues: 1-59; Coverage: 100%)
Gene names: llmg_2363, rpmD
Sequence domains: Ribosomal protein L30p/L7e
Large ribosomal subunit protein bL31B Chain: B3
Molecule details ›
Chain: B3
Length: 81 amino acids
Theoretical weight: 9.37 KDa
Source organism: Lactococcus cremoris subsp. cremoris MG1363
UniProt:
  • Canonical: A2RJP7 (Residues: 1-81; Coverage: 100%)
Gene names: llmg_0906, rpmE2
Sequence domains: Ribosomal protein L31
Large ribosomal subunit protein bL32 Chain: B4
Molecule details ›
Chain: B4
Length: 57 amino acids
Theoretical weight: 6.68 KDa
Source organism: Lactococcus cremoris subsp. cremoris MG1363
UniProt:
  • Canonical: A2RHH0 (Residues: 1-57; Coverage: 100%)
Gene names: llmg_0099, rpmF
Sequence domains: Ribosomal L32p protein family
Large ribosomal subunit protein bL33C Chain: B5
Molecule details ›
Chain: B5
Length: 49 amino acids
Theoretical weight: 5.57 KDa
Source organism: Lactococcus cremoris subsp. cremoris MG1363
UniProt:
  • Canonical: A2RNR2 (Residues: 1-49; Coverage: 100%)
Gene names: llmg_2390, rpmG3, rpmGC
Sequence domains: Ribosomal protein L33
Large ribosomal subunit protein bL34 Chain: B6
Molecule details ›
Chain: B6
Length: 44 amino acids
Theoretical weight: 5.2 KDa
Source organism: Lactococcus cremoris subsp. cremoris MG1363
UniProt:
  • Canonical: A2RHL6 (Residues: 1-44; Coverage: 100%)
Gene names: llmg_0145, rpmH
Sequence domains: Ribosomal protein L34
Large ribosomal subunit protein bL35 Chain: B7
Molecule details ›
Chain: B7
Length: 66 amino acids
Theoretical weight: 7.84 KDa
Source organism: Lactococcus cremoris subsp. cremoris MG1363
UniProt:
  • Canonical: A2RMR2 (Residues: 1-66; Coverage: 100%)
Gene names: llmg_2030, rpmI
Sequence domains: Ribosomal protein L35
Large ribosomal subunit protein bL36 Chain: B8
Molecule details ›
Chain: B8
Length: 38 amino acids
Theoretical weight: 4.43 KDa
Source organism: Lactococcus cremoris subsp. cremoris MG1363
UniProt:
  • Canonical: A2RNN0 (Residues: 1-38; Coverage: 100%)
Gene names: llmg_2357, rpmJ
Sequence domains: Ribosomal protein L36
Large ribosomal subunit protein uL2 Chain: BD
Molecule details ›
Chain: BD
Length: 276 amino acids
Theoretical weight: 29.64 KDa
Source organism: Lactococcus cremoris subsp. cremoris MG1363
UniProt:
  • Canonical: A2RNQ2 (Residues: 1-276; Coverage: 100%)
Gene names: llmg_2380, rplB
Sequence domains:
Large ribosomal subunit protein uL3 Chain: BE
Molecule details ›
Chain: BE
Length: 207 amino acids
Theoretical weight: 21.96 KDa
Source organism: Lactococcus cremoris subsp. cremoris MG1363
UniProt:
  • Canonical: A2RNQ5 (Residues: 1-207; Coverage: 100%)
Gene names: llmg_2383, rplC
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL4 Chain: BF
Molecule details ›
Chain: BF
Length: 208 amino acids
Theoretical weight: 22.39 KDa
Source organism: Lactococcus cremoris subsp. cremoris MG1363
UniProt:
  • Canonical: A2RNQ4 (Residues: 1-208; Coverage: 100%)
Gene names: llmg_2382, rplD
Sequence domains: Ribosomal protein L4/L1 family
Large ribosomal subunit protein uL5 Chain: BG
Molecule details ›
Chain: BG
Length: 180 amino acids
Theoretical weight: 20.03 KDa
Source organism: Lactococcus cremoris subsp. cremoris MG1363
UniProt:
  • Canonical: A2RNP3 (Residues: 1-180; Coverage: 100%)
Gene names: llmg_2371, rplE
Sequence domains:
Large ribosomal subunit protein uL6 Chain: BH
Molecule details ›
Chain: BH
Length: 178 amino acids
Theoretical weight: 19.31 KDa
Source organism: Lactococcus cremoris subsp. cremoris MG1363
UniProt:
  • Canonical: A2RNN8 (Residues: 1-178; Coverage: 100%)
Gene names: llmg_2366, rplF
Sequence domains: Ribosomal protein L6
Large ribosomal subunit protein uL13 Chain: BM
Molecule details ›
Chain: BM
Length: 148 amino acids
Theoretical weight: 16.19 KDa
Source organism: Lactococcus cremoris subsp. cremoris MG1363
UniProt:
  • Canonical: A2RP62 (Residues: 1-148; Coverage: 100%)
Gene names: llmg_2546, rplM
Sequence domains: Ribosomal protein L13
Large ribosomal subunit protein uL14 Chain: BN
Molecule details ›
Chain: BN
Length: 122 amino acids
Theoretical weight: 12.94 KDa
Source organism: Lactococcus cremoris subsp. cremoris MG1363
UniProt:
  • Canonical: A2RNP5 (Residues: 1-122; Coverage: 100%)
Gene names: llmg_2373, rplN
Sequence domains: Ribosomal protein L14p/L23e
Large ribosomal subunit protein uL15 Chain: BO
Molecule details ›
Chain: BO
Length: 147 amino acids
Theoretical weight: 15.38 KDa
Source organism: Lactococcus cremoris subsp. cremoris MG1363
UniProt:
  • Canonical: A2RNN4 (Residues: 1-147; Coverage: 100%)
Gene names: llmg_2362, rplO
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
Large ribosomal subunit protein uL16 Chain: BP
Molecule details ›
Chain: BP
Length: 137 amino acids
Theoretical weight: 15.38 KDa
Source organism: Lactococcus cremoris subsp. cremoris MG1363
UniProt:
  • Canonical: A2RNP8 (Residues: 1-137; Coverage: 100%)
Gene names: llmg_2376, rplP
Sequence domains: Ribosomal protein L16p/L10e
Large ribosomal subunit protein bL17 Chain: BQ
Molecule details ›
Chain: BQ
Length: 126 amino acids
Theoretical weight: 14.28 KDa
Source organism: Lactococcus cremoris subsp. cremoris MG1363
UniProt:
  • Canonical: A2RNM6 (Residues: 1-126; Coverage: 100%)
Gene names: llmg_2353, rplQ
Sequence domains: Ribosomal protein L17
Large ribosomal subunit protein uL18 Chain: BR
Molecule details ›
Chain: BR
Length: 115 amino acids
Theoretical weight: 12.43 KDa
Source organism: Lactococcus cremoris subsp. cremoris MG1363
UniProt:
  • Canonical: A2RNN7 (Residues: 1-115; Coverage: 100%)
Gene names: llmg_2365, rplR
Sequence domains: Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
Large ribosomal subunit protein bL19 Chain: BS
Molecule details ›
Chain: BS
Length: 114 amino acids
Theoretical weight: 13.13 KDa
Source organism: Lactococcus cremoris subsp. cremoris MG1363
UniProt:
  • Canonical: A2RLS5 (Residues: 1-114; Coverage: 100%)
Gene names: llmg_1671, rplS
Sequence domains: Ribosomal protein L19
Large ribosomal subunit protein bL20 Chain: BT
Molecule details ›
Chain: BT
Length: 119 amino acids
Theoretical weight: 13.73 KDa
Source organism: Lactococcus cremoris subsp. cremoris MG1363
UniProt:
  • Canonical: A2RMR1 (Residues: 1-119; Coverage: 100%)
Gene names: llmg_2029, rplT
Sequence domains: Ribosomal protein L20
Large ribosomal subunit protein bL21 Chain: BU
Molecule details ›
Chain: BU
Length: 104 amino acids
Theoretical weight: 11.44 KDa
Source organism: Lactococcus cremoris subsp. cremoris MG1363
UniProt:
  • Canonical: A2RLA4 (Residues: 1-104; Coverage: 100%)
Gene names: llmg_1493, rplU
Sequence domains: Ribosomal prokaryotic L21 protein
Large ribosomal subunit protein uL22 Chain: BV
Molecule details ›
Chain: BV
Length: 115 amino acids
Theoretical weight: 12.49 KDa
Source organism: Lactococcus cremoris subsp. cremoris MG1363
UniProt:
  • Canonical: A2RNQ0 (Residues: 1-115; Coverage: 100%)
Gene names: llmg_2378, rplV
Sequence domains: Ribosomal protein L22p/L17e
Large ribosomal subunit protein uL23 Chain: BW
Molecule details ›
Chain: BW
Length: 97 amino acids
Theoretical weight: 10.82 KDa
Source organism: Lactococcus cremoris subsp. cremoris MG1363
UniProt:
  • Canonical: A2RNQ3 (Residues: 1-97; Coverage: 100%)
Gene names: llmg_2381, rplW
Sequence domains: Ribosomal protein L23
Large ribosomal subunit protein uL24 Chain: BX
Molecule details ›
Chain: BX
Length: 101 amino acids
Theoretical weight: 10.9 KDa
Source organism: Lactococcus cremoris subsp. cremoris MG1363
UniProt:
  • Canonical: A2RNP4 (Residues: 1-101; Coverage: 100%)
Gene names: llmg_2372, rplX
Sequence domains:
Large ribosomal subunit protein bL27 Chain: BZ
Molecule details ›
Chain: BZ
Length: 94 amino acids
Theoretical weight: 10.05 KDa
Source organism: Lactococcus cremoris subsp. cremoris MG1363
UniProt:
  • Canonical: A2RLA2 (Residues: 1-94; Coverage: 100%)
Gene names: llmg_1491, rpmA
Sequence domains: Ribosomal L27 protein
Ribosome hibernation promotion factor Chain: A
Molecule details ›
Chain: A
Length: 185 amino acids
Theoretical weight: 21.35 KDa
Source organism: Lactococcus cremoris subsp. cremoris MG1363
UniProt:
  • Canonical: A2RIX0 (Residues: 1-185; Coverage: 100%)
Gene names: hpf, llmg_0616, yfiA
Sequence domains:
16S ribosomal RNA Chain: AA
Molecule details ›
Chain: AA
Length: 1535 nucleotides
Theoretical weight: 497.14 KDa
Sequence domains: Bacterial small subunit ribosomal RNA
23S ribosomal RNA Chain: BA
Molecule details ›
Chain: BA
Length: 2897 nucleotides
Theoretical weight: 938.59 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
5S ribosomal RNA Chain: BB
Molecule details ›
Chain: BB
Length: 115 nucleotides
Theoretical weight: 37.07 KDa
Sequence domains: 5S ribosomal RNA

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 5.6Å
Relevant EMDB volumes: EMD-3581

Quick links

Citations

7 review citations

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

3 mentions without citation

A general mechanism of ribosome dimerization revealed by single-particle cryo-electron microscopy.
Franken et al. (2017)
2 more