› 6tnn

Electron Microscopy
3.07Å resolution

Mini-RNase III (Mini-III) bound to 50S ribosome with precursor 23S rRNA

Released:
DOI: 10.2210/pdb6tnn/pdb
PDB entry 6tnn coloured by chain, front view.
PDB entry 6tnn coloured by chain, side view.
PDB entry 6tnn coloured by chain, top view.
Source organism: Bacillus subtilis subsp. subtilis str. 168
Primary publication:
Structures of B. subtilis Maturation RNases Captured on 50S Ribosome with Pre-rRNAs.
Oerum S, Dendooven T, Catala M, Gilet L, Dégut C, Trinquier A, Bourguet M, Barraud P, Cianferani S, Luisi BF, Condon C, Tisné C
Mol Cell 80 227-236.e5 (2020)
PMID: 32991829
Related structures: EMD-10535

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 31-mer (preferred)
PDBe Complex ID:
PDB-CPX-128285 (preferred)
Entry contents:
28 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (30 distinct):
Large ribosomal subunit protein uL10 Chain: b
Molecule details ›
Chain: b
Length: 166 amino acids
Theoretical weight: 18.1 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
UniProt:
  • Canonical: P42923 (Residues: 1-166; Coverage: 100%)
Gene names: BSU01040, rplJ
Sequence domains: Ribosomal protein L10
Mini-ribonuclease 3 Chains: H, I
Molecule details ›
Chains: H, I
Length: 143 amino acids
Theoretical weight: 16.25 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
Expression system: Escherichia coli
UniProt:
  • Canonical: O31418 (Residues: 1-143; Coverage: 100%)
Gene names: BSU00950, mrnC, yazC
Sequence domains: Ribonuclease III domain
Large ribosomal subunit protein uL2 Chain: W
Molecule details ›
Chain: W
Length: 277 amino acids
Theoretical weight: 30.34 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
UniProt:
  • Canonical: P42919 (Residues: 1-277; Coverage: 100%)
Gene names: BSU01190, rplB
Sequence domains:
Large ribosomal subunit protein uL3 Chain: X
Molecule details ›
Chain: X
Length: 209 amino acids
Theoretical weight: 22.72 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
UniProt:
  • Canonical: P42920 (Residues: 1-209; Coverage: 100%)
Gene names: BSU01160, rplC
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL4 Chain: Y
Molecule details ›
Chain: Y
Length: 207 amino acids
Theoretical weight: 22.42 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
UniProt:
  • Canonical: P42921 (Residues: 1-207; Coverage: 100%)
Gene names: BSU01170, rplD
Sequence domains: Ribosomal protein L4/L1 family
Large ribosomal subunit protein uL5 Chain: Z
Molecule details ›
Chain: Z
Length: 179 amino acids
Theoretical weight: 20.18 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
UniProt:
  • Canonical: P12877 (Residues: 1-179; Coverage: 100%)
Gene names: BSU01280, rplE
Sequence domains:
Large ribosomal subunit protein uL6 Chain: a
Molecule details ›
Chain: a
Length: 179 amino acids
Theoretical weight: 19.54 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
UniProt:
  • Canonical: P46898 (Residues: 1-179; Coverage: 100%)
Gene names: BSU01310, rplF
Sequence domains: Ribosomal protein L6
Large ribosomal subunit protein uL13 Chain: c
Molecule details ›
Chain: c
Length: 145 amino acids
Theoretical weight: 16.41 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
UniProt:
  • Canonical: P70974 (Residues: 1-145; Coverage: 100%)
Gene names: BSU01490, rplM
Sequence domains: Ribosomal protein L13
Large ribosomal subunit protein uL14 Chain: d
Molecule details ›
Chain: d
Length: 122 amino acids
Theoretical weight: 13.18 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
UniProt:
  • Canonical: P12875 (Residues: 1-122; Coverage: 100%)
Gene names: BSU01260, rplN
Sequence domains: Ribosomal protein L14p/L23e
Large ribosomal subunit protein uL15 Chain: e
Molecule details ›
Chain: e
Length: 146 amino acids
Theoretical weight: 15.41 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
UniProt:
  • Canonical: P19946 (Residues: 1-146; Coverage: 100%)
Gene names: BSU01350, rplO
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
Large ribosomal subunit protein uL16 Chain: f
Molecule details ›
Chain: f
Length: 144 amino acids
Theoretical weight: 16.22 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
UniProt:
  • Canonical: P14577 (Residues: 1-144; Coverage: 100%)
Gene names: BSU01230, rplP
Sequence domains: Ribosomal protein L16p/L10e
Large ribosomal subunit protein bL17 Chain: g
Molecule details ›
Chain: g
Length: 120 amino acids
Theoretical weight: 13.77 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
UniProt:
  • Canonical: P20277 (Residues: 1-120; Coverage: 100%)
Gene names: BSU01440, rplQ
Sequence domains: Ribosomal protein L17
Large ribosomal subunit protein uL18 Chain: h
Molecule details ›
Chain: h
Length: 120 amino acids
Theoretical weight: 12.99 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
UniProt:
  • Canonical: P46899 (Residues: 1-120; Coverage: 100%)
Gene names: BSU01320, rplR
Sequence domains: Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
Large ribosomal subunit protein bL19 Chain: i
Molecule details ›
Chain: i
Length: 115 amino acids
Theoretical weight: 13.42 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
UniProt:
  • Canonical: O31742 (Residues: 1-115; Coverage: 100%)
Gene names: BSU16040, rplS
Sequence domains: Ribosomal protein L19
Large ribosomal subunit protein bL20 Chain: j
Molecule details ›
Chain: j
Length: 119 amino acids
Theoretical weight: 13.67 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
UniProt:
  • Canonical: P55873 (Residues: 1-119; Coverage: 100%)
Gene names: BSU28850, rplT
Sequence domains: Ribosomal protein L20
Large ribosomal subunit protein bL21 Chain: k
Molecule details ›
Chain: k
Length: 102 amino acids
Theoretical weight: 11.3 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
UniProt:
  • Canonical: P26908 (Residues: 1-102; Coverage: 100%)
Gene names: BSU27960, rplU
Sequence domains: Ribosomal prokaryotic L21 protein
Large ribosomal subunit protein uL22 Chain: l
Molecule details ›
Chain: l
Length: 113 amino acids
Theoretical weight: 12.48 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
UniProt:
  • Canonical: P42060 (Residues: 1-113; Coverage: 100%)
Gene names: BSU01210, rplV
Sequence domains: Ribosomal protein L22p/L17e
Large ribosomal subunit protein uL23 Chain: m
Molecule details ›
Chain: m
Length: 95 amino acids
Theoretical weight: 10.98 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
UniProt:
  • Canonical: P42924 (Residues: 1-95; Coverage: 100%)
Gene names: BSU01180, rplW
Sequence domains: Ribosomal protein L23
Large ribosomal subunit protein uL24 Chain: n
Molecule details ›
Chain: n
Length: 103 amino acids
Theoretical weight: 11.17 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
UniProt:
  • Canonical: P0CI78 (Residues: 1-103; Coverage: 100%)
Gene names: BSU01270, rplX
Sequence domains:
Large ribosomal subunit protein bL27 Chain: o
Molecule details ›
Chain: o
Length: 94 amino acids
Theoretical weight: 10.39 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
UniProt:
  • Canonical: P05657 (Residues: 1-94; Coverage: 100%)
Gene names: BSU27940, rpmA
Sequence domains: Ribosomal L27 protein
Large ribosomal subunit protein bL32 Chain: p
Molecule details ›
Chain: p
Length: 59 amino acids
Theoretical weight: 6.75 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
UniProt:
  • Canonical: O34687 (Residues: 1-59; Coverage: 100%)
Gene names: BSU15080, rpmF
Sequence domains: Ribosomal L32p protein family
Large ribosomal subunit protein bL33A Chain: q
Molecule details ›
Chain: q
Length: 49 amino acids
Theoretical weight: 5.92 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
UniProt:
  • Canonical: P56849 (Residues: 1-49; Coverage: 100%)
Gene names: BSU24900, rpmG1, rpmGA
Sequence domains: Ribosomal protein L33
Large ribosomal subunit protein bL34 Chain: r
Molecule details ›
Chain: r
Length: 44 amino acids
Theoretical weight: 5.27 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
UniProt:
  • Canonical: P05647 (Residues: 1-44; Coverage: 100%)
Gene names: BSU41060, rpmH
Sequence domains: Ribosomal protein L34
Large ribosomal subunit protein bL35 Chain: s
Molecule details ›
Chain: s
Length: 66 amino acids
Theoretical weight: 7.58 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
UniProt:
  • Canonical: P55874 (Residues: 1-66; Coverage: 100%)
Gene names: BSU28860, rpmI
Sequence domains: Ribosomal protein L35
Large ribosomal subunit protein bL36 Chain: t
Molecule details ›
Chain: t
Length: 37 amino acids
Theoretical weight: 4.32 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
UniProt:
  • Canonical: P20278 (Residues: 1-37; Coverage: 100%)
Gene names: BSU01400, rpmJ
Sequence domains: Ribosomal protein L36
Large ribosomal subunit protein bL28 Chain: u
Molecule details ›
Chain: u
Length: 62 amino acids
Theoretical weight: 6.83 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
UniProt:
  • Canonical: P37807 (Residues: 1-62; Coverage: 100%)
Gene names: BSU15820, rpmB, yloT
Sequence domains: Ribosomal L28 family
Large ribosomal subunit protein uL29 Chain: v
Molecule details ›
Chain: v
Length: 66 amino acids
Theoretical weight: 7.73 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
UniProt:
  • Canonical: P12873 (Residues: 1-66; Coverage: 100%)
Gene names: BSU01240, rpmC
Sequence domains: Ribosomal L29 protein
Large ribosomal subunit protein uL30 Chain: w
Molecule details ›
Chain: w
Length: 59 amino acids
Theoretical weight: 6.65 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
UniProt:
  • Canonical: P19947 (Residues: 1-59; Coverage: 100%)
Gene names: BSU01340, rpmD
Sequence domains: Ribosomal protein L30p/L7e
pre-23S rRNA Chain: U
Molecule details ›
Chain: U
Length: 2930 nucleotides
Theoretical weight: 950.28 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
5S ribosomal RNA Chain: V
Molecule details ›
Chain: V
Length: 116 nucleotides
Theoretical weight: 37.42 KDa
Sequence domains: 5S ribosomal RNA

Ligands and Environments

2 bound ligands:
Ligand MG 221 x MG
Ligand ZN 3 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.07Å
Relevant EMDB volumes: EMD-10535
Expression system: Escherichia coli

Quick links

Citations

3 review citations

A comprehensive review of m6A/m6Am RNA methyltransferase structures.
Oerum et al. (2021)
2 more

2 mentions without citation

The World of Stable Ribonucleoproteins and Its Mapping With Grad-Seq and Related Approaches.
Gerovac et al. (2021)
1 more