6TNN

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.07 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structures of B. subtilis Maturation RNases Captured on 50S Ribosome with Pre-rRNAs.

Oerum, S.Dendooven, T.Catala, M.Gilet, L.Degut, C.Trinquier, A.Bourguet, M.Barraud, P.Cianferani, S.Luisi, B.F.Condon, C.Tisne, C.

(2020) Mol Cell 80: 227

  • DOI: https://doi.org/10.1016/j.molcel.2020.09.008
  • Primary Citation of Related Structures:  
    6TG6, 6TGJ, 6TNN, 6TPQ

  • PubMed Abstract: 

    The pathways for ribosomal RNA (rRNA) maturation diverge greatly among the domains of life. In the Gram-positive model bacterium, Bacillus subtilis, the final maturation steps of the two large ribosomal subunit (50S) rRNAs, 23S and 5S pre-rRNAs, are catalyzed by the double-strand specific ribonucleases (RNases) Mini-RNase III and RNase M5, respectively. Here we present a protocol that allowed us to solve the 3.0 and 3.1 Å resolution cryoelectron microscopy structures of these RNases poised to cleave their pre-rRNA substrates within the B. subtilis 50S particle. These data provide the first structural insights into rRNA maturation in bacteria by revealing how these RNases recognize and process double-stranded pre-rRNA. Our structures further uncover how specific ribosomal proteins act as chaperones to correctly fold the pre-rRNA substrates and, for Mini-III, anchor the RNase to the ribosome. These r-proteins thereby serve a quality-control function in the process from accurate ribosome assembly to rRNA processing.


  • Organizational Affiliation

    Expression Génétique Microbienne, UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique (IBPC), 75005 Paris, France.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L10A [auth b]166Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Mini-ribonuclease 3B [auth H],
C [auth I]
143Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: mrnCyazCBSU00950
EC: 3.1.26
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2F [auth W]277Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3G [auth X]209Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4H [auth Y]207Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5I [auth Z]179Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6J [auth a]179Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13K [auth c]145Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14L [auth d]122Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15M [auth e]146Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16N [auth f]144Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17O [auth g]120Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18P [auth h]120Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19Q [auth i]115Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20R [auth j]119Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21S [auth k]102Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22T [auth l]113Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23U [auth m]95Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24V [auth n]103Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27W [auth o]94Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32X [auth p]59Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33 1Y [auth q]49Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34Z [auth r]44Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35AA [auth s]66Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36BA [auth t]37Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28CA [auth u]62Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29DA [auth v]66Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30EA [auth w]59Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 3
MoleculeChains LengthOrganismImage
pre-23S rRNAD [auth U]2,930Bacillus subtilis subsp. subtilis str. 168
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Entity ID: 4
MoleculeChains LengthOrganismImage
5S rRNAE [auth V]116Bacillus subtilis subsp. subtilis str. 168
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
RI [auth p],
SI [auth q],
TI [auth t]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AB [auth U]
AC [auth U]
AD [auth U]
AE [auth U]
AF [auth U]
AB [auth U],
AC [auth U],
AD [auth U],
AE [auth U],
AF [auth U],
AG [auth U],
AH [auth U],
AI [auth U],
BB [auth U],
BC [auth U],
BD [auth U],
BE [auth U],
BF [auth U],
BG [auth U],
BH [auth U],
BI [auth U],
CB [auth U],
CC [auth U],
CD [auth U],
CE [auth U],
CF [auth U],
CG [auth U],
CH [auth U],
CI [auth U],
DB [auth U],
DC [auth U],
DD [auth U],
DE [auth U],
DF [auth U],
DG [auth U],
DH [auth U],
DI [auth U],
EB [auth U],
EC [auth U],
ED [auth U],
EE [auth U],
EF [auth U],
EG [auth U],
EH [auth U],
EI [auth U],
FA [auth I],
FB [auth U],
FC [auth U],
FD [auth U],
FE [auth U],
FF [auth U],
FG [auth U],
FH [auth U],
FI [auth U],
GA [auth U],
GB [auth U],
GC [auth U],
GD [auth U],
GE [auth U],
GF [auth U],
GG [auth U],
GH [auth U],
GI [auth U],
HA [auth U],
HB [auth U],
HC [auth U],
HD [auth U],
HE [auth U],
HF [auth U],
HG [auth U],
HH [auth U],
HI [auth U],
IA [auth U],
IB [auth U],
IC [auth U],
ID [auth U],
IE [auth U],
IF [auth U],
IG [auth U],
IH [auth U],
II [auth U],
JA [auth U],
JB [auth U],
JC [auth U],
JD [auth U],
JE [auth U],
JF [auth U],
JG [auth U],
JH [auth U],
JI [auth U],
KA [auth U],
KB [auth U],
KC [auth U],
KD [auth U],
KE [auth U],
KF [auth U],
KG [auth U],
KH [auth U],
KI [auth U],
LA [auth U],
LB [auth U],
LC [auth U],
LD [auth U],
LE [auth U],
LF [auth U],
LG [auth U],
LH [auth U],
LI [auth U],
MA [auth U],
MB [auth U],
MC [auth U],
MD [auth U],
ME [auth U],
MF [auth U],
MG [auth U],
MH [auth U],
MI [auth V],
NA [auth U],
NB [auth U],
NC [auth U],
ND [auth U],
NE [auth U],
NF [auth U],
NG [auth U],
NH [auth U],
NI [auth W],
OA [auth U],
OB [auth U],
OC [auth U],
OD [auth U],
OE [auth U],
OF [auth U],
OG [auth U],
OH [auth U],
OI [auth W],
PA [auth U],
PB [auth U],
PC [auth U],
PD [auth U],
PE [auth U],
PF [auth U],
PG [auth U],
PH [auth U],
PI [auth e],
QA [auth U],
QB [auth U],
QC [auth U],
QD [auth U],
QE [auth U],
QF [auth U],
QG [auth U],
QH [auth U],
QI [auth e],
RA [auth U],
RB [auth U],
RC [auth U],
RD [auth U],
RE [auth U],
RF [auth U],
RG [auth U],
RH [auth U],
SA [auth U],
SB [auth U],
SC [auth U],
SD [auth U],
SE [auth U],
SF [auth U],
SG [auth U],
SH [auth U],
TA [auth U],
TB [auth U],
TC [auth U],
TD [auth U],
TE [auth U],
TF [auth U],
TG [auth U],
TH [auth U],
UA [auth U],
UB [auth U],
UC [auth U],
UD [auth U],
UE [auth U],
UF [auth U],
UG [auth U],
UH [auth U],
UI [auth u],
VA [auth U],
VB [auth U],
VC [auth U],
VD [auth U],
VE [auth U],
VF [auth U],
VG [auth U],
VH [auth U],
WA [auth U],
WB [auth U],
WC [auth U],
WD [auth U],
WE [auth U],
WF [auth U],
WG [auth U],
WH [auth U],
XA [auth U],
XB [auth U],
XC [auth U],
XD [auth U],
XE [auth U],
XF [auth U],
XG [auth U],
XH [auth U],
YA [auth U],
YB [auth U],
YC [auth U],
YD [auth U],
YE [auth U],
YF [auth U],
YG [auth U],
YH [auth U],
ZA [auth U],
ZB [auth U],
ZC [auth U],
ZD [auth U],
ZE [auth U],
ZF [auth U],
ZG [auth U],
ZH [auth U]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.07 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.16

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFrance--

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-30
    Type: Initial release
  • Version 1.1: 2020-10-14
    Changes: Database references
  • Version 1.2: 2020-10-28
    Changes: Database references
  • Version 1.3: 2024-05-22
    Changes: Data collection, Database references, Refinement description