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 

wwPDB Validation   3D Report Full Report


This is version 1.2 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

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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