8OM4

Small subunit of yeast mitochondrial ribosome.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.32 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

METTL17 is an Fe-S cluster checkpoint for mitochondrial translation.

Ast, T.Itoh, Y.Sadre, S.McCoy, J.G.Namkoong, G.Wengrod, J.C.Chicherin, I.Joshi, P.R.Kamenski, P.Suess, D.L.M.Amunts, A.Mootha, V.K.

(2024) Mol Cell 84: 359

  • DOI: https://doi.org/10.1016/j.molcel.2023.12.016
  • Primary Citation of Related Structures:  
    8OM2, 8OM3, 8OM4

  • PubMed Abstract: 

    Friedreich's ataxia (FA) is a debilitating, multisystemic disease caused by the depletion of frataxin (FXN), a mitochondrial iron-sulfur (Fe-S) cluster biogenesis factor. To understand the cellular pathogenesis of FA, we performed quantitative proteomics in FXN-deficient human cells. Nearly every annotated Fe-S cluster-containing protein was depleted, indicating that as a rule, cluster binding confers stability to Fe-S proteins. We also observed depletion of a small mitoribosomal assembly factor METTL17 and evidence of impaired mitochondrial translation. Using comparative sequence analysis, mutagenesis, biochemistry, and cryoelectron microscopy, we show that METTL17 binds to the mitoribosomal small subunit during late assembly and harbors a previously unrecognized [Fe 4 S 4 ] 2+ cluster required for its stability. METTL17 overexpression rescued the mitochondrial translation and bioenergetic defects, but not the cellular growth, of FXN-depleted cells. These findings suggest that METTL17 acts as an Fe-S cluster checkpoint, promoting translation of Fe-S cluster-rich oxidative phosphorylation (OXPHOS) proteins only when Fe-S cofactors are replete.


  • Organizational Affiliation

    Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein MRP51, mitochondrial344Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for Q02950 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein MRP4, mitochondrial394Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P32902 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein VAR1, mitochondrial398Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P02381 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein NAM9, mitochondrial486Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P27929 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein S5, mitochondrial307Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P33759 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein MRP17, mitochondrial131Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P28778 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein S7, mitochondrial247Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P47150 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein S8, mitochondrial155Saccharomyces cerevisiaeMutation(s): 1 
UniProt
Find proteins for Q03799 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein S9, mitochondrial278Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P38120 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein S10, mitochondrial203Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for Q03201 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein S18, mitochondrial217Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P42847 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein S12, mitochondrial153Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P53732 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein SWS2, mitochondrial143Saccharomyces cerevisiaeMutation(s): 1 
UniProt
Find proteins for P53937 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein MRP2, mitochondrial115Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P10663 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein S28, mitochondrial286Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P21771 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein S16, mitochondrial121Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for Q02608 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein S17, mitochondrial237Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for Q03246 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein RSM18, mitochondrial138Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P40033 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein S19, mitochondrial91Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P53733 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein MRP21, mitochondrial177Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P38175 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein S25, mitochondrial264Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P40496 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein PET123, mitochondrial318Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P17558 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein S23, mitochondrial450Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for Q01163 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial 37S ribosomal protein S27110Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P53305 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein S24, mitochondrial319Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for Q03976 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein MRP10, mitochondrial95Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for O75012 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial mRNA-processing protein COX24AA [auth 1]111Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P32344 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Protein FYV4, mitochondrialBA [auth 2]130Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P38783 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein S26, mitochondrialCA [auth 3]266Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P47141 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein MRP1, mitochondrialDA [auth 4]321Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P10662 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein MRP13, mitochondrialEA [auth 5]339Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P12686 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein S35, mitochondrialFA [auth 6]345Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P53292 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
3-hydroxyisobutyryl-CoA hydrolase, mitochondrialGA [auth 8]500Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.1.2.4
UniProt
Find proteins for P28817 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 34
MoleculeChains LengthOrganismImage
15S mitochondrial rRNAHA [auth r]1,647Saccharomyces cerevisiae
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LMT
Query on LMT

Download Ideal Coordinates CCD File 
MA [auth O]DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
NA [auth W]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
K
Query on K

Download Ideal Coordinates CCD File 
AE [auth r]
AF [auth r]
BE [auth r]
BF [auth r]
CE [auth r]
AE [auth r],
AF [auth r],
BE [auth r],
BF [auth r],
CE [auth r],
CF [auth r],
DE [auth r],
DF [auth r],
EE [auth r],
EF [auth r],
FE [auth r],
FF [auth r],
GE [auth r],
HE [auth r],
IE [auth r],
JA [auth D],
JE [auth r],
KE [auth r],
LA [auth M],
LE [auth r],
ME [auth r],
NE [auth r],
OE [auth r],
PE [auth r],
QE [auth r],
RE [auth r],
SE [auth r],
TE [auth r],
UE [auth r],
VE [auth r],
WE [auth r],
XD [auth r],
XE [auth r],
YD [auth r],
YE [auth r],
ZD [auth r],
ZE [auth r]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AB [auth r]
AC [auth r]
AD [auth r]
BB [auth r]
BC [auth r]
AB [auth r],
AC [auth r],
AD [auth r],
BB [auth r],
BC [auth r],
BD [auth r],
CB [auth r],
CC [auth r],
CD [auth r],
DB [auth r],
DC [auth r],
DD [auth r],
EB [auth r],
EC [auth r],
ED [auth r],
FB [auth r],
FC [auth r],
FD [auth r],
GB [auth r],
GC [auth r],
GD [auth r],
HB [auth r],
HC [auth r],
HD [auth r],
IA [auth B],
IB [auth r],
IC [auth r],
ID [auth r],
JB [auth r],
JC [auth r],
JD [auth r],
KA [auth K],
KB [auth r],
KC [auth r],
KD [auth r],
LB [auth r],
LC [auth r],
LD [auth r],
MB [auth r],
MC [auth r],
MD [auth r],
NB [auth r],
NC [auth r],
ND [auth r],
OA [auth W],
OB [auth r],
OC [auth r],
OD [auth r],
PA [auth r],
PB [auth r],
PC [auth r],
PD [auth r],
QA [auth r],
QB [auth r],
QC [auth r],
QD [auth r],
RA [auth r],
RB [auth r],
RC [auth r],
RD [auth r],
SA [auth r],
SB [auth r],
SC [auth r],
SD [auth r],
TA [auth r],
TB [auth r],
TC [auth r],
TD [auth r],
UA [auth r],
UB [auth r],
UC [auth r],
UD [auth r],
VA [auth r],
VB [auth r],
VC [auth r],
VD [auth r],
WA [auth r],
WB [auth r],
WC [auth r],
WD [auth r],
XA [auth r],
XB [auth r],
XC [auth r],
YA [auth r],
YB [auth r],
YC [auth r],
ZA [auth r],
ZB [auth r],
ZC [auth r]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.32 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European UnionERC-2018-StG-805230
The Swedish Foundation for Strategic ResearchSwedenFFL15:0325

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-10
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Database references