8OM3

Small subunit of yeast mitochondrial ribosome in complex with IF3/Aim23.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.87 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

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 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein MRP4, mitochondrial394Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein VAR1, mitochondrial398Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein NAM9, mitochondrial486Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein S5, mitochondrial307Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein MRP17, mitochondrial131Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein S7, mitochondrial247Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein S8, mitochondrial155Saccharomyces cerevisiaeMutation(s): 1 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein S9, mitochondrial278Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein S10, mitochondrial203Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein S18, mitochondrial217Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein S12, mitochondrial153Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein SWS2, mitochondrial143Saccharomyces cerevisiaeMutation(s): 1 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein MRP2, mitochondrial115Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein S28, mitochondrial286Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein S16, mitochondrial121Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein S17, mitochondrial237Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein RSM18, mitochondrial138Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein S19, mitochondrial91Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein MRP21, mitochondrial177Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein S25, mitochondrial264Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein PET123, mitochondrial318Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein S23, mitochondrial450Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial 37S ribosomal protein S27110Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein S24, mitochondrial319Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein MRP10, mitochondrial95Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial mRNA-processing protein COX24AA [auth 1]111Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Protein FYV4, mitochondrialBA [auth 2]130Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein S26, mitochondrialCA [auth 3]266Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein MRP1, mitochondrialDA [auth 4]321Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein MRP13, mitochondrialEA [auth 5]339Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein S35, mitochondrialFA [auth 6]345Saccharomyces cerevisiaeMutation(s): 0 
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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
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Altered inheritance of mitochondria protein 23, mitochondrialIA [auth d]364Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: AIM23YJL131CJ0682
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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

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

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

Download Ideal Coordinates CCD File 
AF [auth r]
BF [auth r]
CF [auth r]
EE [auth r]
FE [auth r]
AF [auth r],
BF [auth r],
CF [auth r],
EE [auth r],
FE [auth r],
GE [auth r],
HE [auth r],
IE [auth r],
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],
XE [auth r],
YE [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]
AE [auth r]
BB [auth r]
AB [auth r],
AC [auth r],
AD [auth r],
AE [auth r],
BB [auth r],
BC [auth r],
BD [auth r],
BE [auth r],
CB [auth r],
CC [auth r],
CD [auth r],
CE [auth r],
DB [auth r],
DC [auth r],
DD [auth r],
DE [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],
IB [auth r],
IC [auth r],
ID [auth r],
JA [auth B],
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],
XD [auth r],
YA [auth r],
YB [auth r],
YC [auth r],
YD [auth r],
ZA [auth r],
ZB [auth r],
ZC [auth r],
ZD [auth r]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.87 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
  • Version 1.3: 2024-11-13
    Changes: Data collection, Structure summary