8D8K

Yeast mitochondrial small subunit assembly intermediate (State 2)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.13 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Principles of mitoribosomal small subunit assembly in eukaryotes.

Harper, N.J.Burnside, C.Klinge, S.

(2023) Nature 614: 175-181

  • DOI: https://doi.org/10.1038/s41586-022-05621-0
  • Primary Citation of Related Structures:  
    8CSP, 8CSQ, 8CSR, 8CSS, 8CST, 8CSU, 8D8J, 8D8K, 8D8L

  • PubMed Abstract: 

    Mitochondrial ribosomes (mitoribosomes) synthesize proteins encoded within the mitochondrial genome that are assembled into oxidative phosphorylation complexes. Thus, mitoribosome biogenesis is essential for ATP production and cellular metabolism 1 . Here we used cryo-electron microscopy to determine nine structures of native yeast and human mitoribosomal small subunit assembly intermediates, illuminating the mechanistic basis for how GTPases are used to control early steps of decoding centre formation, how initial rRNA folding and processing events are mediated, and how mitoribosomal proteins have active roles during assembly. Furthermore, this series of intermediates from two species with divergent mitoribosomal architecture uncovers both conserved principles and species-specific adaptations that govern the maturation of mitoribosomal small subunits in eukaryotes. By revealing the dynamic interplay between assembly factors, mitoribosomal proteins and rRNA that are required to generate functional subunits, our structural analysis provides a vignette for how molecular complexity and diversity can evolve in large ribonucleoprotein assemblies.


  • Organizational Affiliation

    Laboratory of Protein and Nucleic Acid Chemistry, The Rockefeller University, New York, NY, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Probable S-adenosyl-L-methionine-dependent RNA methyltransferase RSM22, mitochondrialA [auth 0]628Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.1.1
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein MRP13, mitochondrialB [auth 5]339Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein VAR1, mitochondrial398Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial group I intron splicing factor CCM1D [auth d]864Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein SWS2, mitochondrialE [auth M]143Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein MRP2, mitochondrialF [auth N]115Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein S28, mitochondrialG [auth O]286Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein S16, mitochondrialH [auth P]121Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein S17, mitochondrialI [auth Q]237Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein RSM18, mitochondrialJ [auth R]138Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein S19, mitochondrialK [auth S]91Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein MRP21, mitochondrialL [auth T]177Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein S25, mitochondrialM [auth U]264Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein PET123, mitochondrialN [auth V]318Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein S23, mitochondrialO [auth W]450Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial 37S ribosomal protein S27P [auth X]110Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein S24, mitochondrialQ [auth Y]319Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein MRP10, mitochondrialR [auth Z]95Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein MRP51, mitochondrialS [auth A]344Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein MRP4, mitochondrialT [auth B]394Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Protein FYV4, mitochondrialU [auth 2]130Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein S26, mitochondrialV [auth 3]266Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein NAM9, mitochondrialW [auth D]486Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein MRP1, mitochondrialX [auth 4]321Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein S5, mitochondrialY [auth E]307Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein MRP17, mitochondrialZ [auth F]131Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein S35, mitochondrialAA [auth 6]345Saccharomyces cerevisiaeMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein S7, mitochondrialBA [auth G]247Saccharomyces cerevisiaeMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein S8, mitochondrialCA [auth H]155Saccharomyces cerevisiaeMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein S9, mitochondrialDA [auth I]278Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein S10, mitochondrialFA [auth J]203Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein S18, mitochondrialGA [auth K]217Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
unknown protein sequenceHA [auth c]94Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
MRPS12 isoform 1IA [auth L]153Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 31
MoleculeChains LengthOrganismImage
15S ribosomal RNAEA [auth a]1,713Saccharomyces cerevisiae
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP

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LA [auth W]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
SF4 (Subject of Investigation/LOI)
Query on SF4

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JA [auth 0]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
AB [auth a]
AC [auth a]
AD [auth a]
BB [auth a]
BC [auth a]
AB [auth a],
AC [auth a],
AD [auth a],
BB [auth a],
BC [auth a],
BD [auth a],
CB [auth a],
CC [auth a],
CD [auth a],
DB [auth a],
DC [auth a],
DD [auth a],
EB [auth a],
EC [auth a],
ED [auth a],
FB [auth a],
FC [auth a],
GB [auth a],
GC [auth a],
HB [auth a],
HC [auth a],
IB [auth a],
IC [auth a],
JB [auth a],
JC [auth a],
KA [auth Q],
KB [auth a],
KC [auth a],
LB [auth a],
LC [auth a],
MA [auth W],
MB [auth a],
MC [auth a],
NA [auth B],
NB [auth a],
NC [auth a],
OA [auth a],
OB [auth a],
OC [auth a],
PA [auth a],
PB [auth a],
PC [auth a],
QA [auth a],
QB [auth a],
QC [auth a],
RA [auth a],
RB [auth a],
RC [auth a],
SA [auth a],
SB [auth a],
SC [auth a],
TA [auth a],
TB [auth a],
TC [auth a],
UA [auth a],
UB [auth a],
UC [auth a],
VA [auth a],
VB [auth a],
VC [auth a],
WA [auth a],
WB [auth a],
WC [auth a],
XA [auth a],
XB [auth a],
XC [auth a],
YA [auth a],
YB [auth a],
YC [auth a],
ZA [auth a],
ZB [auth a],
ZC [auth a]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.13 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONPHENIX1.19
MODEL REFINEMENTPHENIX1.19

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other private--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States5T32GM136640-02

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-21
    Type: Initial release
  • Version 1.1: 2023-02-15
    Changes: Database references