8CSP

Human mitochondrial small subunit assembly intermediate (State A)

  • Classification: RIBOSOME
  • Organism(s): Homo sapiens
  • Mutation(s): No 

  • Deposited: 2022-05-13 Released: 2022-12-14 
  • Deposition Author(s): Harper, N.J., Burnside, C., Klinge, S.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), The Robertson Foundation

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.66 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

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
28S ribosomal protein S34, mitochondrialA [auth 0]218Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000074071 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S35, mitochondrialB [auth 1]323Homo sapiensMutation(s): 0 
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PHAROS:  P82673
GTEx:  ENSG00000061794 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Pentatricopeptide repeat domain-containing protein 3, mitochondrialC [auth 4]689Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000132300 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Dimethyladenosine transferase 1, mitochondrialD [auth 5]346Homo sapiensMutation(s): 0 
EC: 2.1.1
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GTEx:  ENSG00000029639 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Methyltransferase-like protein 17, mitochondrialE [auth 7]456Homo sapiensMutation(s): 0 
EC: 2.1.1
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GTEx:  ENSG00000165792 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Malonyl-CoA-acyl carrier protein transacylase, mitochondrialF [auth 8]390Homo sapiensMutation(s): 0 
EC: 2.3.1.39
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GTEx:  ENSG00000100294 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Nitric oxide-associated protein 1G [auth 9]698Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000084092 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S2, mitochondrialI [auth B]296Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000122140 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S24, mitochondrialJ [auth C]167Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000062582 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S5, mitochondrialK [auth D]430Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000144029 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S6, mitochondrialL [auth E]125Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000243927 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S7, mitochondrialM [auth F]242Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125445 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S9, mitochondrialN [auth G]396Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000135972 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S10, mitochondrialO [auth H]201Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000048544 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S12, mitochondrialP [auth J]138Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000128626 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S14, mitochondrialQ [auth K]128Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000120333 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S15, mitochondrialR [auth L]257Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000116898 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S16, mitochondrialS [auth M]137Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182180 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S17, mitochondrialT [auth N]130Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000239789 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S18b, mitochondrialU [auth O]258Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000204568 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S18c, mitochondrialV [auth P]142Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000163319 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S21, mitochondrialW [auth Q]87Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000266472 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S22, mitochondrialX [auth R]360Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000175110 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S23, mitochondrialY [auth S]190Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000181610 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S25, mitochondrialZ [auth T]173Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000131368 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S26, mitochondrialAA [auth U]205Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125901 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S27, mitochondrialBA [auth V]414Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000113048 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S28, mitochondrialCA [auth W]187Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000147586 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S29, mitochondrialDA [auth X]398Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000132676 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S31, mitochondrialEA [auth Y]395Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000102738 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S33, mitochondrialFA [auth Z]106Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000090263 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
GTPase Era, mitochondrialGA [auth a]437Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000132591 
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Entity ID: 8
MoleculeChains LengthOrganismImage
12S mitochondrial rRNAH [auth A]955Homo sapiens
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Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

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RB [auth X]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
GDP
Query on GDP

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TB [auth X]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
SAM (Subject of Investigation/LOI)
Query on SAM

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IA [auth 7]S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
SF4 (Subject of Investigation/LOI)
Query on SF4

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HA [auth 7]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FES
Query on FES

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OB [auth E],
QB [auth T]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
ZN
Query on ZN

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PB [auth O]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K

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JA [auth A],
KA [auth A],
LA [auth A],
MA [auth A]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

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AB [auth A]
BB [auth A]
CB [auth A]
DB [auth A]
EB [auth A]
AB [auth A],
BB [auth A],
CB [auth A],
DB [auth A],
EB [auth A],
FB [auth A],
GB [auth A],
HB [auth A],
IB [auth A],
JB [auth A],
KB [auth A],
LB [auth A],
MB [auth A],
NA [auth A],
NB [auth B],
OA [auth A],
PA [auth A],
QA [auth A],
RA [auth A],
SA [auth A],
SB [auth X],
TA [auth A],
UA [auth A],
VA [auth A],
WA [auth A],
XA [auth A],
YA [auth A],
ZA [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
AYA
Query on AYA
W [auth Q]L-PEPTIDE LINKINGC5 H9 N O3ALA
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.66 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19
RECONSTRUCTIONPHENIX1.19

Structure Validation

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Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-14
    Type: Initial release
  • Version 1.1: 2022-12-21
    Changes: Database references
  • Version 1.2: 2023-02-15
    Changes: Database references