RCSB PDB - 7PNV: Assembly intermediate of mouse mitochondrial ribosome small subunit without mS37 in complex with RbfA and Mettl15

 7PNV

Assembly intermediate of mouse mitochondrial ribosome small subunit without mS37 in complex with RbfA and Mettl15


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.06 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 2.2 of the entry. See complete history


Literature

Mechanism of mitoribosomal small subunit biogenesis and preinitiation.

Itoh, Y.Khawaja, A.Laptev, I.Cipullo, M.Atanassov, I.Sergiev, P.Rorbach, J.Amunts, A.

(2022) Nature 606: 603-608

  • DOI: https://doi.org/10.1038/s41586-022-04795-x
  • Primary Citation of Related Structures:  
    7PNT, 7PNU, 7PNV, 7PNW, 7PNX, 7PNY, 7PNZ, 7PO0, 7PO1, 7PO2, 7PO3, 7PO4

  • PubMed Abstract: 

    Mitoribosomes are essential for the synthesis and maintenance of bioenergetic proteins. Here we use cryo-electron microscopy to determine a series of the small mitoribosomal subunit (SSU) intermediates in complex with auxiliary factors, revealing a sequential assembly mechanism. The methyltransferase TFB1M binds to partially unfolded rRNA h45 that is promoted by RBFA, while the mRNA channel is blocked. This enables binding of METTL15 that promotes further rRNA maturation and a large conformational change of RBFA. The new conformation allows initiation factor mtIF3 to already occupy the subunit interface during the assembly. Finally, the mitochondria-specific ribosomal protein mS37 (ref. 1 ) outcompetes RBFA to complete the assembly with the SSU-mS37-mtIF3 complex 2 that proceeds towards mtIF2 binding and translation initiation. Our results explain how the action of step-specific factors modulate the dynamic assembly of the SSU, and adaptation of a unique protein, mS37, links the assembly to initiation to establish the catalytic human mitoribosome.


  • Organizational Affiliation

    Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S2, mitochondrial291Mus musculusMutation(s): 0 
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Find proteins for Q924T2 (Mus musculus)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S24, mitochondrial167Mus musculusMutation(s): 0 
UniProt
Find proteins for Q9CQV5 (Mus musculus)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S5, mitochondrial432Mus musculusMutation(s): 0 
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IMPC:  MGI:1924971
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S6, mitochondrial125Mus musculusMutation(s): 0 
UniProt
Find proteins for P58064 (Mus musculus)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S7, mitochondrial242Mus musculusMutation(s): 0 
UniProt
Find proteins for Q80X85 (Mus musculus)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S9, mitochondrial390Mus musculusMutation(s): 0 
UniProt
Find proteins for Q9D7N3 (Mus musculus)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S10, mitochondrial160Mus musculusMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S11, mitochondrial191Mus musculusMutation(s): 0 
UniProt
Find proteins for Q9DCA2 (Mus musculus)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S12, mitochondrial139Mus musculusMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O35680 (Mus musculus)
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IMPC:  MGI:1346333
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S14, mitochondrial128Mus musculusMutation(s): 0 
UniProt
Find proteins for Q9CR88 (Mus musculus)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S15, mitochondrial258Mus musculusMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S16, mitochondrial135Mus musculusMutation(s): 0 
UniProt
Find proteins for Q9CPX7 (Mus musculus)
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S17, mitochondrial120Mus musculusMutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S18b, mitochondrial254Mus musculusMutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S18c, mitochondrial143Mus musculusMutation(s): 0 
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IMPC:  MGI:1915985
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S21, mitochondrial86Mus musculusMutation(s): 0 
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IMPC:  MGI:1913542
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S22, mitochondrial359Mus musculusMutation(s): 0 
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IMPC:  MGI:1928137
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S23, mitochondrial177Mus musculusMutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S25, mitochondrial171Mus musculusMutation(s): 0 
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Find proteins for Q9D125 (Mus musculus)
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IMPC:  MGI:1928140
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S26, mitochondrial200Mus musculusMutation(s): 0 
UniProt
Find proteins for Q80ZS3 (Mus musculus)
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S27, mitochondrial415Mus musculusMutation(s): 0 
UniProt
Find proteins for Q8BK72 (Mus musculus)
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S28, mitochondrial186Mus musculusMutation(s): 0 
UniProt
Find proteins for Q9CY16 (Mus musculus)
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S29, mitochondrial391Mus musculusMutation(s): 0 
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Find proteins for Q9ER88 (Mus musculus)
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IMPC:  MGI:1929538
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S31, mitochondrial384Mus musculusMutation(s): 0 
UniProt
Find proteins for Q61733 (Mus musculus)
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S33, mitochondrial106Mus musculusMutation(s): 0 
UniProt
Find proteins for Q9D2R8 (Mus musculus)
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S34, mitochondrialAA [auth 0]218Mus musculusMutation(s): 0 
UniProt
Find proteins for Q9JIK9 (Mus musculus)
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S35, mitochondrialBA [auth 1]320Mus musculusMutation(s): 0 
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IMPC:  MGI:2385255
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Aurora kinase A-interacting proteinCA [auth 3]200Mus musculusMutation(s): 0 
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IMPC:  MGI:1913327
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Pentatricopeptide repeat domain-containing protein 3, mitochondrialDA [auth 4]685Mus musculusMutation(s): 0 
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IMPC:  MGI:1917206
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Putative ribosome-binding factor A, mitochondrialEA [auth a]350Mus musculusMutation(s): 0 
UniProt
Find proteins for Q6P3B9 (Mus musculus)
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
12S rRNA N4-methylcytidine methyltransferaseFA [auth b]406Mus musculusMutation(s): 0 
EC: 2.1.1
UniProt
Find proteins for Q9DCL4 (Mus musculus)
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Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

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

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UC [auth b]S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
FES
Query on FES

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PC [auth P],
QC [auth T]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
ZN
Query on ZN

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

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AC [auth A]
BC [auth A]
CC [auth A]
DC [auth A]
EC [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]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
AYA
Query on AYA
Q
L-PEPTIDE LINKINGC5 H9 N O3ALA
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.06 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.18
RECONSTRUCTIONRELION3.1

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 ResearchEuropean UnionFFL15:0325
European CommissionEuropean Union799399-Itohribo

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-15
    Type: Initial release
  • Version 1.1: 2022-06-22
    Changes: Database references
  • Version 1.2: 2022-06-29
    Changes: Database references
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Derived calculations, Refinement description
  • Version 2.1: 2024-01-17
    Changes: Structure summary
  • Version 2.2: 2024-04-24
    Changes: Data collection