7PNY

Assembly intermediate of human mitochondrial ribosome small subunit without mS37 in complex with RBFA and METTL15 conformation b

  • Classification: RIBOSOME
  • Organism(s): Homo sapiens
  • Mutation(s): Yes 

  • Deposited: 2021-09-08 Released: 2022-06-15 
  • Deposition Author(s): Itoh, Y., Khawaja, A., Rorbach, J., Amunts, A.
  • Funding Organization(s): European Research Council (ERC), The Swedish Foundation for Strategic Research, European Commission

Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 2.1 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, mitochondrial296Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000122140 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S24, mitochondrial167Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000062582 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S5, mitochondrial430Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000144029 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S6, mitochondrial125Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000243927 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S7, mitochondrial242Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125445 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S9, mitochondrial396Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000135972 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S10, mitochondrial201Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000048544 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S11, mitochondrial194Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000181991 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S12, mitochondrial138Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000128626 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S14, mitochondrial128Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000120333 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S15, mitochondrial257Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000116898 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S16, mitochondrial137Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182180 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S17, mitochondrial130Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000239789 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S18b, mitochondrial258Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000204568 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S18c, mitochondrial142Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000163319 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S21, mitochondrial86Homo sapiensMutation(s): 1 
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GTEx:  ENSG00000266472 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S22, mitochondrial360Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000175110 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S23, mitochondrial190Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000181610 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S25, mitochondrial173Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000131368 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S26, mitochondrial205Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125901 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S27, mitochondrial414Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000113048 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S28, mitochondrial187Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000147586 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S29, mitochondrial398Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000132676 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S31, mitochondrial395Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000102738 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S33, mitochondrial106Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000090263 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S34, mitochondrialAA [auth 0]218Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000074071 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S35, mitochondrialBA [auth 1]323Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000061794 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Aurora kinase A-interacting proteinCA [auth 3]199Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000175756 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Pentatricopeptide repeat domain-containing protein 3, mitochondrialDA [auth 4]689Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000132300 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Putative ribosome-binding factor A, mitochondrialEA [auth a]343Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000101546 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
12S rRNA N4-methylcytidine (m4C) methyltransferaseFA [auth b]407Homo sapiensMutation(s): 0 
EC: 2.1.1
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GTEx:  ENSG00000169519 
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Entity ID: 1
MoleculeChains LengthOrganismImage
12S mitochondrial rRNA955Homo sapiens
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Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

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GA [auth A]NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
ATP
Query on ATP

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

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MD [auth X]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
SAH
Query on SAH

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PD [auth b]S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
FES (Subject of Investigation/LOI)
Query on FES

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

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

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AD [auth A]
BD [auth A]
CD [auth A]
DD [auth A]
ED [auth A]
AD [auth A],
BD [auth A],
CD [auth A],
DD [auth A],
ED [auth A],
FD [auth A],
GD [auth A],
NC [auth A],
OC [auth A],
PC [auth A],
QC [auth A],
RC [auth A],
SC [auth A],
TC [auth A],
UC [auth A],
VC [auth A],
WC [auth A],
XC [auth A],
YC [auth A],
ZC [auth A]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

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AB [auth A]
AC [auth A]
BB [auth A]
BC [auth A]
CB [auth A]
AB [auth A],
AC [auth A],
BB [auth A],
BC [auth A],
CB [auth A],
CC [auth A],
DB [auth A],
DC [auth A],
EB [auth A],
EC [auth A],
FB [auth A],
FC [auth A],
GB [auth A],
GC [auth A],
HA [auth A],
HB [auth A],
HC [auth A],
HD [auth B],
IA [auth A],
IB [auth A],
IC [auth A],
JA [auth A],
JB [auth A],
JC [auth A],
KA [auth A],
KB [auth A],
KC [auth A],
LA [auth A],
LB [auth A],
LC [auth A],
MA [auth A],
MB [auth A],
MC [auth A],
NA [auth A],
NB [auth A],
ND [auth X],
OA [auth A],
OB [auth A],
OD [auth 3],
PA [auth A],
PB [auth A],
QA [auth A],
QB [auth A],
RA [auth A],
RB [auth A],
SA [auth A],
SB [auth A],
TA [auth A],
TB [auth A],
UA [auth A],
UB [auth A],
VA [auth A],
VB [auth A],
WA [auth A],
WB [auth A],
XA [auth A],
XB [auth A],
YA [auth A],
YB [auth A],
ZA [auth A],
ZB [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