6RW4

Structure of human mitochondrial 28S ribosome in complex with mitochondrial IF3


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.97 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

Distinct pre-initiation steps in human mitochondrial translation.

Khawaja, A.Itoh, Y.Remes, C.Spahr, H.Yukhnovets, O.Hofig, H.Amunts, A.Rorbach, J.

(2020) Nat Commun 11: 2932-2932

  • DOI: 10.1038/s41467-020-16503-2
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Translation initiation in human mitochondria relies upon specialized mitoribosomes and initiation factors, mtIF2 and mtIF3, which have diverged from their bacterial counterparts. Here we report two distinct mitochondrial pre-initiation assembly steps ...

    Translation initiation in human mitochondria relies upon specialized mitoribosomes and initiation factors, mtIF2 and mtIF3, which have diverged from their bacterial counterparts. Here we report two distinct mitochondrial pre-initiation assembly steps involving those factors. Single-particle cryo-EM revealed that in the first step, interactions between mitochondria-specific protein mS37 and mtIF3 keep the small mitoribosomal subunit in a conformation favorable for a subsequent accommodation of mtIF2 in the second step. Combination with fluorescence cross-correlation spectroscopy analyses suggests that mtIF3 promotes complex assembly without mRNA or initiator tRNA binding, where exclusion is achieved by the N-terminal and C-terminal domains of mtIF3. Finally, the association of large mitoribosomal subunit is required for initiator tRNA and leaderless mRNA recruitment to form a stable initiation complex. These data reveal fundamental aspects of mammalian protein synthesis that are specific to mitochondria.


    Organizational Affiliation

    Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden. joanna.rorbach@ki.se.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
28S ribosomal protein S2, mitochondrialB296Homo sapiensMutation(s): 0 
Gene Names: MRPS2CGI-91
Find proteins for Q9Y399 (Homo sapiens)
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PHAROS  Q9Y399
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
28S ribosomal protein S24, mitochondrialC167Homo sapiensMutation(s): 0 
Gene Names: MRPS24HSPC335
Find proteins for Q96EL2 (Homo sapiens)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
28S ribosomal protein S5, mitochondrialD430Homo sapiensMutation(s): 0 
Gene Names: MRPS5
Find proteins for P82675 (Homo sapiens)
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PHAROS  P82675
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
28S ribosomal protein S6, mitochondrialE125Homo sapiensMutation(s): 0 
Gene Names: MRPS6C21orf101RPMS6
Find proteins for P82932 (Homo sapiens)
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PHAROS  P82932
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
28S ribosomal protein S7, mitochondrialF242Homo sapiensMutation(s): 0 
Gene Names: MRPS7
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PHAROS  Q9Y2R9
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
28S ribosomal protein S9, mitochondrialG396Homo sapiensMutation(s): 0 
Gene Names: MRPS9RPMS9
Find proteins for P82933 (Homo sapiens)
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PHAROS  P82933
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
28S ribosomal protein S10, mitochondrialH201Homo sapiensMutation(s): 0 
Gene Names: MRPS10MSTP040
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PHAROS  P82664
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
28S ribosomal protein S11, mitochondrialI194Homo sapiensMutation(s): 0 
Gene Names: MRPS11RPMS11HCC2
Find proteins for P82912 (Homo sapiens)
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PHAROS  P82912
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
28S ribosomal protein S12, mitochondrialJ138Homo sapiensMutation(s): 0 
Gene Names: MRPS12RPMS12RPSM12
Find proteins for O15235 (Homo sapiens)
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PHAROS  O15235
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
28S ribosomal protein S14, mitochondrialK128Homo sapiensMutation(s): 0 
Gene Names: MRPS14
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PHAROS  O60783
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
28S ribosomal protein S15, mitochondrialL257Homo sapiensMutation(s): 0 
Gene Names: MRPS15RPMS15DC37
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
28S ribosomal protein S16, mitochondrialM137Homo sapiensMutation(s): 0 
Gene Names: MRPS16RPMS16CGI-132
Find proteins for Q9Y3D3 (Homo sapiens)
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PHAROS  Q9Y3D3
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
28S ribosomal protein S17, mitochondrialN130Homo sapiensMutation(s): 0 
Gene Names: MRPS17RPMS17HSPC011
Find proteins for Q9Y2R5 (Homo sapiens)
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
28S ribosomal protein S18b, mitochondrialO258Homo sapiensMutation(s): 0 
Gene Names: MRPS18BC6orf14HSPC183PTD017
Find proteins for Q9Y676 (Homo sapiens)
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PHAROS  Q9Y676
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
28S ribosomal protein S18c, mitochondrialP142Homo sapiensMutation(s): 0 
Gene Names: MRPS18CCGI-134
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PHAROS  Q9Y3D5
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
28S ribosomal protein S21, mitochondrialQ86Homo sapiensMutation(s): 1 
Gene Names: MRPS21RPMS21MDS016
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PHAROS  P82921
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
28S ribosomal protein S22, mitochondrialR360Homo sapiensMutation(s): 0 
Gene Names: MRPS22C3orf5RPMS22GK002
Find proteins for P82650 (Homo sapiens)
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PHAROS  P82650
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
28S ribosomal protein S23, mitochondrialS190Homo sapiensMutation(s): 0 
Gene Names: MRPS23CGI-138HSPC329
Find proteins for Q9Y3D9 (Homo sapiens)
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PHAROS  Q9Y3D9
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
28S ribosomal protein S25, mitochondrialT173Homo sapiensMutation(s): 0 
Gene Names: MRPS25RPMS25
Find proteins for P82663 (Homo sapiens)
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PHAROS  P82663
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
28S ribosomal protein S26, mitochondrialU205Homo sapiensMutation(s): 0 
Gene Names: MRPS26C20orf193RPMS13
Find proteins for Q9BYN8 (Homo sapiens)
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PHAROS  Q9BYN8
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
28S ribosomal protein S27, mitochondrialV414Homo sapiensMutation(s): 0 
Gene Names: MRPS27KIAA0264
Find proteins for Q92552 (Homo sapiens)
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PHAROS  Q92552
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
28S ribosomal protein S28, mitochondrialW187Homo sapiensMutation(s): 0 
Gene Names: MRPS28MRPS35HSPC007
Find proteins for Q9Y2Q9 (Homo sapiens)
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PHAROS  Q9Y2Q9
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
28S ribosomal protein S29, mitochondrialX398Homo sapiensMutation(s): 0 
Gene Names: DAP3MRPS29
Find proteins for P51398 (Homo sapiens)
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PHAROS  P51398
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
28S ribosomal protein S31, mitochondrialY395Homo sapiensMutation(s): 0 
Gene Names: MRPS31IMOGN38
Find proteins for Q92665 (Homo sapiens)
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PHAROS  Q92665
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
28S ribosomal protein S33, mitochondrialZ106Homo sapiensMutation(s): 0 
Gene Names: MRPS33CGI-139PTD003
Find proteins for Q9Y291 (Homo sapiens)
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PHAROS  Q9Y291
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
28S ribosomal protein S34, mitochondrial0218Homo sapiensMutation(s): 0 
Gene Names: MRPS34
Find proteins for P82930 (Homo sapiens)
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PHAROS  P82930
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
28S ribosomal protein S35, mitochondrial1323Homo sapiensMutation(s): 0 
Gene Names: MRPS35MRPS28HDCMD11PMDS023PSEC0213
Find proteins for P82673 (Homo sapiens)
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PHAROS  P82673
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
Coiled-coil-helix-coiled-coil-helix domain-containing protein 12117Homo sapiensMutation(s): 0 
Gene Names: CHCHD1C10orf34MRPS37
Find proteins for Q96BP2 (Homo sapiens)
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PHAROS  Q96BP2
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
Aurora kinase A-interacting protein3199Homo sapiensMutation(s): 0 
Gene Names: AURKAIP1AIPAKIPMRPS38
Find proteins for Q9NWT8 (Homo sapiens)
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PHAROS  Q9NWT8
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
Pentatricopeptide repeat domain-containing protein 3, mitochondrial4689Homo sapiensMutation(s): 0 
Gene Names: PTCD3MRPS39TRG15
Find proteins for Q96EY7 (Homo sapiens)
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PHAROS  Q96EY7
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
Translation initiation factor IF-3, mitochondrial8285Homo sapiensMutation(s): 2 
Gene Names: MTIF3DC38
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PHAROS  Q9H2K0
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Entity ID: 1
MoleculeChainsLengthOrganism
12S mitochondrial rRNAA955Homo sapiens
Small Molecules
Ligands 9 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

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A
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
SRY
Query on SRY

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A
STREPTOMYCIN
C21 H39 N7 O12
UCSJYZPVAKXKNQ-HZYVHMACSA-N
 Ligand Interaction
GNP
Query on GNP

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X
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
 Ligand Interaction
ATP
Query on ATP

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X
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
SPM
Query on SPM

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A
SPERMINE
C10 H26 N4
PFNFFQXMRSDOHW-UHFFFAOYSA-N
 Ligand Interaction
FES
Query on FES

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P, T
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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O
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

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A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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3, A, B, X
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
AYA
Query on AYA
QL-PEPTIDE LINKINGC5 H9 N O3ALA
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.97 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-06-03
    Type: Initial release
  • Version 1.1: 2020-07-01
    Changes: Database references