6RW5

Structure of human mitochondrial 28S ribosome in complex with mitochondrial IF2 and IF3


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.14 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
  • Primary Citation of Related Structures:  
    6RW4, 6RW5

  • 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 inv ...

    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 LengthOrganismDetailsImage
28S ribosomal protein S2, mitochondrial B296Homo sapiensMutation(s): 0 
Gene Names: MRPS2CGI-91
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S24, mitochondrial C167Homo sapiensMutation(s): 0 
Gene Names: MRPS24HSPC335
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S5, mitochondrial D430Homo sapiensMutation(s): 0 
Gene Names: MRPS5
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S6, mitochondrial E125Homo sapiensMutation(s): 0 
Gene Names: MRPS6C21orf101RPMS6
Find proteins for P82932 (Homo sapiens)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S7, mitochondrial F242Homo sapiensMutation(s): 0 
Gene Names: MRPS7
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S9, mitochondrial G396Homo sapiensMutation(s): 0 
Gene Names: MRPS9RPMS9
Find proteins for P82933 (Homo sapiens)
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S10, mitochondrial H201Homo sapiensMutation(s): 0 
Gene Names: MRPS10MSTP040
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S11, mitochondrial I194Homo sapiensMutation(s): 0 
Gene Names: MRPS11RPMS11HCC2
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S12, mitochondrial J138Homo sapiensMutation(s): 0 
Gene Names: MRPS12RPMS12RPSM12
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S14, mitochondrial K128Homo sapiensMutation(s): 0 
Gene Names: MRPS14
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S15, mitochondrial L257Homo sapiensMutation(s): 0 
Gene Names: MRPS15RPMS15DC37
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S16, mitochondrial M137Homo sapiensMutation(s): 0 
Gene Names: MRPS16RPMS16CGI-132
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S17, mitochondrial N130Homo sapiensMutation(s): 0 
Gene Names: MRPS17RPMS17HSPC011
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S18b, mitochondrial O258Homo sapiensMutation(s): 0 
Gene Names: MRPS18BC6orf14HSPC183PTD017
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S18c, mitochondrial P142Homo sapiensMutation(s): 0 
Gene Names: MRPS18CCGI-134
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S21, mitochondrial Q86Homo sapiensMutation(s): 1 
Gene Names: MRPS21RPMS21MDS016
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S22, mitochondrial R360Homo sapiensMutation(s): 0 
Gene Names: MRPS22C3orf5RPMS22GK002
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S23, mitochondrial S190Homo sapiensMutation(s): 0 
Gene Names: MRPS23CGI-138HSPC329
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S25, mitochondrial T173Homo sapiensMutation(s): 0 
Gene Names: MRPS25RPMS25
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S26, mitochondrial U205Homo sapiensMutation(s): 0 
Gene Names: MRPS26C20orf193RPMS13
Find proteins for Q9BYN8 (Homo sapiens)
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S27, mitochondrial V414Homo sapiensMutation(s): 0 
Gene Names: MRPS27KIAA0264
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S28, mitochondrial W187Homo sapiensMutation(s): 0 
Gene Names: MRPS28MRPS35HSPC007
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S29, mitochondrial X398Homo sapiensMutation(s): 0 
Gene Names: DAP3MRPS29
Find proteins for P51398 (Homo sapiens)
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S31, mitochondrial Y395Homo sapiensMutation(s): 0 
Gene Names: MRPS31IMOGN38
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S33, mitochondrial Z106Homo sapiensMutation(s): 0 
Gene Names: MRPS33CGI-139PTD003
Find proteins for Q9Y291 (Homo sapiens)
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S34, mitochondrial 0218Homo sapiensMutation(s): 0 
Gene Names: MRPS34
Find proteins for P82930 (Homo sapiens)
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S35, mitochondrial 1323Homo sapiensMutation(s): 0 
Gene Names: MRPS35MRPS28HDCMD11PMDS023PSEC0213
Find proteins for P82673 (Homo sapiens)
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
Coiled-coil-helix-coiled-coil-helix domain-containing protein 1 2117Homo sapiensMutation(s): 0 
Gene Names: CHCHD1C10orf34MRPS37
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
Aurora kinase A-interacting protein 3199Homo sapiensMutation(s): 0 
Gene Names: AURKAIP1AIPAKIPMRPS38
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
Pentatricopeptide repeat domain-containing protein 3, mitochondrial 4689Homo sapiensMutation(s): 0 
Gene Names: PTCD3MRPS39TRG15
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
Translation initiation factor IF-2, mitochondrial 7699Homo sapiensMutation(s): 0 
Gene Names: MTIF2
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
Translation initiation factor IF-3, mitochondrial 8285Homo sapiensMutation(s): 2 
Gene Names: MTIF3DC38
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Entity ID: 1
MoleculeChainsLengthOrganismImage
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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7, 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, 7, 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: 3.14 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