6GAZ

Unique features of mammalian mitochondrial translation initiation revealed by cryo-EM. This file contains the 28S ribosomal subunit.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 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

Unique features of mammalian mitochondrial translation initiation revealed by cryo-EM.

Kummer, E.Leibundgut, M.Rackham, O.Lee, R.G.Boehringer, D.Filipovska, A.Ban, N.

(2018) Nature 560: 263-267

  • DOI: 10.1038/s41586-018-0373-y
  • Primary Citation of Related Structures:  
    6GAW, 6GAZ, 6GB2

  • PubMed Abstract: 
  • Mitochondria maintain their own specialized protein synthesis machinery, which in mammals is used exclusively for the synthesis of the membrane proteins responsible for oxidative phosphorylation 1,2 . The initiation of protein synthesis in mitochondria differs substantially from bacterial or cytosolic translation systems ...

    Mitochondria maintain their own specialized protein synthesis machinery, which in mammals is used exclusively for the synthesis of the membrane proteins responsible for oxidative phosphorylation 1,2 . The initiation of protein synthesis in mitochondria differs substantially from bacterial or cytosolic translation systems. Mitochondrial translation initiation lacks initiation factor 1, which is essential in all other translation systems from bacteria to mammals 3,4 . Furthermore, only one type of methionyl transfer RNA (tRNA Met ) is used for both initiation and elongation 4,5 , necessitating that the initiation factor specifically recognizes the formylated version of tRNA Met (fMet-tRNA Met ). Lastly, most mitochondrial mRNAs do not possess 5' leader sequences to promote mRNA binding to the ribosome 2 . There is currently little mechanistic insight into mammalian mitochondrial translation initiation, and it is not clear how mRNA engagement, initiator-tRNA recruitment and start-codon selection occur. Here we determine the cryo-EM structure of the complete translation initiation complex from mammalian mitochondria at 3.2 Å. We describe the function of an additional domain insertion that is present in the mammalian mitochondrial initiation factor 2 (mtIF2). By closing the decoding centre, this insertion stabilizes the binding of leaderless mRNAs and induces conformational changes in the rRNA nucleotides involved in decoding. We identify unique features of mtIF2 that are required for specific recognition of fMet-tRNA Met and regulation of its GTPase activity. Finally, we observe that the ribosomal tunnel in the initiating ribosome is blocked by insertion of the N-terminal portion of mitochondrial protein mL45, which becomes exposed as the ribosome switches to elongation mode and may have an additional role in targeting of mitochondrial ribosomes to the protein-conducting pore in the inner mitochondrial membrane.


    Organizational Affiliation

    Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland. ban@mol.biol.ethz.ch.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Translation initiation factor IF-2, mitochondrialA [auth BC]657Homo sapiensMutation(s): 0 
Gene Names: MTIF2
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PHAROS:  P46199
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L19B [auth BT]292Sus scrofaMutation(s): 0 
Gene Names: MRPL19
UniProt
Find proteins for I3LNJ0 (Sus scrofa)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S2D [auth AB]289Sus scrofaMutation(s): 0 
Gene Names: MRPS2
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S24E [auth AC]167Sus scrofaMutation(s): 0 
Gene Names: MRPS24
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S5F [auth AE]430Sus scrofaMutation(s): 0 
Gene Names: MRPS5
UniProt
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S6G [auth AF]124Sus scrofaMutation(s): 0 
Gene Names: MRPS6
UniProt
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S7H [auth AG]242Sus scrofaMutation(s): 0 
Gene Names: MRPS7
UniProt
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S9I [auth AI]397Sus scrofaMutation(s): 0 
Gene Names: MRPS9
UniProt
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S10J [auth AJ]201Sus scrofaMutation(s): 0 
Gene Names: MRPS10
UniProt
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S11K [auth AK]196Sus scrofaMutation(s): 0 
Gene Names: MRPS11
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S12L [auth AL]139Sus scrofaMutation(s): 0 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S14M [auth AN]128Sus scrofaMutation(s): 0 
Gene Names: MRPS14
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S15N [auth AO]239Sus scrofaMutation(s): 0 
Gene Names: MRPS15
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
bS16m, MRPS16O [auth AP]135Sus scrofaMutation(s): 0 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S17P [auth AQ]130Sus scrofaMutation(s): 0 
Gene Names: MRPS17
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S18CQ [auth AR]143Sus scrofaMutation(s): 0 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S21R [auth AU]87Sus scrofaMutation(s): 0 
Gene Names: MRPS21
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
unassigned secondary structure elementsU [auth AZ]18Sus scrofaMutation(s): 0 
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S22V [auth Aa]382Sus scrofaMutation(s): 0 
Gene Names: MRPS22
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S23W [auth Ab]190Sus scrofaMutation(s): 0 
Gene Names: MRPS23
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S25X [auth Ac]173Sus scrofaMutation(s): 0 
Gene Names: MRPS25
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S26Y [auth Ad]205Sus scrofaMutation(s): 0 
Gene Names: GNRH2
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S27Z [auth Ae]390Sus scrofaMutation(s): 0 
Gene Names: MRPS27
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
Mitoribosomal protein ms28, mrps28AA [auth Af]188Sus scrofaMutation(s): 0 
Gene Names: MRPS28
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
Death associated protein 3BA [auth Ag]397Sus scrofaMutation(s): 0 
Gene Names: DAP3
UniProt
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
mS31, MRPS31CA [auth Ah]387Sus scrofaMutation(s): 0 
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S33DA [auth Ai]106Sus scrofaMutation(s): 0 
Gene Names: MRPS33
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S34EA [auth Aj]218Sus scrofaMutation(s): 0 
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S35FA [auth Ak]325Sus scrofaMutation(s): 0 
Gene Names: MRPS35
UniProt
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S37GA [auth Am]118Sus scrofaMutation(s): 0 
Gene Names: CHCHD1
UniProt
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
Aurora kinase A interacting protein 1HA [auth An]199Sus scrofaMutation(s): 0 
Gene Names: AURKAIP1
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S39IA [auth Ao]692Sus scrofaMutation(s): 0 
Gene Names: PTCD3
UniProt
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S18b, mitochondrialJA [auth Ap]258Sus scrofaMutation(s): 0 
Gene Names: MRPS18B
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Entity ID: 3
MoleculeChainsLengthOrganismImage
12S ribosomal RNA, mitochondrialC [auth AA]962Sus scrofa
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Entity ID: 19
MoleculeChainsLengthOrganismImage
P-site fMet-tRNAMet, mitochondrialS [auth AV]71Homo sapiens
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Entity ID: 20
MoleculeChainsLengthOrganismImage
MT-CO3 mRNA, mitochondrialT [auth AX]201Homo sapiens
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Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GSP (Subject of Investigation/LOI)
Query on GSP

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KA [auth BC]5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE
C10 H16 N5 O13 P3 S
XOFLBQFBSOEHOG-UUOKFMHZSA-N
 Ligand Interaction
GTP (Subject of Investigation/LOI)
Query on GTP

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VE [auth Ag]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
SPM (Subject of Investigation/LOI)
Query on SPM

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OA [auth AA]SPERMINE
C10 H26 N4
PFNFFQXMRSDOHW-UHFFFAOYSA-N
 Ligand Interaction
FME (Subject of Investigation/LOI)
Query on FME

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SE [auth AV]N-FORMYLMETHIONINE
C6 H11 N O3 S
PYUSHNKNPOHWEZ-YFKPBYRVSA-N
 Ligand Interaction
ZN
Query on ZN

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RE [auth AR], UE [auth Ac], YE [auth Ap]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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AB [auth AA] , AC [auth AA] , AD [auth AA] , AE [auth AA] , BB [auth AA] , BC [auth AA] , BD [auth AA] , BE [auth AA] , 
AB [auth AA], AC [auth AA], AD [auth AA], AE [auth AA], BB [auth AA], BC [auth AA], BD [auth AA], BE [auth AA], CB [auth AA], CC [auth AA], CD [auth AA], CE [auth AA], DB [auth AA], DC [auth AA], DD [auth AA], DE [auth AA], EB [auth AA], EC [auth AA], ED [auth AA], EE [auth AA], FB [auth AA], FC [auth AA], FD [auth AA], FE [auth AA], GB [auth AA], GC [auth AA], GD [auth AA], GE [auth AA], HB [auth AA], HC [auth AA], HD [auth AA], HE [auth AA], IB [auth AA], IC [auth AA], ID [auth AA], IE [auth AA], JB [auth AA], JC [auth AA], JD [auth AA], JE [auth AA], KB [auth AA], KC [auth AA], KD [auth AA], KE [auth AA], LA [auth BC], LB [auth AA], LC [auth AA], LD [auth AA], LE [auth AA], MB [auth AA], MC [auth AA], MD [auth AA], ME [auth AA], NA [auth BC], NB [auth AA], NC [auth AA], ND [auth AA], NE [auth AA], OB [auth AA], OC [auth AA], OD [auth AA], OE [auth AA], PA [auth AA], PB [auth AA], PC [auth AA], PD [auth AA], PE [auth AA], QA [auth AA], QB [auth AA], QC [auth AA], QD [auth AA], QE [auth AB], RA [auth AA], RB [auth AA], RC [auth AA], RD [auth AA], SA [auth AA], SB [auth AA], SC [auth AA], SD [auth AA], TA [auth AA], TB [auth AA], TC [auth AA], TD [auth AA], TE [auth AX], UA [auth AA], UB [auth AA], UC [auth AA], UD [auth AA], VA [auth AA], VB [auth AA], VC [auth AA], VD [auth AA], WA [auth AA], WB [auth AA], WC [auth AA], WD [auth AA], WE [auth Ag], XA [auth AA], XB [auth AA], XC [auth AA], XD [auth AA], XE [auth An], YA [auth AA], YB [auth AA], YC [auth AA], YD [auth AA], ZA [auth AA], ZB [auth AA], ZC [auth AA], ZD [auth AA]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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MA [auth BC]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Molecular Biology OrganizationSwitzerlandALTF 1196-2014
Swiss National Science FoundationSwitzerland310030B_163478
Swiss National Science FoundationSwitzerland138262

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-08
    Type: Initial release
  • Version 1.1: 2018-08-22
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-18
    Changes: Other