6GB2

Unique features of mammalian mitochondrial translation initiation revealed by cryo-EM. This file contains the 39S ribosomal subunit.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 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
  • Structures With Same Primary Citation

  • 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 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: 2
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein L27B0148Sus scrofaMutation(s): 0 
Gene Names: MRPL27
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein L28B1256Sus scrofaMutation(s): 0 
Gene Names: MRPL28
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
'Mitochondrial ribosomal protein L30B3161Sus scrofaMutation(s): 0 
Gene Names: MRPL30
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
'Mitochondrial ribosomal protein L55B4126Sus scrofaMutation(s): 0 
Gene Names: MRPL55
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein L32B5188Sus scrofaMutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein L33B665Sus scrofaMutation(s): 0 
Gene Names: MRPL33
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein L34B795Sus scrofaMutation(s): 0 
Gene Names: MRPL34
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein L35B8188Sus scrofaMutation(s): 0 
Gene Names: MRPL35
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
ICT1BE348Sus scrofaMutation(s): 0 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein L9BI268Sus scrofaMutation(s): 0 
Gene Names: MRPL9
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein L10BJ262Sus scrofaMutation(s): 0 
Gene Names: MRPL10
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein L14BO145Sus scrofaMutation(s): 0 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein L15BP296Sus scrofaMutation(s): 0 
Gene Names: MRPL15
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein L16BQ251Sus scrofaMutation(s): 0 
Gene Names: MRPL16
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein L17BR169Sus scrofaMutation(s): 0 
Gene Names: MRPL17
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein L18BS180Sus scrofaMutation(s): 0 
Gene Names: MRPL18
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein L19BT292Sus scrofaMutation(s): 0 
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein L20BU149Sus scrofaMutation(s): 0 
Gene Names: MRPL20
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein L22BW210Sus scrofaMutation(s): 0 
Gene Names: MRPL22
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein L24BY216Sus scrofaMutation(s): 0 
Gene Names: MRPL24
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein L37Ba423Sus scrofaMutation(s): 0 
Gene Names: MRPL37
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein L38Bb380Sus scrofaMutation(s): 0 
Gene Names: MRPL38
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein L39Bc334Sus scrofaMutation(s): 0 
Gene Names: MRPL39
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein L40Bd206Sus scrofaMutation(s): 0 
Gene Names: MRPL40
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein L41Be135Sus scrofaMutation(s): 0 
Gene Names: MRPL41
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein L42Bf142Sus scrofaMutation(s): 0 
Gene Names: MRPL42
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein L43Bg159Sus scrofaMutation(s): 0 
Gene Names: MRPL43
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein L44Bh332Sus scrofaMutation(s): 0 
Gene Names: MRPL44
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein L48Bk212Sus scrofaMutation(s): 0 
Gene Names: MRPL48
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
Mrpl34Bl166Sus scrofaMutation(s): 0 
Gene Names: MRPL49
Find proteins for A0A0R4J8D6 (Sus scrofa)
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein L50Bm159Sus scrofaMutation(s): 0 
Gene Names: MRPL50
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein L51Bn128Sus scrofaMutation(s): 0 
Gene Names: MRPL51
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein L52Bo124Sus scrofaMutation(s): 0 
Gene Names: MRPL52
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
mL53, MRPL53Bp112Sus scrofaMutation(s): 0 
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized proteinBq138Sus scrofaMutation(s): 0 
Gene Names: MRPL54
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein L57Bt102Sus scrofaMutation(s): 0 
Gene Names: MRPL57
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein L58Bu205Sus scrofaMutation(s): 0 
Gene Names: MRPL58
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
'Mitochondrial ribosomal protein L59Bv222Sus scrofaMutation(s): 0 
Gene Names: GADD45GIP1
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
mL65, MRPS30Bw433Sus scrofaMutation(s): 0 
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein S18ABx196Sus scrofaMutation(s): 0 
Gene Names: MRPS18A
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
unassigned secondary structure elementsBz82Sus scrofaMutation(s): 0 
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein L12BL, CL, DL, EL, FL, GL, HL198Sus scrofaMutation(s): 0 
Gene Names: MRPL12
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Ribosomal proteinB9100Sus scrofaMutation(s): 0 
Gene Names: MRPL36
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Translation initiation factor IF-2, mitochondrialBC657Homo sapiensMutation(s): 0 
Gene Names: MTIF2
Find proteins for P46199 (Homo sapiens)
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NIH Common Fund Data Resources
PHAROS  P46199
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein L2BD306Sus scrofaMutation(s): 0 
Gene Names: MRPL2
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein L4BF294Sus scrofaMutation(s): 0 
Gene Names: MRPL4
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein L11BK192Sus scrofaMutation(s): 0 
Gene Names: MRPL11
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein L13BN178Sus scrofaMutation(s): 0 
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein L21BV209Sus scrofaMutation(s): 0 
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein L23BX150Sus scrofaMutation(s): 0 
Gene Names: MRPL23
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein L47B2252Sus scrofaMutation(s): 0 
Gene Names: MRPL47
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein L45Bi306Sus scrofaMutation(s): 0 
Gene Names: MRPL45
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein L46Bj279Sus scrofaMutation(s): 0 
Gene Names: MRPL46
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Entity ID: 12
MoleculeChainsLengthOrganism
16S ribosomal RNA, mitochondrialBA1571Sus scrofa

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Entity ID: 13
MoleculeChainsLengthOrganism
CP tRNAPhe, mitochondrialBB73Sus scrofa

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Entity ID: 56
MoleculeChainsLengthOrganism
P-site fMet-tRNAMet, mitochondrialAV71Homo sapiens
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GSP
Query on GSP

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BC
5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE
C10 H16 N5 O13 P3 S
XOFLBQFBSOEHOG-UUOKFMHZSA-N
 Ligand Interaction
5GP
Query on 5GP

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BA
GUANOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O8 P
RQFCJASXJCIDSX-UUOKFMHZSA-N
 Ligand Interaction
SPM
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BA, BR
SPERMINE
C10 H26 N4
PFNFFQXMRSDOHW-UHFFFAOYSA-N
 Ligand Interaction
FME
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AV
N-FORMYLMETHIONINE
C6 H11 N O3 S
PYUSHNKNPOHWEZ-YFKPBYRVSA-N
 Ligand Interaction
ZN
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B5, B9, BJ
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
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B3, BA, BB, BC, BD, BP, BQ, Be, Bl, Bt
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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BC
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 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 

  • Version 1.0: 2018-08-08
    Type: Initial release
  • Version 1.1: 2018-08-22
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-11
    Changes: Other