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
  • 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 L19
BT
292Sus scrofaMutation(s): 0 
Gene Names: MRPL19
Find proteins for I3LNJ0 (Sus scrofa)
Go to UniProtKB:  I3LNJ0

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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein S7
AG
242Sus scrofaMutation(s): 0 
Gene Names: MRPS7
Find proteins for A0A286ZJ25 (Sus scrofa)
Go to UniProtKB:  A0A286ZJ25

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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein S9
AI
397Sus scrofaMutation(s): 0 
Gene Names: MRPS9
Find proteins for I3LU08 (Sus scrofa)
Go to UniProtKB:  I3LU08

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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein S11
AK
196Sus scrofaMutation(s): 0 
Gene Names: MRPS11
Find proteins for A0A286ZJJ6 (Sus scrofa)
Go to UniProtKB:  A0A286ZJJ6

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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein S15
AO
239Sus scrofaMutation(s): 0 
Gene Names: MRPS15
Find proteins for A0A287BMP0 (Sus scrofa)
Go to UniProtKB:  A0A287BMP0

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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein S17
AQ
130Sus scrofaMutation(s): 0 
Gene Names: MRPS17
Find proteins for F1RIU0 (Sus scrofa)
Go to UniProtKB:  F1RIU0

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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein S18C
AR
143Sus scrofaMutation(s): 0 
Find proteins for A0A0M3KL54 (Sus scrofa)
Go to UniProtKB:  A0A0M3KL54
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
unassigned secondary structure elements
AZ
18Sus scrofaMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
Mitoribosomal protein ms28, mrps28
Af
188Sus scrofaMutation(s): 0 
Gene Names: MRPS28
Find proteins for A0A0M3KL56 (Sus scrofa)
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein S35
Ak
325Sus scrofaMutation(s): 0 
Gene Names: MRPS35
Find proteins for F1SG95 (Sus scrofa)
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein S37
Am
118Sus scrofaMutation(s): 0 
Gene Names: CHCHD1
Find proteins for F1SU49 (Sus scrofa)
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein S39
Ao
692Sus scrofaMutation(s): 0 
Find proteins for K7GKS8 (Sus scrofa)
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
28S ribosomal protein S18b, mitochondrial
Ap
258Sus scrofaMutation(s): 0 
Gene Names: MRPS18B
Find proteins for Q767K8 (Sus scrofa)
Go to UniProtKB:  Q767K8

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Translation initiation factor IF-2, mitochondrial
BC
657Homo sapiensMutation(s): 0 
Gene Names: MTIF2
Find proteins for P46199 (Homo sapiens)
Go to UniProtKB:  P46199
NIH Common Fund Data Resources
PHAROS  P46199

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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein S10
AJ
201Sus scrofaMutation(s): 0 
Gene Names: MRPS10
Find proteins for F1RUU2 (Sus scrofa)
Go to UniProtKB:  F1RUU2

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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein S12
AL
139Sus scrofaMutation(s): 0 
Find proteins for A0A0M3KL52 (Sus scrofa)
Go to UniProtKB:  A0A0M3KL52

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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein S14
AN
128Sus scrofaMutation(s): 0 
Gene Names: MRPS14
Find proteins for A0A0M3KL53 (Sus scrofa)
Go to UniProtKB:  A0A0M3KL53

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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
bS16m, MRPS16
AP
135Sus scrofaMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein S21
AU
87Sus scrofaMutation(s): 0 
Gene Names: MRPS21
Find proteins for A0A286ZNB3 (Sus scrofa)
Go to UniProtKB:  A0A286ZNB3

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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein S22
Aa
382Sus scrofaMutation(s): 0 
Gene Names: MRPS22
Find proteins for A0A287AQT5 (Sus scrofa)
Go to UniProtKB:  A0A287AQT5

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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein S23
Ab
190Sus scrofaMutation(s): 0 
Gene Names: MRPS23
Find proteins for A0A287AEW3 (Sus scrofa)
Go to UniProtKB:  A0A287AEW3

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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein S25
Ac
173Sus scrofaMutation(s): 0 
Gene Names: MRPS25
Find proteins for A0A0M3KL55 (Sus scrofa)
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein S26
Ad
205Sus scrofaMutation(s): 0 
Gene Names: GNRH2
Find proteins for A0A287AY01 (Sus scrofa)
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein S27
Ae
390Sus scrofaMutation(s): 0 
Gene Names: MRPS27
Find proteins for I3LK09 (Sus scrofa)
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
Death associated protein 3
Ag
397Sus scrofaMutation(s): 0 
Gene Names: DAP3
Find proteins for I3LS10 (Sus scrofa)
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
mS31, MRPS31
Ah
387Sus scrofaMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein S33
Ai
106Sus scrofaMutation(s): 0 
Gene Names: MRPS33
Find proteins for F1S8G3 (Sus scrofa)
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein S34
Aj
218Sus scrofaMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
Aurora kinase A interacting protein 1
An
199Sus scrofaMutation(s): 0 
Gene Names: AURKAIP1
Find proteins for A0A287B3R8 (Sus scrofa)
Go to UniProtKB:  A0A287B3R8

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein S2
AB
289Sus scrofaMutation(s): 0 
Gene Names: MRPS2
Find proteins for F1S001 (Sus scrofa)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein S24
AC
167Sus scrofaMutation(s): 0 
Gene Names: MRPS24
Find proteins for A0A287ANU4 (Sus scrofa)
Go to UniProtKB:  A0A287ANU4

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein S5
AE
430Sus scrofaMutation(s): 0 
Gene Names: MRPS5
Find proteins for F1SU66 (Sus scrofa)
Go to UniProtKB:  F1SU66

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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein S6
AF
124Sus scrofaMutation(s): 0 
Gene Names: MRPS6
Find proteins for I3LEJ9 (Sus scrofa)
Go to UniProtKB:  I3LEJ9

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Entity ID: 3
MoleculeChainsLengthOrganism
12S ribosomal RNA, mitochondrialAA962Sus scrofa

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Entity ID: 19
MoleculeChainsLengthOrganism
P-site fMet-tRNAMet, mitochondrialAV71Homo sapiens

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Entity ID: 20
MoleculeChainsLengthOrganism
MT-CO3 mRNA, mitochondrialAX201Homo sapiens
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GSP
Query on GSP

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

Download CCD File 
Ag
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
SPM
Query on SPM

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AA
SPERMINE
C10 H26 N4
PFNFFQXMRSDOHW-UHFFFAOYSA-N
 Ligand Interaction
FME
Query on FME

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AV
N-FORMYLMETHIONINE
C6 H11 N O3 S
PYUSHNKNPOHWEZ-YFKPBYRVSA-N
 Ligand Interaction
ZN
Query on ZN

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AR, Ac, Ap
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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AA, AB, AX, Ag, An, BC
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: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



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: 2019-12-18
    Changes: Other