4V19

Structure of the large subunit of the mammalian mitoribosome, part 1 of 2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.4 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 2.2 of the entry. See complete history

Literature

The Complete Structure of the Large Subunit of the Mammalian Mitochondrial Ribosome

Greber, B.J.Boehringer, D.Leibundgut, M.Bieri, P.Leitner, A.Schmitz, N.Aebersold, R.Ban, N.

(2014) Nature 515: 283

  • DOI: 10.1038/nature13895
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Mitochondrial ribosomes (mitoribosomes) are extensively modified ribosomes of bacterial descent specialized for the synthesis and insertion of membrane proteins that are critical for energy conversion and ATP production inside mitochondria. Mammalian ...

    Mitochondrial ribosomes (mitoribosomes) are extensively modified ribosomes of bacterial descent specialized for the synthesis and insertion of membrane proteins that are critical for energy conversion and ATP production inside mitochondria. Mammalian mitoribosomes, which comprise 39S and 28S subunits, have diverged markedly from the bacterial ribosomes from which they are derived, rendering them unique compared to bacterial, eukaryotic cytosolic and fungal mitochondrial ribosomes. We have previously determined at 4.9 Å resolution the architecture of the porcine (Sus scrofa) 39S subunit, which is highly homologous to the human mitoribosomal large subunit. Here we present the complete atomic structure of the porcine 39S large mitoribosomal subunit determined in the context of a stalled translating mitoribosome at 3.4 Å resolution by cryo-electron microscopy and chemical crosslinking/mass spectrometry. The structure reveals the locations and the detailed folds of 50 mitoribosomal proteins, shows the highly conserved mitoribosomal peptidyl transferase active site in complex with its substrate transfer RNAs, and defines the path of the nascent chain in mammalian mitoribosomes along their idiosyncratic exit tunnel. Furthermore, we present evidence that a mitochondrial tRNA has become an integral component of the central protuberance of the 39S subunit where it architecturally substitutes for the absence of the 5S ribosomal RNA, a ubiquitous component of all cytoplasmic ribosomes.


    Organizational Affiliation

    Department of Biology, Institute of Molecular Systems Biology, Auguste-Piccard-Hof 1, ETH Zurich, CH-8093 Zurich, Switzerland.,Department of Biology, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, ETH Zurich, CH-8093 Zurich, Switzerland.,1] Department of Biology, Institute of Molecular Systems Biology, Auguste-Piccard-Hof 1, ETH Zurich, CH-8093 Zurich, Switzerland [2] Faculty of Science, University of Zurich, CH-8057 Zurich, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN BL27M, MRPL27
0
148Sus scrofaMutation(s): 0 
Gene Names: MRPL27
Find proteins for F1RT79 (Sus scrofa)
Go to Gene View: MRPL27
Go to UniProtKB:  F1RT79
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN BL28M, MRPL28
1
256Sus scrofaMutation(s): 0 
Gene Names: MRPL18
Find proteins for A0A0R4J8D5 (Sus scrofa)
Go to Gene View: MRPL18
Go to UniProtKB:  A0A0R4J8D5
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN UL29M, MRPL47
2
252Sus scrofaMutation(s): 0 
Gene Names: MRPL47
Find proteins for F1SGC7 (Sus scrofa)
Go to Gene View: MRPL47
Go to UniProtKB:  F1SGC7
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN UL30M, MRPL30
3
161Sus scrofaMutation(s): 0 
Gene Names: MRPL30
Find proteins for F1STE5 (Sus scrofa)
Go to Gene View: MRPL30
Go to UniProtKB:  F1STE5
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN BL31M, MRPL55
4
126N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN BL32M, MRPL32
5
188Sus scrofaMutation(s): 0 
Gene Names: MRPL32
Find proteins for I3LTC4 (Sus scrofa)
Go to Gene View: MRPL32
Go to UniProtKB:  I3LTC4
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN BL33M, MRPL33
6
65N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN BL34M, MRPL34
7
95Sus scrofa domesticusMutation(s): 0 
Gene Names: MRPL34
Find proteins for W5IDC1 (Sus scrofa domesticus)
Go to Gene View: MRPL34
Go to UniProtKB:  W5IDC1
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN BL35M, MRPL35
8
188Sus scrofaMutation(s): 0 
Gene Names: MRPL35
Find proteins for F1SVC5 (Sus scrofa)
Go to Gene View: MRPL35
Go to UniProtKB:  F1SVC5
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN BL36M, MRPL36
9
100N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN UL2M, MRPL2
D
306Sus scrofaMutation(s): 0 
Gene Names: MRPL2
Find proteins for F1RRN2 (Sus scrofa)
Go to Gene View: MRPL2
Go to UniProtKB:  F1RRN2
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN UL3M, MRPL3
E
348Sus scrofaMutation(s): 0 
Gene Names: MRPL18
Find proteins for A0A0R4J8D5 (Sus scrofa)
Go to Gene View: MRPL18
Go to UniProtKB:  A0A0R4J8D5
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN UL4M, MRPL4
F
294Sus scrofaMutation(s): 0 
Gene Names: MRPL4
Find proteins for F1S3J8 (Sus scrofa)
Go to Gene View: MRPL4
Go to UniProtKB:  F1S3J8
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN BL9M, MRPL9
I
268Sus scrofaMutation(s): 0 
Gene Names: MRPL9
Find proteins for I3LR45 (Sus scrofa)
Go to Gene View: MRPL9
Go to UniProtKB:  I3LR45
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN UL10M, MRPL10
J
262Sus scrofaMutation(s): 0 
Gene Names: MRPL10
Find proteins for F1RWJ0 (Sus scrofa)
Go to Gene View: MRPL10
Go to UniProtKB:  F1RWJ0
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN UL11M, MRPL11
K
192Sus scrofaMutation(s): 0 
Gene Names: MRPL11
Find proteins for F1RU54 (Sus scrofa)
Go to Gene View: MRPL11
Go to UniProtKB:  F1RU54
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN UL13M, MRPL13
N
178N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN UL14M, MRPL14
O
145Sus scrofaMutation(s): 0 
Gene Names: MRPL14
Find proteins for F1RQV7 (Sus scrofa)
Go to Gene View: MRPL14
Go to UniProtKB:  F1RQV7
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN UL15M, MRPL15
P
296Sus scrofaMutation(s): 0 
Gene Names: MRPL15
Find proteins for F1RSH0 (Sus scrofa)
Go to Gene View: MRPL15
Go to UniProtKB:  F1RSH0
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN UL16M, MRPL16
Q
251Sus scrofaMutation(s): 0 
Gene Names: MRPL16
Find proteins for F1RI89 (Sus scrofa)
Go to Gene View: MRPL16
Go to UniProtKB:  F1RI89
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN BL17M, MRPL17
R
169Sus scrofaMutation(s): 0 
Gene Names: MRPL17
Find proteins for F1RMQ4 (Sus scrofa)
Go to Gene View: MRPL17
Go to UniProtKB:  F1RMQ4
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN UL18M, MRPL18
S
180Sus scrofaMutation(s): 0 
Gene Names: MRPL18
Find proteins for A0A0R4J8D5 (Sus scrofa)
Go to Gene View: MRPL18
Go to UniProtKB:  A0A0R4J8D5
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN BL19M, MRPL19
T
292Sus scrofaMutation(s): 0 
Gene Names: MRPL19
Find proteins for I3LNJ0 (Sus scrofa)
Go to Gene View: MRPL19
Go to UniProtKB:  I3LNJ0
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN BL20M, MRPL20
U
149N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN BL21M, MRPL21
V
209Sus scrofaMutation(s): 0 
Gene Names: MRPL21
Find proteins for F1RY70 (Sus scrofa)
Go to Gene View: MRPL21
Go to UniProtKB:  F1RY70
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN UL22M, MRPL22
W
210N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN UL23M, MRPL23
X
150N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN UL24M, MRPL24
Y
216Sus scrofaMutation(s): 0 
Gene Names: MRPL24
Find proteins for F1RHJ1 (Sus scrofa)
Go to Gene View: MRPL24
Go to UniProtKB:  F1RHJ1
Entity ID: 11
MoleculeChainsLengthOrganism
MITORIBOSOMAL 16S RRNAA1570Sus scrofa
Entity ID: 12
MoleculeChainsLengthOrganism
MITORIBOSOMAL CP TRNAB62Sus scrofa
Entity ID: 13
MoleculeChainsLengthOrganism
TRNAC,Z3Sus scrofa
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
5, 9
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, D, P, Q, R
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
Y5P
Query on Y5P
B
RNA LINKINGC9 H15 N2 O7 P

--

P5P
Query on P5P
B
RNA LINKINGC10 H13 N4 O7 PA
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.4 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-10-08
    Type: Initial release
  • Version 1.1: 2014-10-15
    Type: Database references
  • Version 1.2: 2014-11-19
    Type: Database references
  • Version 2.0: 2017-08-02
    Type: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2019-10-02
    Type: Data collection, Derived calculations, Other
  • Version 2.2: 2019-10-23
    Type: Data collection, Other