4V19 | pdb_00004v19

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 2.3 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: https://doi.org/10.1038/nature13895
  • Primary Citation Related Structures: 
    4V19, 4V1A

  • 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 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 Biology and Biophysics, Otto-Stern-Weg 5, ETH Zurich, CH-8093 Zurich, Switzerland.

Macromolecule Content 

  • Total Structure Weight: 1,176.43 kDa 
  • Atom Count: 69,409 
  • Modeled Residue Count: 5,944 
  • Deposited Residue Count: 7,332 
  • Unique protein chains: 28
  • Unique nucleic acid chains: 3

Macromolecules


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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN BL27M, MRPL27A [auth 0]148Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A4X1U0F6 (Sus scrofa)
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN BL28M, MRPL28B [auth 1]256Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A286ZTW8 (Sus scrofa)
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN UL29M, MRPL47C [auth 2]252Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN UL30M, MRPL30D [auth 3]161Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN BL31M, MRPL55E [auth 4]126Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN BL32M, MRPL32F [auth 5]188Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN BL33M, MRPL33G [auth 6]65Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A4X1TLP9 (Sus scrofa)
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN BL34M, MRPL34H [auth 7]95Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A4X1UFR4 (Sus scrofa)
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN BL35M, MRPL35I [auth 8]188Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A5G2QZK0 (Sus scrofa)
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN BL36M, MRPL36J [auth 9]100Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A287A731 (Sus scrofa)
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN UL2M, MRPL2N [auth D]306Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A287A143 (Sus scrofa)
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN UL3M, MRPL3O [auth E]348Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A140UHW4 (Sus scrofa)
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN UL4M, MRPL4P [auth F]294Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A287B2W3 (Sus scrofa)
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN BL9M, MRPL9Q [auth I]268Sus scrofaMutation(s): 0 
UniProt
Find proteins for I3LR45 (Sus scrofa)
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN UL10M, MRPL10R [auth J]262Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A480VPY3 (Sus scrofa)
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN UL11M, MRPL11S [auth K]192Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A480KRD0 (Sus scrofa)
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN UL13M, MRPL13T [auth N]178Sus scrofaMutation(s): 0 
UniProt
Find proteins for K7GP19 (Sus scrofa)
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN UL14M, MRPL14U [auth O]145Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A287BMZ6 (Sus scrofa)
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Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN UL15M, MRPL15V [auth P]296Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A8D0HMG9 (Sus scrofa)
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Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN UL16M, MRPL16W [auth Q]251Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A480MAF3 (Sus scrofa)
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Entity ID: 24
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN BL17M, MRPL17X [auth R]169Sus scrofaMutation(s): 0 
UniProt
Find proteins for F1RMQ4 (Sus scrofa)
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Entity ID: 25
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN UL18M, MRPL18Y [auth S]180Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A0R4J8D5 (Sus scrofa)
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Entity ID: 26
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN BL19M, MRPL19Z [auth T]292Sus scrofaMutation(s): 0 
UniProt
Find proteins for I3LNJ0 (Sus scrofa)
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Entity ID: 27
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN BL20M, MRPL20AA [auth U]149Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A286ZU56 (Sus scrofa)
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Entity ID: 28
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN BL21M, MRPL21BA [auth V]209Sus scrofaMutation(s): 0 
UniProt
Find proteins for F1RY70 (Sus scrofa)
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Entity ID: 29
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN UL22M, MRPL22CA [auth W]210Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A4X1TXR4 (Sus scrofa)
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Entity ID: 30
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN UL23M, MRPL23DA [auth X]150Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A480JJI1 (Sus scrofa)
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Entity ID: 31
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN UL24M, MRPL24EA [auth Y]216Sus scrofaMutation(s): 0 
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Entity ID: 11
MoleculeChains LengthOrganismImage
MITORIBOSOMAL 16S RRNAK [auth A]1,570Sus scrofa
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Entity ID: 12
MoleculeChains LengthOrganismImage
MITORIBOSOMAL CP TRNAL [auth B]62Sus scrofa
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Entity ID: 13
MoleculeChains LengthOrganismImage
TRNAFA [auth Z],
M [auth C]
3Sus scrofa
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN

Query on ZN



Download:Ideal Coordinates CCD File
GA [auth 5],
HA [auth 9]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
AB [auth A]
AC [auth A]
AD [auth A]
AE [auth A]
AF [auth A]
AB [auth A],
AC [auth A],
AD [auth A],
AE [auth A],
AF [auth A],
AG [auth A],
BB [auth A],
BC [auth A],
BD [auth A],
BE [auth A],
BF [auth A],
BG [auth A],
CB [auth A],
CC [auth A],
CD [auth A],
CE [auth A],
CF [auth A],
CG [auth A],
DB [auth A],
DC [auth A],
DD [auth A],
DE [auth A],
DF [auth A],
DG [auth A],
EB [auth A],
EC [auth A],
ED [auth A],
EE [auth A],
EF [auth A],
EG [auth A],
FB [auth A],
FC [auth A],
FD [auth A],
FE [auth A],
FF [auth A],
FG [auth A],
GB [auth A],
GC [auth A],
GD [auth A],
GE [auth A],
GF [auth A],
GG [auth A],
HB [auth A],
HC [auth A],
HD [auth A],
HE [auth A],
HF [auth A],
HG [auth A],
IA [auth A],
IB [auth A],
IC [auth A],
ID [auth A],
IE [auth A],
IF [auth A],
IG [auth A],
JA [auth A],
JB [auth A],
JC [auth A],
JD [auth A],
JE [auth A],
JF [auth A],
JG [auth A],
KA [auth A],
KB [auth A],
KC [auth A],
KD [auth A],
KE [auth A],
KF [auth A],
KG [auth A],
LA [auth A],
LB [auth A],
LC [auth A],
LD [auth A],
LE [auth A],
LF [auth A],
LG [auth A],
MA [auth A],
MB [auth A],
MC [auth A],
MD [auth A],
ME [auth A],
MF [auth A],
MG [auth A],
NA [auth A],
NB [auth A],
NC [auth A],
ND [auth A],
NE [auth A],
NF [auth A],
NG [auth A],
OA [auth A],
OB [auth A],
OC [auth A],
OD [auth A],
OE [auth A],
OF [auth A],
OG [auth A],
PA [auth A],
PB [auth A],
PC [auth A],
PD [auth A],
PE [auth A],
PF [auth A],
PG [auth D],
QA [auth A],
QB [auth A],
QC [auth A],
QD [auth A],
QE [auth A],
QF [auth A],
QG [auth D],
RA [auth A],
RB [auth A],
RC [auth A],
RD [auth A],
RE [auth A],
RF [auth A],
RG [auth P],
SA [auth A],
SB [auth A],
SC [auth A],
SD [auth A],
SE [auth A],
SF [auth A],
SG [auth P],
TA [auth A],
TB [auth A],
TC [auth A],
TD [auth A],
TE [auth A],
TF [auth A],
TG [auth Q],
UA [auth A],
UB [auth A],
UC [auth A],
UD [auth A],
UE [auth A],
UF [auth A],
UG [auth R],
VA [auth A],
VB [auth A],
VC [auth A],
VD [auth A],
VE [auth A],
VF [auth A],
WA [auth A],
WB [auth A],
WC [auth A],
WD [auth A],
WE [auth A],
WF [auth A],
XA [auth A],
XB [auth A],
XC [auth A],
XD [auth A],
XE [auth A],
XF [auth A],
YA [auth A],
YB [auth A],
YC [auth A],
YD [auth A],
YE [auth A],
YF [auth A],
ZA [auth A],
ZB [auth A],
ZC [auth A],
ZD [auth A],
ZE [auth A],
ZF [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONEMAN1.9
RECONSTRUCTIONRELION

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-08
    Type: Initial release
  • Version 1.1: 2014-10-15
    Changes: Database references
  • Version 1.2: 2014-11-19
    Changes: Database references
  • Version 2.0: 2017-08-02
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2019-10-02
    Changes: Data collection, Derived calculations, Other
  • Version 2.2: 2019-10-23
    Changes: Data collection, Other
  • Version 2.3: 2024-05-08
    Changes: Data collection, Database references, Derived calculations