7NSH

39S mammalian mitochondrial large ribosomal subunit with mtRRF (post) and mtEFG2


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

Structural basis of translation termination, rescue, and recycling in mammalian mitochondria.

Kummer, E.Schubert, K.N.Schoenhut, T.Scaiola, A.Ban, N.

(2021) Mol Cell 81: 2566-2582.e6

  • DOI: https://doi.org/10.1016/j.molcel.2021.03.042
  • Primary Citation of Related Structures:  
    7NQH, 7NQL, 7NSH, 7NSI, 7NSJ

  • PubMed Abstract: 

    The mitochondrial translation system originates from a bacterial ancestor but has substantially diverged in the course of evolution. Here, we use single-particle cryo-electron microscopy (cryo-EM) as a screening tool to identify mitochondrial translation termination mechanisms and to describe them in molecular detail. We show how mitochondrial release factor 1a releases the nascent chain from the ribosome when it encounters the canonical stop codons UAA and UAG. Furthermore, we define how the peptidyl-tRNA hydrolase ICT1 acts as a rescue factor on mitoribosomes that have stalled on truncated messages to recover them for protein synthesis. Finally, we present structural models detailing the process of mitochondrial ribosome recycling to explain how a dedicated elongation factor, mitochondrial EFG2 (mtEFG2), has specialized for cooperation with the mitochondrial ribosome recycling factor to dissociate the mitoribosomal subunits at the end of the translation process.


  • Organizational Affiliation

    Swiss Federal Institute of Technology, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, 8093 Zurich, Switzerland. Electronic address: eva.kummer@cpr.ku.dk.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L27A [auth B0]148Sus scrofaMutation(s): 0 
UniProt
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UniProt GroupA0A4X1U0F6
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
uL24mB [auth BY]216Sus scrofaMutation(s): 0 
UniProt
Find proteins for F1RHJ1 (Sus scrofa)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L37C [auth Ba]423Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L35D [auth B8]188Sus scrofaMutation(s): 0 
UniProt
Find proteins for F1SVC5 (Sus scrofa)
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L38E [auth Bb]380Sus scrofaMutation(s): 0 
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Find proteins for F1RW03 (Sus scrofa)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L39F [auth Bc]334Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L40G [auth Bd]206Sus scrofaMutation(s): 0 
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Find proteins for A0A5G2R2V2 (Sus scrofa)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L41H [auth Be]135Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A8D1F1K9 (Sus scrofa)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
mL42I [auth Bf]142Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L43J [auth Bg]159Sus scrofaMutation(s): 0 
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Find proteins for F1S8U4 (Sus scrofa)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
mL44K [auth Bh]332Sus scrofaMutation(s): 0 
UniProt
Find proteins for F1SR64 (Sus scrofa)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L45L [auth Bi]306Sus scrofaMutation(s): 0 
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Find proteins for I3LGM5 (Sus scrofa)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L46M [auth Bj]279Sus scrofaMutation(s): 0 
UniProt
Find proteins for F1SRT0 (Sus scrofa)
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L48, mitochondrialN [auth Bk]269Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A480J9Z6 (Sus scrofa)
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Mrpl34O [auth Bl]166Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A0R4J8D6 (Sus scrofa)
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L50P [auth Bm]198Sus scrofaMutation(s): 0 
UniProt
Find proteins for I3L9H6 (Sus scrofa)
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L51Q [auth Bn]128Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A8D1P1C8 (Sus scrofa)
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
mL52R [auth Bo]124Sus scrofaMutation(s): 0 
UniProt
Find proteins for F1S9B7 (Sus scrofa)
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
mL53S [auth Bp]112Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A341D604 (Neophocaena asiaeorientalis asiaeorientalis)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
mL54T [auth Bq]138Sus scrofaMutation(s): 0 
UniProt
Find proteins for I3LN63 (Sus scrofa)
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L57U [auth Bt]102Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A287BP93 (Sus scrofa)
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
mL62 (ICT1)V [auth Bu]205Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A286ZJR2 (Sus scrofa)
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
mL64W [auth Bv]222Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A286ZXA6 (Sus scrofa)
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein S30, mitochondrialX [auth Bw]433Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A480QIM3 (Sus scrofa)
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S18AY [auth Bx]196Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L12198Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A4X1U6S6 (Sus scrofa)
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L28AA [auth B1]256Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A286ZTW8 (Sus scrofa)
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal proteinEA [auth B9]100Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A287A731 (Sus scrofa)
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L47IA [auth B2]252Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
uL30mJA [auth B3]161Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
bL31mKA [auth B4]126Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A4X1ULI6 (Sus scrofa)
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
bL32mLA [auth B5]188Sus scrofaMutation(s): 0 
UniProt
Find proteins for I3LTC4 (Sus scrofa)
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
bL33mMA [auth B6]65Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A4X1TLP9 (Sus scrofa)
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L34NA [auth B7]95Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome-releasing factor 2, mitochondrialPA [auth BC]755Homo sapiensMutation(s): 0 
Gene Names: GFM2EFG2MSTP027
UniProt & NIH Common Fund Data Resources
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GTEx:  ENSG00000164347 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
uL2mQA [auth BD]306Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome-recycling factor, mitochondrialRA [auth BG]257Homo sapiensMutation(s): 0 
Gene Names: MRRF
UniProt & NIH Common Fund Data Resources
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PHAROS:  Q96E11
GTEx:  ENSG00000148187 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
uL16mSA [auth BQ]251Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
ICT1UA [auth BE]399Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A140UHW4 (Sus scrofa)
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L4VA [auth BF]294Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A287B9C4 (Sus scrofa)
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L9WA [auth BI]268Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L10XA [auth BJ]262Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L11YA [auth BK]192Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
uL13mZA [auth BN]178Sus scrofaMutation(s): 0 
UniProt
Find proteins for K7GP19 (Sus scrofa)
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
uL14mAB [auth BO]145Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A287BMZ6 (Sus scrofa)
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UniProt GroupA0A287BMZ6
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
uL15mBB [auth BP]296Sus scrofaMutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
bL17mCB [auth BR]169Sus scrofaMutation(s): 0 
UniProt
Find proteins for F1RMQ4 (Sus scrofa)
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L18DB [auth BS]180Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A286ZNK1 (Sus scrofa)
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L19EB [auth BT]292Sus scrofaMutation(s): 0 
UniProt
Find proteins for I3LNJ0 (Sus scrofa)
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UniProt GroupI3LNJ0
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L20FB [auth BU]149Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A286ZU56 (Sus scrofa)
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L21GB [auth BV]209Sus scrofaMutation(s): 0 
UniProt
Find proteins for F1RY70 (Sus scrofa)
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
uL22mHB [auth BW]210Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A4X1TXR4 (Sus scrofa)
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
uL23mIB [auth BX]150Sus scrofaMutation(s): 0 
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Entity ID: 29
MoleculeChains LengthOrganismImage
16S rRNAHA [auth BA]1,571Sus scrofa
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Entity ID: 36
MoleculeChains LengthOrganismImage
CP tRNAPheOA [auth BB]73Sus scrofa
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Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GNP (Subject of Investigation/LOI)
Query on GNP

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TJ [auth BC]PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
5GP
Query on 5GP

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NJ [auth BA],
OJ [auth BA]
GUANOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O8 P
RQFCJASXJCIDSX-UUOKFMHZSA-N
SPM
Query on SPM

Download Ideal Coordinates CCD File 
PJ [auth BA],
QJ [auth BA]
SPERMINE
C10 H26 N4
PFNFFQXMRSDOHW-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
OB [auth Bx],
PB [auth B9],
SJ [auth B5]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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AC [auth BA]
AD [auth BA]
AE [auth BA]
AF [auth BA]
AG [auth BA]
AC [auth BA],
AD [auth BA],
AE [auth BA],
AF [auth BA],
AG [auth BA],
AH [auth BA],
AI [auth BA],
AJ [auth BA],
AK [auth BJ],
BC [auth BA],
BD [auth BA],
BE [auth BA],
BF [auth BA],
BG [auth BA],
BH [auth BA],
BI [auth BA],
BJ [auth BA],
BK [auth BP],
CC [auth BA],
CD [auth BA],
CE [auth BA],
CF [auth BA],
CG [auth BA],
CH [auth BA],
CI [auth BA],
CJ [auth BA],
CK [auth BP],
DC [auth BA],
DD [auth BA],
DE [auth BA],
DF [auth BA],
DG [auth BA],
DH [auth BA],
DI [auth BA],
DJ [auth BA],
DK [auth BR],
EC [auth BA],
ED [auth BA],
EE [auth BA],
EF [auth BA],
EG [auth BA],
EH [auth BA],
EI [auth BA],
EJ [auth BA],
FC [auth BA],
FD [auth BA],
FE [auth BA],
FF [auth BA],
FG [auth BA],
FH [auth BA],
FI [auth BA],
FJ [auth BA],
GC [auth BA],
GD [auth BA],
GE [auth BA],
GF [auth BA],
GG [auth BA],
GH [auth BA],
GI [auth BA],
GJ [auth BA],
HC [auth BA],
HD [auth BA],
HE [auth BA],
HF [auth BA],
HG [auth BA],
HH [auth BA],
HI [auth BA],
HJ [auth BA],
IC [auth BA],
ID [auth BA],
IE [auth BA],
IF [auth BA],
IG [auth BA],
IH [auth BA],
II [auth BA],
IJ [auth BA],
JB [auth B0],
JC [auth BA],
JD [auth BA],
JE [auth BA],
JF [auth BA],
JG [auth BA],
JH [auth BA],
JI [auth BA],
JJ [auth BA],
KB [auth Bb],
KC [auth BA],
KD [auth BA],
KE [auth BA],
KF [auth BA],
KG [auth BA],
KH [auth BA],
KI [auth BA],
KJ [auth BA],
LB [auth Be],
LC [auth BA],
LD [auth BA],
LE [auth BA],
LF [auth BA],
LG [auth BA],
LH [auth BA],
LI [auth BA],
LJ [auth BA],
MB [auth Bl],
MC [auth BA],
MD [auth BA],
ME [auth BA],
MF [auth BA],
MG [auth BA],
MH [auth BA],
MI [auth BA],
MJ [auth BA],
NB [auth Bt],
NC [auth BA],
ND [auth BA],
NE [auth BA],
NF [auth BA],
NG [auth BA],
NH [auth BA],
NI [auth BA],
OC [auth BA],
OD [auth BA],
OE [auth BA],
OF [auth BA],
OG [auth BA],
OH [auth BA],
OI [auth BA],
PC [auth BA],
PD [auth BA],
PE [auth BA],
PF [auth BA],
PG [auth BA],
PH [auth BA],
PI [auth BA],
QB [auth BA],
QC [auth BA],
QD [auth BA],
QE [auth BA],
QF [auth BA],
QG [auth BA],
QH [auth BA],
QI [auth BA],
RB [auth BA],
RC [auth BA],
RD [auth BA],
RE [auth BA],
RF [auth BA],
RG [auth BA],
RH [auth BA],
RI [auth BA],
RJ [auth B3],
SB [auth BA],
SC [auth BA],
SD [auth BA],
SE [auth BA],
SF [auth BA],
SG [auth BA],
SH [auth BA],
SI [auth BA],
TB [auth BA],
TC [auth BA],
TD [auth BA],
TE [auth BA],
TF [auth BA],
TG [auth BA],
TH [auth BA],
TI [auth BA],
UB [auth BA],
UC [auth BA],
UD [auth BA],
UE [auth BA],
UF [auth BA],
UG [auth BA],
UH [auth BA],
UI [auth BA],
UJ [auth BC],
VB [auth BA],
VC [auth BA],
VD [auth BA],
VE [auth BA],
VF [auth BA],
VG [auth BA],
VH [auth BA],
VI [auth BA],
VJ [auth BD],
WB [auth BA],
WC [auth BA],
WD [auth BA],
WE [auth BA],
WF [auth BA],
WG [auth BA],
WH [auth BA],
WI [auth BA],
WJ [auth BD],
XB [auth BA],
XC [auth BA],
XD [auth BA],
XE [auth BA],
XF [auth BA],
XG [auth BA],
XH [auth BA],
XI [auth BA],
XJ [auth BD],
YB [auth BA],
YC [auth BA],
YD [auth BA],
YE [auth BA],
YF [auth BA],
YG [auth BA],
YH [auth BA],
YI [auth BA],
YJ [auth BQ],
ZB [auth BA],
ZC [auth BA],
ZD [auth BA],
ZE [auth BA],
ZF [auth BA],
ZG [auth BA],
ZH [auth BA],
ZI [auth BA],
ZJ [auth BE]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 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 Organization (EMBO)Switzerland--
Swiss National Science FoundationSwitzerland--

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-05
    Type: Initial release
  • Version 1.1: 2021-12-15
    Changes: Database references
  • Version 1.2: 2024-07-10
    Changes: Data collection