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 1.1 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 ...

    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: ban@mol.biol.ethz.ch.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L27A [auth B0]148Sus scrofaMutation(s): 0 
Gene Names: MRPL27
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
uL24mB [auth BY]216Sus scrofaMutation(s): 0 
Gene Names: MRPL24
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Find proteins for F1RHJ1 (Sus scrofa)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L37C [auth Ba]423Sus scrofaMutation(s): 0 
Gene Names: MRPL37
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L35D [auth B8]188Sus scrofaMutation(s): 0 
Gene Names: MRPL35
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L38E [auth Bb]380Sus scrofaMutation(s): 0 
Gene Names: MRPL38
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L39F [auth Bc]334Sus scrofaMutation(s): 0 
Gene Names: MRPL39
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L40G [auth Bd]206Sus scrofaMutation(s): 0 
Gene Names: MRPL40
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L41H [auth Be]135Sus scrofaMutation(s): 0 
Gene Names: MRPL41
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
mL42I [auth Bf]142Sus scrofaMutation(s): 0 
Gene Names: MRPL42
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Entity ID: 10
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Mitochondrial ribosomal protein L43J [auth Bg]159Sus scrofaMutation(s): 0 
Gene Names: MRPL43
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Entity ID: 11
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mL44K [auth Bh]332Sus scrofaMutation(s): 0 
Gene Names: MRPL44
UniProt
Find proteins for F1SR64 (Sus scrofa)
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L45L [auth Bi]306Sus scrofaMutation(s): 0 
Gene Names: MRPL45
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Entity ID: 13
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Mitochondrial ribosomal protein L46M [auth Bj]279Sus scrofaMutation(s): 0 
Gene Names: MRPL46
UniProt
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L48, mitochondrialN [auth Bk]269Sus scrofaMutation(s): 0 
Gene Names: MRPL48
UniProt
Find proteins for A0A480J9Z6 (Sus scrofa)
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Mrpl34O [auth Bl]166Sus scrofaMutation(s): 0 
Gene Names: MRPL49
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L50P [auth Bm]198Sus scrofaMutation(s): 0 
Gene Names: MRPL50
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Entity ID: 17
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Mitochondrial ribosomal protein L51Q [auth Bn]128Sus scrofaMutation(s): 0 
Gene Names: MRPL51
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
mL52R [auth Bo]124Sus scrofaMutation(s): 0 
Gene Names: MRPL52
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
mL53S [auth Bp]112Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A341D604 (Neophocaena asiaeorientalis asiaeorientalis)
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
mL54T [auth Bq]138Sus scrofaMutation(s): 0 
Gene Names: MRPL54
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L57U [auth Bt]102Sus scrofaMutation(s): 0 
Gene Names: MRPL57
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
mL62 (ICT1)V [auth Bu]205Sus scrofaMutation(s): 0 
Gene Names: MRPL58
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
mL64W [auth Bv]222Sus scrofaMutation(s): 0 
Gene Names: GADD45GIP1
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein S30, mitochondrialX [auth Bw]433Sus scrofaMutation(s): 0 
Gene Names: MRPS30
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S18AY [auth Bx]196Sus scrofaMutation(s): 0 
Gene Names: MRPS18A
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L12198Sus scrofaMutation(s): 0 
Gene Names: MRPL12
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L28AA [auth B1]256Sus scrofaMutation(s): 0 
Gene Names: MRPL28
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal proteinEA [auth B9]100Sus scrofaMutation(s): 0 
Gene Names: MRPL36
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L47IA [auth B2]252Sus scrofaMutation(s): 0 
Gene Names: MRPL47
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
uL30mJA [auth B3]161Sus scrofaMutation(s): 0 
Gene Names: MRPL30
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
bL31mKA [auth B4]126Sus scrofaMutation(s): 0 
Gene Names: MRPL55
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
bL32mLA [auth B5]188Sus scrofaMutation(s): 0 
Gene Names: MRPL32
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Entity ID: 34
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bL33mMA [auth B6]65Sus scrofaMutation(s): 0 
Gene Names: MRPL33
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L34NA [auth B7]95Sus scrofaMutation(s): 0 
Gene Names: MRPL34
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosome-releasing factor 2, mitochondrialPA [auth BC]755Homo sapiensMutation(s): 0 
Gene Names: GFM2EFG2MSTP027
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
uL2mQA [auth BD]306Sus scrofaMutation(s): 0 
Gene Names: MRPL2
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Entity ID: 39
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Ribosome-recycling factor, mitochondrialRA [auth BG]257Homo sapiensMutation(s): 0 
Gene Names: MRRF
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
uL16mSA [auth BQ]251Sus scrofaMutation(s): 0 
Gene Names: MRPL16
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
ICT1UA [auth BE]399Sus scrofaMutation(s): 0 
Gene Names: MRPL3
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Entity ID: 42
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Mitochondrial ribosomal protein L4VA [auth BF]294Sus scrofaMutation(s): 0 
Gene Names: MRPL4
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L9WA [auth BI]268Sus scrofaMutation(s): 0 
Gene Names: MRPL9
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L10XA [auth BJ]262Sus scrofaMutation(s): 0 
Gene Names: MRPL10
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L11YA [auth BK]192Sus scrofaMutation(s): 0 
Gene Names: MRPL11
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetailsImage
uL13mZA [auth BN]178Sus scrofaMutation(s): 0 
Gene Names: MRPL13
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetailsImage
uL14mAB [auth BO]145Sus scrofaMutation(s): 0 
Gene Names: MRPL14
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetailsImage
uL15mBB [auth BP]296Sus scrofaMutation(s): 0 
Gene Names: MRPL15
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetailsImage
bL17mCB [auth BR]169Sus scrofaMutation(s): 0 
Gene Names: MRPL17
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L18DB [auth BS]180Sus scrofaMutation(s): 0 
Gene Names: MRPL18
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Find proteins for A0A286ZNK1 (Sus scrofa)
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Entity ID: 51
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Mitochondrial ribosomal protein L19EB [auth BT]292Sus scrofaMutation(s): 0 
Gene Names: MRPL19
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Entity ID: 52
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Mitochondrial ribosomal protein L20FB [auth BU]149Sus scrofaMutation(s): 0 
Gene Names: MRPL20
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Find proteins for A0A286ZU56 (Sus scrofa)
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Entity ID: 53
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Mitochondrial ribosomal protein L21GB [auth BV]209Sus scrofaMutation(s): 0 
UniProt
Find proteins for F1RY70 (Sus scrofa)
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Go to UniProtKB:  F1RY70
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UniProt GroupF1RY70
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetailsImage
uL22mHB [auth BW]210Sus scrofaMutation(s): 0 
Gene Names: MRPL22
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetailsImage
uL23mIB [auth BX]150Sus scrofaMutation(s): 0 
Gene Names: MRPL23
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Entity ID: 29
MoleculeChainsLengthOrganismImage
16S rRNAHA [auth BA]1,571Sus scrofa
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Entity ID: 36
MoleculeChainsLengthOrganismImage
CP tRNAPheOA [auth BB]73Sus scrofa
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / 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
 Ligand Interaction
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
 Ligand Interaction
SPM
Query on SPM

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PJ [auth BA],
QJ [auth BA]
SPERMINE
C10 H26 N4
PFNFFQXMRSDOHW-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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OB [auth Bx],
PB [auth B9],
SJ [auth B5]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
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
 Ligand Interaction
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