7A5H

Structure of the split human mitoribosomal large subunit with rescue factors mtRF-R and MTRES1

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history. 


Literature

Elongational stalling activates mitoribosome-associated quality control.

Desai, N., Yang, H., Chandrasekaran, V., Kazi, R., Minczuk, M., Ramakrishnan, V.

(2020) Science 370: 1105-1110

  • DOI: https://doi.org/10.1126/science.abc7782
  • Primary Citation of Related Structures:  
    7A5F, 7A5G, 7A5H, 7A5I, 7A5J, 7A5K

  • PubMed Abstract: 

    • The human mitochondrial ribosome (mitoribosome) and associated proteins regulate the synthesis of 13 essential subunits of the oxidative phosphorylation complexes. We report the discovery of a mitoribosome-associated quality control pathway that responds to interruptions during elongation, and we present structures at 3 ...

    The human mitochondrial ribosome (mitoribosome) and associated proteins regulate the synthesis of 13 essential subunits of the oxidative phosphorylation complexes. We report the discovery of a mitoribosome-associated quality control pathway that responds to interruptions during elongation, and we present structures at 3.1- to 3.3-angstrom resolution of mitoribosomal large subunits trapped during ribosome rescue. Release factor homolog C12orf65 (mtRF-R) and RNA binding protein C6orf203 (MTRES1) eject the nascent chain and peptidyl transfer RNA (tRNA), respectively, from stalled ribosomes. Recruitment of mitoribosome biogenesis factors to these quality control intermediates suggests additional roles for these factors during mitoribosome rescue. We also report related cryo-electron microscopy structures (3.7 to 4.4 angstrom resolution) of elongating mitoribosomes bound to tRNAs, nascent polypeptides, the guanosine triphosphatase elongation factors mtEF-Tu and mtEF-G1, and the Oxa1L translocase.

    Organizational Affiliation: 

    MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK. ramak@mrc-lmb.cam.ac.uk.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L2, mitochondrialA [auth D]305Homo sapiensMutation(s): 0 
Gene Names: MRPL2, CGI-22
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Entity ID: 2
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39S ribosomal protein L3, mitochondrialB [auth E]348Homo sapiensMutation(s): 0 
Gene Names: MRPL3, MRL3, RPML3
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Entity ID: 3
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39S ribosomal protein L4, mitochondrialC [auth F]311Homo sapiensMutation(s): 0 
Gene Names: MRPL4, CDABP0091, CGI-28
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Entity ID: 4
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39S ribosomal protein L9, mitochondrialD [auth H]267Homo sapiensMutation(s): 0 
Gene Names: MRPL9
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Entity ID: 5
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39S ribosomal protein L10, mitochondrialE [auth I]261Homo sapiensMutation(s): 0 
Gene Names: MRPL10, MRPL8, RPML8
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Entity ID: 6
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39S ribosomal protein L11, mitochondrialF [auth J]192Homo sapiensMutation(s): 0 
Gene Names: MRPL11, CGI-113
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Entity ID: 7
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39S ribosomal protein L13, mitochondrialG [auth K]178Homo sapiensMutation(s): 0 
Gene Names: MRPL13
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Entity ID: 8
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39S ribosomal protein L14, mitochondrialH [auth L]145Homo sapiensMutation(s): 0 
Gene Names: MRPL14, MRPL32, RPML32
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39S ribosomal protein L15, mitochondrialI [auth M]296Homo sapiensMutation(s): 0 
Gene Names: MRPL15, HSPC145
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39S ribosomal protein L16, mitochondrialJ [auth N]251Homo sapiensMutation(s): 0 
Gene Names: MRPL16, PNAS-111
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Entity ID: 11
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39S ribosomal protein L17, mitochondrialK [auth O]175Homo sapiensMutation(s): 0 
Gene Names: MRPL17, LIP2
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Entity ID: 12
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Mitochondrial ribosomal protein L18, isoform CRA_bL [auth P]179Homo sapiensMutation(s): 0 
Gene Names: MRPL18, hCG_34030
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39S ribosomal protein L19, mitochondrialM [auth Q]292Homo sapiensMutation(s): 0 
Gene Names: MRPL19, KIAA0104, MRPL15
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39S ribosomal protein L20, mitochondrialN [auth R]149Homo sapiensMutation(s): 0 
Gene Names: MRPL20
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Entity ID: 15
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39S ribosomal protein L21, mitochondrialO [auth S]205Homo sapiensMutation(s): 0 
Gene Names: MRPL21
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39S ribosomal protein L22, mitochondrialP [auth T]212Homo sapiensMutation(s): 0 
Gene Names: MRPL22
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39S ribosomal protein L23, mitochondrialQ [auth U]153Homo sapiensMutation(s): 0 
Gene Names: MRPL23, L23MRP, RPL23L
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39S ribosomal protein L24, mitochondrialR [auth V]216Homo sapiensMutation(s): 0 
Gene Names: MRPL24
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Entity ID: 19
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39S ribosomal protein L27, mitochondrialS [auth W]148Homo sapiensMutation(s): 0 
Gene Names: MRPL27, HSPC250
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Entity ID: 20
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39S ribosomal protein L28, mitochondrialT [auth X]256Homo sapiensMutation(s): 0 
Gene Names: MRPL28, MAAT1
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39S ribosomal protein L47, mitochondrialU [auth Y]250Homo sapiensMutation(s): 0 
Gene Names: MRPL47, NCM1, CGI-204
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Entity ID: 22
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39S ribosomal protein L30, mitochondrialV [auth Z]161Homo sapiensMutation(s): 0 
Gene Names: MRPL30, MRPL28, RPML28, HSPC249
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39S ribosomal protein L32, mitochondrialW [auth 0]188Homo sapiensMutation(s): 0 
Gene Names: MRPL32, HSPC283
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39S ribosomal protein L33, mitochondrialX [auth 1]65Homo sapiensMutation(s): 0 
Gene Names: MRPL33, C2orf1
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39S ribosomal protein L34, mitochondrialY [auth 2]92Homo sapiensMutation(s): 0 
Gene Names: MRPL34
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39S ribosomal protein L35, mitochondrialZ [auth 3]188Homo sapiensMutation(s): 0 
Gene Names: MRPL35, BM-007
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Entity ID: 27
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39S ribosomal protein L37, mitochondrialAA [auth 5]423Homo sapiensMutation(s): 0 
Gene Names: MRPL37, MRPL2, RPML2, HSPC235
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Entity ID: 28
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39S ribosomal protein L38, mitochondrialBA [auth 6]380Homo sapiensMutation(s): 0 
Gene Names: MRPL38, HSPC262
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Entity ID: 29
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39S ribosomal protein L39, mitochondrialCA [auth 7]338Homo sapiensMutation(s): 0 
Gene Names: MRPL39, C21orf92, MRPL5, RPML5, MSTP003, PRED22
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39S ribosomal protein L40, mitochondrialDA [auth 8]206Homo sapiensMutation(s): 0 
Gene Names: MRPL40, NLVCF, URIM
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39S ribosomal protein L41, mitochondrialEA [auth 9]137Homo sapiensMutation(s): 0 
Gene Names: MRPL41, BMRP, MRPL27, RPML27, PIG3
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Entity ID: 32
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39S ribosomal protein L42, mitochondrialFA [auth a]142Homo sapiensMutation(s): 0 
Gene Names: MRPL42, MRPL31, MRPS32, RPML31, HSPC204, PTD007
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Entity ID: 33
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39S ribosomal protein L43, mitochondrialGA [auth b]155Homo sapiensMutation(s): 0 
Gene Names: MRPL43
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Entity ID: 34
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39S ribosomal protein L44, mitochondrialHA [auth c]332Homo sapiensMutation(s): 0 
Gene Names: MRPL44
EC: 3.1.26
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Entity ID: 35
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39S ribosomal protein L45, mitochondrialIA [auth d]306Homo sapiensMutation(s): 0 
Gene Names: MRPL45
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Entity ID: 36
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39S ribosomal protein L46, mitochondrialJA [auth e]279Homo sapiensMutation(s): 0 
Gene Names: MRPL46, C15orf4, LIECG2
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Entity ID: 37
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39S ribosomal protein L48, mitochondrialKA [auth f]194Homo sapiensMutation(s): 0 
Gene Names: MRPL48, CGI-118, HSPC290
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39S ribosomal protein L49, mitochondrialLA [auth g]166Homo sapiensMutation(s): 0 
Gene Names: MRPL49, C11orf4, NOF1, OK/SW-cl.67
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L50, mitochondrialMA [auth h]158Homo sapiensMutation(s): 0 
Gene Names: MRPL50
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Entity ID: 40
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39S ribosomal protein L51, mitochondrialNA [auth i]128Homo sapiensMutation(s): 0 
Gene Names: MRPL51, MRP64, CDA09, HSPC241
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
cDNA FLJ76418, highly similar to Homo sapiens mitochondrial ribosomal protein L52 (MRPL52), transcript variant 1, mRNAOA [auth j]123Homo sapiensMutation(s): 0 
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Entity ID: 42
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39S ribosomal protein L53, mitochondrialPA [auth k]112Homo sapiensMutation(s): 0 
Gene Names: MRPL53
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Entity ID: 43
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39S ribosomal protein L54, mitochondrialQA [auth l]138Homo sapiensMutation(s): 0 
Gene Names: MRPL54
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Entity ID: 44
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39S ribosomal protein L55, mitochondrialRA [auth m]128Homo sapiensMutation(s): 0 
Gene Names: MRPL55, UNQ5835/PRO19675
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Entity ID: 45
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Ribosomal protein 63, mitochondrialSA [auth o]102Homo sapiensMutation(s): 0 
Gene Names: MRPL57, MRP63
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Entity ID: 46
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Peptidyl-tRNA hydrolase ICT1, mitochondrialTA [auth p]206Homo sapiensMutation(s): 0 
Gene Names: MRPL58, DS1, ICT1
EC: 3.1.1.29
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Entity ID: 47
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Growth arrest and DNA damage-inducible proteins-interacting protein 1UA [auth q]222Homo sapiensMutation(s): 0 
Gene Names: GADD45GIP1, MRPL59, PLINP1, PRG6
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Entity ID: 48
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39S ribosomal protein S18a, mitochondrialVA [auth r]196Homo sapiensMutation(s): 0 
Gene Names: MRPS18A
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Entity ID: 49
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39S ribosomal protein S30, mitochondrialWA [auth s]439Homo sapiensMutation(s): 0 
Gene Names: MRPS30, PDCD9, BM-047
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Entity ID: 50
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Unknown protein/protein extensionXA [auth t]28Homo sapiensMutation(s): 0 
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Entity ID: 51
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Mitochondrial assembly of ribosomal large subunit protein 1YA [auth u]234Homo sapiensMutation(s): 0 
Gene Names: MALSU1, C7orf30
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Entity ID: 52
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MIEF1 upstream open reading frame proteinZA [auth v]70Homo sapiensMutation(s): 0 
Gene Names: MIEF1
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Entity ID: 53
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Acyl carrier protein, mitochondrialAB [auth w]156Homo sapiensMutation(s): 0 
Gene Names: NDUFAB1
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Entity ID: 57
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nascent chainEB [auth Y2]29Homo sapiensMutation(s): 0 
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Entity ID: 58
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Probable peptide chain release factor C12orf65, mitochondrialFB [auth C]166Homo sapiensMutation(s): 0 
Gene Names: MTRFR, C12orf65, My030
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Entity ID: 59
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Mitochondrial transcription rescue factor 1GB [auth G]240Homo sapiensMutation(s): 0 
Gene Names: MTRES1, C6orf203, HSPC230
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Entity ID: 54
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16S rRNABB [auth A]1,559Homo sapiens
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Entity ID: 55
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mt-tRNAValCB [auth B]73Homo sapiens
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Entity ID: 56
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mt-tRNADB [auth 24]73Homo sapiens
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PNS
Query on PNS
Download Ideal Coordinates CCD File 
MB [auth v]4'-PHOSPHOPANTETHEINE
C11 H23 N2 O7 P S
JDMUPRLRUUMCTL-VIFPVBQESA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
JB [auth 0],
LB [auth r]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
AC [auth A],
AD [auth A],
AE [auth A],
BC [auth A],
BD [auth A],
AC [auth A],
AD [auth A],
AE [auth A],
BC [auth A],
BD [auth A],
BE [auth A],
CC [auth A],
CD [auth A],
CE [auth A],
DC [auth A],
DD [auth A],
DE [auth A],
EC [auth A],
ED [auth A],
EE [auth A],
FC [auth A],
FD [auth A],
FE [auth A],
GC [auth A],
GD [auth A],
GE [auth A],
HB [auth D],
HC [auth A],
HD [auth A],
HE [auth A],
IB [auth W],
IC [auth A],
ID [auth A],
IE [auth A],
JC [auth A],
JD [auth A],
JE [auth A],
KB [auth g],
KC [auth A],
KD [auth A],
KE [auth A],
LC [auth A],
LD [auth A],
LE [auth A],
MC [auth A],
MD [auth A],
ME [auth A],
NB [auth A],
NC [auth A],
ND [auth A],
NE [auth A],
OB [auth A],
OC [auth A],
OD [auth A],
OE [auth A],
PB [auth A],
PC [auth A],
PD [auth A],
PE [auth A],
QB [auth A],
QC [auth A],
QD [auth A],
QE [auth A],
RB [auth A],
RC [auth A],
RD [auth A],
RE [auth A],
SB [auth A],
SC [auth A],
SD [auth A],
SE [auth A],
TB [auth A],
TC [auth A],
TD [auth A],
TE [auth A],
UB [auth A],
UC [auth A],
UD [auth A],
UE [auth A],
VB [auth A],
VC [auth A],
VD [auth A],
VE [auth A],
WB [auth A],
WC [auth A],
WD [auth A],
WE [auth A],
XB [auth A],
XC [auth A],
XD [auth A],
XE [auth A],
YB [auth A],
YC [auth A],
YD [auth A],
ZB [auth A],
ZC [auth A],
ZD [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MEQ
Query on MEQ		FB [auth C]L-PEPTIDE LINKINGC6 H12 N2 O3GLN
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMC_U105184332
Wellcome TrustUnited KingdomWT096570
Louis-Jeantet FoundationUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-23
    Type: Initial release
  • Version 2.0: 2023-03-01
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary