7L20

Cryo-EM structure of the human 39S mitoribosomal subunit in complex with RRFmt and EF-G2mt.

  • Classification: RIBOSOME
  • Organism(s): Homo sapiens
  • Mutation(s): Yes 

  • Deposited: 2020-12-15 Released: 2021-05-12 
  • Deposition Author(s): Agrawal, E., Koripella, R.
  • Funding Organization(s): National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.15 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

Distinct mechanisms of the human mitoribosome recycling and antibiotic resistance.

Koripella, R.K., Deep, A., Agrawal, E.K., Keshavan, P., Banavali, N.K., Agrawal, R.K.

(2021) Nat Commun 12: 3607-3607

  • DOI: 10.1038/s41467-021-23726-4
  • Primary Citation of Related Structures:  
    7L08, 7L20

  • PubMed Abstract: 

    • Ribosomes are recycled for a new round of translation initiation by dissociation of ribosomal subunits, messenger RNA and transfer RNA from their translational post-termination complex. Here we present cryo-EM structures of the human 55S mitochondrial ribosome (mitoribosome) and the mitoribosomal large 39S subunit in complex with mitoribosome recycling factor (RRF mt ) and a recycling-specific homolog of elongation factor G (EF-G2 mt ) ...

    Ribosomes are recycled for a new round of translation initiation by dissociation of ribosomal subunits, messenger RNA and transfer RNA from their translational post-termination complex. Here we present cryo-EM structures of the human 55S mitochondrial ribosome (mitoribosome) and the mitoribosomal large 39S subunit in complex with mitoribosome recycling factor (RRF mt ) and a recycling-specific homolog of elongation factor G (EF-G2 mt ). These structures clarify an unusual role of a mitochondria-specific segment of RRF mt , identify the structural distinctions that confer functional specificity to EF-G2 mt , and show that the deacylated tRNA remains with the dissociated 39S subunit, suggesting a distinct sequence of events in mitoribosome recycling. Furthermore, biochemical and structural analyses reveal that the molecular mechanism of antibiotic fusidic acid resistance for EF-G2 mt is markedly different from that of mitochondrial elongation factor EF-G1 mt , suggesting that the two human EF-G mt s have evolved diversely to negate the effect of a bacterial antibiotic.

    Organizational Affiliation: 

    Department of Biomedical Sciences, University at Albany, Albany, NY, USA. rajendra.agrawal@health.ny.gov.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L2, mitochondrialC [auth D]305Homo sapiensMutation(s): 0 
Gene Names: MRPL2, CGI-22
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Entity ID: 4
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39S ribosomal protein L4, mitochondrialD [auth F]311Homo sapiensMutation(s): 0 
Gene Names: MRPL4, CDABP0091, CGI-28
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Entity ID: 5
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39S ribosomal protein L9, mitochondrialE [auth H]267Homo sapiensMutation(s): 0 
Gene Names: MRPL9
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Entity ID: 6
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39S ribosomal protein L13, mitochondrialF [auth K]178Homo sapiensMutation(s): 0 
Gene Names: MRPL13
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Entity ID: 7
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39S ribosomal protein L14, mitochondrialG [auth L]145Homo sapiensMutation(s): 0 
Gene Names: MRPL14, MRPL32, RPML32
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Entity ID: 8
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39S ribosomal protein L15, mitochondrialH [auth M]296Homo sapiensMutation(s): 0 
Gene Names: MRPL15, HSPC145
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Entity ID: 9
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39S ribosomal protein L17, mitochondrialI [auth O]175Homo sapiensMutation(s): 0 
Gene Names: MRPL17, LIP2
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Entity ID: 10
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39S ribosomal protein L20, mitochondrialJ [auth R]149Homo sapiensMutation(s): 0 
Gene Names: MRPL20
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Entity ID: 11
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39S ribosomal protein L21, mitochondrialK [auth S]205Homo sapiensMutation(s): 0 
Gene Names: MRPL21
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Entity ID: 12
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39S ribosomal protein L22, mitochondrialL [auth T]212Homo sapiensMutation(s): 0 
Gene Names: MRPL22
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Entity ID: 13
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39S ribosomal protein L27, mitochondrialM [auth W]148Homo sapiensMutation(s): 0 
Gene Names: MRPL27, HSPC250
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Entity ID: 14
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39S ribosomal protein L28, mitochondrialN [auth X]256Homo sapiensMutation(s): 3 
Gene Names: MRPL28, MAAT1
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Entity ID: 15
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39S ribosomal protein L47, mitochondrialO [auth Y]250Homo sapiensMutation(s): 0 
Gene Names: MRPL47, NCM1, CGI-204
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Entity ID: 16
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39S ribosomal protein L30, mitochondrialP [auth Z]161Homo sapiensMutation(s): 0 
Gene Names: MRPL30, MRPL28, RPML28, HSPC249
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Entity ID: 17
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39S ribosomal protein L32, mitochondrialQ [auth 0]188Homo sapiensMutation(s): 0 
Gene Names: MRPL32, HSPC283
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Entity ID: 18
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39S ribosomal protein L33, mitochondrialR [auth 1]65Homo sapiensMutation(s): 0 
Gene Names: MRPL33, C2orf1
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Entity ID: 19
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39S ribosomal protein L34, mitochondrialS [auth 2]92Homo sapiensMutation(s): 0 
Gene Names: MRPL34
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Entity ID: 20
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39S ribosomal protein L35, mitochondrialT [auth 3]188Homo sapiensMutation(s): 0 
Gene Names: MRPL35, BM-007
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Entity ID: 21
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39S ribosomal protein L36, mitochondrialU [auth 4]103Homo sapiensMutation(s): 0 
Gene Names: MRPL36, BRIP1
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Entity ID: 22
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39S ribosomal protein L40, mitochondrialV [auth 8]206Homo sapiensMutation(s): 0 
Gene Names: MRPL40, NLVCF, URIM
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Entity ID: 23
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39S ribosomal protein L43, mitochondrialW [auth b]155Homo sapiensMutation(s): 0 
Gene Names: MRPL43
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Entity ID: 24
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39S ribosomal protein L46, mitochondrialX [auth e]279Homo sapiensMutation(s): 0 
Gene Names: MRPL46, C15orf4, LIECG2
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Entity ID: 25
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39S ribosomal protein L49, mitochondrialY [auth g]166Homo sapiensMutation(s): 0 
Gene Names: MRPL49, C11orf4, NOF1, OK/SW-cl.67
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Entity ID: 26
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39S ribosomal protein L51, mitochondrialZ [auth i]128Homo sapiensMutation(s): 0 
Gene Names: MRPL51, MRP64, CDA09, HSPC241
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Entity ID: 27
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cDNA FLJ76418, highly similar to Homo sapiens mitochondrial ribosomal protein L52 (MRPL52), transcript variant 1, mRNAAA [auth j]123Homo sapiensMutation(s): 0 
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Entity ID: 28
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39S ribosomal protein L55, mitochondrialBA [auth m]128Homo sapiensMutation(s): 0 
Gene Names: MRPL55, UNQ5835/PRO19675
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Entity ID: 29
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Ribosomal protein 63, mitochondrialCA [auth o]102Homo sapiensMutation(s): 0 
Gene Names: MRPL57, MRP63
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Entity ID: 30
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Growth arrest and DNA damage-inducible proteins-interacting protein 1DA [auth q]222Homo sapiensMutation(s): 0 
Gene Names: GADD45GIP1, MRPL59, PLINP1, PRG6
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Entity ID: 31
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39S ribosomal protein S18a, mitochondrialEA [auth r]196Homo sapiensMutation(s): 0 
Gene Names: MRPS18A
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Entity ID: 32
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39S ribosomal protein L11, mitochondrialFA [auth J]192Homo sapiensMutation(s): 0 
Gene Names: MRPL11, CGI-113
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Entity ID: 33
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39S ribosomal protein L10, mitochondrialGA [auth I]261Homo sapiensMutation(s): 0 
Gene Names: MRPL10, MRPL8, RPML8
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Entity ID: 34
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39S ribosomal protein L16, mitochondrialHA [auth N]251Homo sapiensMutation(s): 0 
Gene Names: MRPL16, PNAS-111
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Entity ID: 35
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Mitochondrial ribosomal protein L18, isoform CRA_bIA [auth P]179Homo sapiensMutation(s): 0 
Gene Names: MRPL18, hCG_34030
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Entity ID: 36
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39S ribosomal protein L23, mitochondrialJA [auth U]153Homo sapiensMutation(s): 0 
Gene Names: MRPL23, L23MRP, RPL23L
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Entity ID: 37
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39S ribosomal protein L24, mitochondrialKA [auth V]216Homo sapiensMutation(s): 0 
Gene Names: MRPL24
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Entity ID: 38
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39S ribosomal protein L3, mitochondrialLA [auth E]348Homo sapiensMutation(s): 0 
Gene Names: MRPL3, MRL3, RPML3
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Entity ID: 39
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39S ribosomal protein L37, mitochondrialMA [auth 5]423Homo sapiensMutation(s): 0 
Gene Names: MRPL37, MRPL2, RPML2, HSPC235
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L38, mitochondrialNA [auth 6]380Homo sapiensMutation(s): 0 
Gene Names: MRPL38, HSPC262
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Entity ID: 41
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39S ribosomal protein L39, mitochondrialOA [auth 7]338Homo sapiensMutation(s): 0 
Gene Names: MRPL39, C21orf92, MRPL5, RPML5, MSTP003, PRED22
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Entity ID: 42
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39S ribosomal protein L41, mitochondrialPA [auth 9]137Homo sapiensMutation(s): 0 
Gene Names: MRPL41, BMRP, MRPL27, RPML27, PIG3
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Entity ID: 43
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39S ribosomal protein L42, mitochondrialQA [auth a]142Homo sapiensMutation(s): 0 
Gene Names: MRPL42, MRPL31, MRPS32, RPML31, HSPC204, PTD007
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Entity ID: 44
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39S ribosomal protein L44, mitochondrialRA [auth c]332Homo sapiensMutation(s): 0 
Gene Names: MRPL44
EC: 3.1.26
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Entity ID: 45
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39S ribosomal protein L45, mitochondrialSA [auth d]306Homo sapiensMutation(s): 0 
Gene Names: MRPL45
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Entity ID: 46
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39S ribosomal protein L48, mitochondrialTA [auth f]194Homo sapiensMutation(s): 0 
Gene Names: MRPL48, CGI-118, HSPC290
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Entity ID: 47
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39S ribosomal protein L50, mitochondrialUA [auth h]158Homo sapiensMutation(s): 0 
Gene Names: MRPL50
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Entity ID: 48
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39S ribosomal protein L53, mitochondrialVA [auth k]112Homo sapiensMutation(s): 0 
Gene Names: MRPL53
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Entity ID: 49
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39S ribosomal protein L54, mitochondrialWA [auth l]138Homo sapiensMutation(s): 0 
Gene Names: MRPL54
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Entity ID: 50
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Peptidyl-tRNA hydrolase ICT1, mitochondrialXA [auth p]206Homo sapiensMutation(s): 0 
Gene Names: MRPL58, DS1, ICT1
EC: 3.1.1.29
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Entity ID: 51
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39S ribosomal protein S30, mitochondrialYA [auth s]439Homo sapiensMutation(s): 0 
Gene Names: MRPS30, PDCD9, BM-047
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Entity ID: 52
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39S ribosomal protein L19, mitochondrialZA [auth Q]292Homo sapiensMutation(s): 0 
Gene Names: MRPL19, KIAA0104, MRPL15
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Entity ID: 53
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39 S P-site fingerAB [auth u]65Homo sapiensMutation(s): 0 
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Entity ID: 54
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39S ribosomal protein L12, mitochondrialBB [auth TA],
CB [auth TB],
DB [auth TC]		198Homo sapiensMutation(s): 0 
Gene Names: MRPL12, MRPL7, RPML12
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Entity ID: 55
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Ribosome-recycling factor, mitochondrialEB [auth z]204Homo sapiensMutation(s): 0 
Gene Names: MRRF
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Entity ID: 56
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Ribosome-releasing factor 2, mitochondrialFB [auth w]696Homo sapiensMutation(s): 0 
Gene Names: GFM2, EFG2, MSTP027
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Entity ID: 1
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16S rRNA mitochondrialA 1559Homo sapiens
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Entity ID: 2
MoleculeChainsLengthOrganismImage
tRNAvalB 73Homo sapiens
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GCP
Query on GCP
Download Ideal Coordinates CCD File 
GF [auth w]PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
C11 H18 N5 O13 P3
PHBDHXOBFUBCJD-KQYNXXCUSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
BF [auth 0],
CF [auth 4],
EF [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],
AF [auth W],
BC [auth A],
AC [auth A],
AD [auth A],
AE [auth A],
AF [auth W],
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],
DF [auth g],
EC [auth A],
ED [auth A],
EE [auth A],
FC [auth A],
FD [auth A],
FE [auth A],
FF [auth E],
GB [auth A],
GC [auth A],
GD [auth A],
GE [auth A],
HB [auth A],
HC [auth A],
HD [auth A],
HE [auth A],
HF [auth w],
IB [auth A],
IC [auth A],
ID [auth A],
IE [auth A],
JB [auth A],
JC [auth A],
JD [auth A],
JE [auth A],
KB [auth A],
KC [auth A],
KD [auth A],
KE [auth A],
LB [auth A],
LC [auth A],
LD [auth A],
LE [auth A],
MB [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],
YE [auth A],
ZB [auth A],
ZC [auth A],
ZD [auth A],
ZE [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.15 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
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)United StatesR01 GM61576

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-12
    Type: Initial release
  • Version 1.1: 2021-12-01
    Changes: Database references