6I9R

Large subunit of the human mitochondrial ribosome in complex with Virginiamycin M and Quinupristin

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 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

Inhibition of mitochondrial translation suppresses glioblastoma stem cell growth.

Sighel, D., Notarangelo, M., Aibara, S., Re, A., Ricci, G., Guida, M., Soldano, A., Adami, V., Ambrosini, C., Broso, F., Rosatti, E.F., Longhi, S., Buccarelli, M., D'Alessandris, Q.G., Giannetti, S., Pacioni, S., Ricci-Vitiani, L., Rorbach, J., Pallini, R., Roulland, S., Amunts, A., Mancini, I., Modelska, A., Quattrone, A.

(2021) Cell Rep 35: 109024-109024

  • DOI: https://doi.org/10.1016/j.celrep.2021.109024
  • Primary Citation of Related Structures:  
    6I9R

  • PubMed Abstract: 

    • Glioblastoma stem cells (GSCs) resist current glioblastoma (GBM) therapies. GSCs rely highly on oxidative phosphorylation (OXPHOS), whose function requires mitochondrial translation. Here we explore the therapeutic potential of targeting mitochondrial translation and report the results of high-content screening with putative blockers of mitochondrial ribosomes ...

    Glioblastoma stem cells (GSCs) resist current glioblastoma (GBM) therapies. GSCs rely highly on oxidative phosphorylation (OXPHOS), whose function requires mitochondrial translation. Here we explore the therapeutic potential of targeting mitochondrial translation and report the results of high-content screening with putative blockers of mitochondrial ribosomes. We identify the bacterial antibiotic quinupristin/dalfopristin (Q/D) as an effective suppressor of GSC growth. Q/D also decreases the clonogenicity of GSCs in vitro, consequently dysregulating the cell cycle and inducing apoptosis. Cryoelectron microscopy (cryo-EM) reveals that Q/D binds to the large mitoribosomal subunit, inhibiting mitochondrial protein synthesis and functionally dysregulating OXPHOS complexes. These data suggest that targeting mitochondrial translation could be explored to therapeutically suppress GSC growth in GBM and that Q/D could potentially be repurposed for cancer treatment.

    Organizational Affiliation: 

    Department CIBIO, University of Trento, Trento 38123, Italy. Electronic address: alessandro.quattrone@unitn.it.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L32, mitochondrialA [auth 0]188Homo sapiensMutation(s): 0 
Gene Names: MRPL32, HSPC283
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L33, mitochondrialB [auth 1]65Homo sapiensMutation(s): 0 
Gene Names: MRPL33, C2orf1
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L34, mitochondrialC [auth 2]92Homo sapiensMutation(s): 0 
Gene Names: MRPL34
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L35, mitochondrialD [auth 3]188Homo sapiensMutation(s): 0 
Gene Names: MRPL35, BM-007
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Entity ID: 5
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39S ribosomal protein L36, mitochondrialE [auth 4]103Homo sapiensMutation(s): 0 
Gene Names: MRPL36, BRIP1
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Entity ID: 6
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39S ribosomal protein L37, mitochondrialF [auth 5]423Homo sapiensMutation(s): 0 
Gene Names: MRPL37, MRPL2, RPML2, HSPC235
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Entity ID: 7
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39S ribosomal protein L38, mitochondrialG [auth 6]380Homo sapiensMutation(s): 0 
Gene Names: MRPL38, HSPC262
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Entity ID: 8
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39S ribosomal protein L39, mitochondrialH [auth 7]338Homo sapiensMutation(s): 0 
Gene Names: MRPL39, C21orf92, MRPL5, RPML5, MSTP003, PRED22
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Entity ID: 9
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39S ribosomal protein L40, mitochondrialI [auth 8]206Homo sapiensMutation(s): 0 
Gene Names: MRPL40, NLVCF, URIM
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Entity ID: 10
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39S ribosomal protein L41, mitochondrialJ [auth 9]137Homo sapiensMutation(s): 0 
Gene Names: MRPL41, BMRP, MRPL27, RPML27, PIG3
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Entity ID: 13
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39S ribosomal protein L2, mitochondrialM [auth D]305Homo sapiensMutation(s): 0 
Gene Names: MRPL2, CGI-22
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Entity ID: 14
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39S ribosomal protein L3, mitochondrialN [auth E]348Homo sapiensMutation(s): 0 
Gene Names: MRPL3, MRL3, RPML3
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Entity ID: 15
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39S ribosomal protein L4, mitochondrialO [auth F]311Homo sapiensMutation(s): 0 
Gene Names: MRPL4, CDABP0091, CGI-28
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L9, mitochondrialP [auth H]267Homo sapiensMutation(s): 0 
Gene Names: MRPL9
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Entity ID: 17
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39S ribosomal protein L10, mitochondrialQ [auth I]261Homo sapiensMutation(s): 0 
Gene Names: MRPL10, MRPL8, RPML8
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Entity ID: 18
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39S ribosomal protein L11, mitochondrialR [auth J]192Homo sapiensMutation(s): 0 
Gene Names: MRPL11, CGI-113
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Entity ID: 19
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39S ribosomal protein L13, mitochondrialS [auth K]178Homo sapiensMutation(s): 0 
Gene Names: MRPL13
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Entity ID: 20
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39S ribosomal protein L14, mitochondrialT [auth L]145Homo sapiensMutation(s): 0 
Gene Names: MRPL14, MRPL32, RPML32
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Entity ID: 21
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39S ribosomal protein L15, mitochondrialU [auth M]296Homo sapiensMutation(s): 0 
Gene Names: MRPL15, HSPC145
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Entity ID: 22
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39S ribosomal protein L16, mitochondrialV [auth N]251Homo sapiensMutation(s): 0 
Gene Names: MRPL16, PNAS-111
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Entity ID: 23
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39S ribosomal protein L17, mitochondrialW [auth O]175Homo sapiensMutation(s): 0 
Gene Names: MRPL17, LIP2
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Entity ID: 24
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Mitochondrial ribosomal protein L18, isoform CRA_bX [auth P]179Homo sapiensMutation(s): 0 
Gene Names: MRPL18, hCG_34030
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Entity ID: 25
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39S ribosomal protein L19, mitochondrialY [auth Q]292Homo sapiensMutation(s): 0 
Gene Names: MRPL19, KIAA0104, MRPL15
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Entity ID: 26
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39S ribosomal protein L20, mitochondrialZ [auth R]149Homo sapiensMutation(s): 0 
Gene Names: MRPL20
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Entity ID: 27
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39S ribosomal protein L21, mitochondrialAA [auth S]205Homo sapiensMutation(s): 0 
Gene Names: MRPL21
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Entity ID: 28
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39S ribosomal protein L22, mitochondrialBA [auth T]212Homo sapiensMutation(s): 0 
Gene Names: MRPL22
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Entity ID: 29
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39S ribosomal protein L23, mitochondrialCA [auth U]153Homo sapiensMutation(s): 0 
Gene Names: MRPL23, L23MRP, RPL23L
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Entity ID: 30
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39S ribosomal protein L24, mitochondrialDA [auth V]216Homo sapiensMutation(s): 0 
Gene Names: MRPL24
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Entity ID: 31
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39S ribosomal protein L27, mitochondrialEA [auth W]148Homo sapiensMutation(s): 0 
Gene Names: MRPL27, HSPC250
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Entity ID: 32
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39S ribosomal protein L28, mitochondrialFA [auth X]256Homo sapiensMutation(s): 0 
Gene Names: MRPL28, MAAT1
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Entity ID: 33
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39S ribosomal protein L47, mitochondrialGA [auth Y]250Homo sapiensMutation(s): 0 
Gene Names: MRPL47, NCM1, CGI-204
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Entity ID: 34
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39S ribosomal protein L30, mitochondrialHA [auth Z]161Homo sapiensMutation(s): 0 
Gene Names: MRPL30, MRPL28, RPML28, HSPC249
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Entity ID: 35
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39S ribosomal protein L42, mitochondrialIA [auth a]142Homo sapiensMutation(s): 0 
Gene Names: MRPL42, MRPL31, MRPS32, RPML31, HSPC204, PTD007
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Entity ID: 36
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39S ribosomal protein L43, mitochondrialJA [auth b]215Homo sapiensMutation(s): 0 
Gene Names: MRPL43
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Entity ID: 37
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39S ribosomal protein L44, mitochondrialKA [auth c]332Homo sapiensMutation(s): 0 
Gene Names: MRPL44
EC: 3.1.26
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Entity ID: 38
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39S ribosomal protein L45, mitochondrialLA [auth d]306Homo sapiensMutation(s): 0 
Gene Names: MRPL45
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Entity ID: 39
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39S ribosomal protein L46, mitochondrialMA [auth e]279Homo sapiensMutation(s): 0 
Gene Names: MRPL46, C15orf4, LIECG2
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Entity ID: 40
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39S ribosomal protein L48, mitochondrialNA [auth f]212Homo sapiensMutation(s): 0 
Gene Names: MRPL48, CGI-118, HSPC290
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L49, mitochondrialOA [auth g]166Homo sapiensMutation(s): 0 
Gene Names: MRPL49, C11orf4, NOF1, OK/SW-cl.67
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L50, mitochondrialPA [auth h]158Homo sapiensMutation(s): 0 
Gene Names: MRPL50
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L51, mitochondrialQA [auth i]128Homo sapiensMutation(s): 0 
Gene Names: MRPL51, MRP64, CDA09, HSPC241
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
cDNA FLJ76418, highly similar to Homo sapiens mitochondrial ribosomal protein L52 (MRPL52), transcript variant 1, mRNARA [auth j]123Homo sapiensMutation(s): 0 
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Entity ID: 45
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39S ribosomal protein L53, mitochondrialSA [auth k]112Homo sapiensMutation(s): 0 
Gene Names: MRPL53
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L54, mitochondrialTA [auth l]138Homo sapiensMutation(s): 0 
Gene Names: MRPL54
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L55, mitochondrialUA [auth m]128Homo sapiensMutation(s): 0 
Gene Names: MRPL55, UNQ5835/PRO19675
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Entity ID: 48
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Ribosomal protein 63, mitochondrialVA [auth o]102Homo sapiensMutation(s): 0 
Gene Names: MRPL57, MRP63
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetailsImage
Peptidyl-tRNA hydrolase ICT1, mitochondrialWA [auth p]206Homo sapiensMutation(s): 0 
Gene Names: MRPL58, DS1, ICT1
EC: 3.1.1.29
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetailsImage
Growth arrest and DNA damage-inducible proteins-interacting protein 1XA [auth q]222Homo sapiensMutation(s): 0 
Gene Names: GADD45GIP1, MRPL59, PLINP1, PRG6
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Entity ID: 51
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39S ribosomal protein S18a, mitochondrialYA [auth r]196Homo sapiensMutation(s): 0 
Gene Names: MRPS18A
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Entity ID: 52
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39S ribosomal protein S30, mitochondrialZA [auth s]439Homo sapiensMutation(s): 0 
Gene Names: MRPS30, PDCD9, BM-047
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetailsImage
QuinupristinAB [auth C]8synthetic constructMutation(s): 0 
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Entity ID: 11
MoleculeChainsLengthOrganismImage
16S rRNAK [auth A]1,557Homo sapiens
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Entity ID: 12
MoleculeChainsLengthOrganismImage
tRNA ValL [auth B]69Homo sapiens
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Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
H8T
Query on H8T
Download Ideal Coordinates CCD File 
DG [auth A]Virginiamycin M
C28 H33 N3 O7
CNTGCXRBDCXZRN-FQTGFAPKSA-N		 Ligand Interaction
G
Query on G
Download Ideal Coordinates CCD File 
CG [auth A]GUANOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O8 P
RQFCJASXJCIDSX-UUOKFMHZSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
BB [auth 0],
CB [auth 4],
FG [auth I]		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 A],
AG [auth A],
AC [auth A],
AD [auth A],
AE [auth A],
AF [auth A],
AG [auth A],
BC [auth A],
BD [auth A],
BE [auth A],
BF [auth A],
BG [auth A],
CC [auth A],
CD [auth A],
CE [auth A],
CF [auth A],
DB [auth 9],
DC [auth A],
DD [auth A],
DE [auth A],
DF [auth A],
EB [auth A],
EC [auth A],
ED [auth A],
EE [auth A],
EF [auth A],
EG [auth D],
FB [auth A],
FC [auth A],
FD [auth A],
FE [auth A],
FF [auth A],
GB [auth A],
GC [auth A],
GD [auth A],
GE [auth A],
GF [auth A],
GG [auth L],
HB [auth A],
HC [auth A],
HD [auth A],
HE [auth A],
HF [auth A],
HG [auth M],
IB [auth A],
IC [auth A],
ID [auth A],
IE [auth A],
IF [auth A],
IG [auth g],
JB [auth A],
JC [auth A],
JD [auth A],
JE [auth A],
JF [auth A],
JG [auth o],
KB [auth A],
KC [auth A],
KD [auth A],
KE [auth A],
KF [auth A],
LB [auth A],
LC [auth A],
LD [auth A],
LE [auth A],
LF [auth A],
MB [auth A],
MC [auth A],
MD [auth A],
ME [auth A],
MF [auth A],
NB [auth A],
NC [auth A],
ND [auth A],
NE [auth A],
NF [auth A],
OB [auth A],
OC [auth A],
OD [auth A],
OE [auth A],
OF [auth A],
PB [auth A],
PC [auth A],
PD [auth A],
PE [auth A],
PF [auth A],
QB [auth A],
QC [auth A],
QD [auth A],
QE [auth A],
QF [auth A],
RB [auth A],
RC [auth A],
RD [auth A],
RE [auth A],
RF [auth A],
SB [auth A],
SC [auth A],
SD [auth A],
SE [auth A],
SF [auth A],
TB [auth A],
TC [auth A],
TD [auth A],
TE [auth A],
TF [auth A],
UB [auth A],
UC [auth A],
UD [auth A],
UE [auth A],
UF [auth A],
VB [auth A],
VC [auth A],
VD [auth A],
VE [auth A],
VF [auth A],
WB [auth A],
WC [auth A],
WD [auth A],
WE [auth A],
WF [auth A],
XB [auth A],
XC [auth A],
XD [auth A],
XE [auth A],
XF [auth A],
YB [auth A],
YC [auth A],
YD [auth A],
YE [auth A],
YF [auth A],
ZB [auth A],
ZC [auth A],
ZD [auth A],
ZE [auth A],
ZF [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MHU
Query on MHU		AB [auth C]L-PEPTIDE LINKINGC12 H18 N2 O2PHE
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 53
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000505
Query on PRD_000505		AB [auth C]QuinupristinOligopeptide / Antibiotic Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Swedish Research CouncilSwedenNT_2015-04107

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-08
    Type: Initial release
  • Version 1.1: 2020-07-15
    Changes: Structure summary
  • Version 1.2: 2020-07-22
    Changes: Database references
  • Version 1.3: 2021-07-28
    Changes: Database references
  • Version 1.4: 2021-09-08
    Changes: Database references, Derived calculations
  • Version 2.0: 2023-01-11
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Source and taxonomy, Structure summary