7OF0

Structure of a human mitochondrial ribosome large subunit assembly intermediate in complex with MTERF4-NSUN4 (dataset1).

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.20 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 GTPase-mediated mitochondrial ribosome biogenesis and recycling.

Hillen, H.S., Lavdovskaia, E., Nadler, F., Hanitsch, E., Linden, A., Bohnsack, K.E., Urlaub, H., Richter-Dennerlein, R.

(2021) Nat Commun 12: 3672-3672

  • DOI: https://doi.org/10.1038/s41467-021-23702-y
  • Primary Citation of Related Structures:  
    7OF0, 7OF2, 7OF3, 7OF4, 7OF5, 7OF6, 7OF7

  • PubMed Abstract: 

    • Ribosome biogenesis requires auxiliary factors to promote folding and assembly of ribosomal proteins and RNA. Particularly, maturation of the peptidyl transferase center (PTC) is mediated by conserved GTPases, but the molecular basis is poorly understood ...

    Ribosome biogenesis requires auxiliary factors to promote folding and assembly of ribosomal proteins and RNA. Particularly, maturation of the peptidyl transferase center (PTC) is mediated by conserved GTPases, but the molecular basis is poorly understood. Here, we define the mechanism of GTPase-driven maturation of the human mitochondrial large ribosomal subunit (mtLSU) using endogenous complex purification, in vitro reconstitution and cryo-EM. Structures of transient native mtLSU assembly intermediates that accumulate in GTPBP6-deficient cells reveal how the biogenesis factors GTPBP5, MTERF4 and NSUN4 facilitate PTC folding. Addition of recombinant GTPBP6 reconstitutes late mtLSU biogenesis in vitro and shows that GTPBP6 triggers a molecular switch and progression to a near-mature PTC state. Additionally, cryo-EM analysis of GTPBP6-treated mature mitochondrial ribosomes reveals the structural basis for the dual-role of GTPBP6 in ribosome biogenesis and recycling. Together, these results provide a framework for understanding step-wise PTC folding as a critical conserved quality control checkpoint.

    Related Citations: 
    • Structural basis of GTPase-mediated mitochondrial ribosome biogenesis and recycling
      Hillen, H.S., Lavdovskaia, E., Nadler, F., Hanitsch, E., Linden, A., Bohnsack, K.E., Urlaub, H., Richter-Dennerlein, R.
      (2021) Biorxiv --: --
    Organizational Affiliation: 

    Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Goettingen, Goettingen, Germany. ricarda.richter@med.uni-goettingen.de.



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
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39S ribosomal protein L33, mitochondrialB [auth 1]65Homo sapiensMutation(s): 0 
Gene Names: MRPL33, C2orf1
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Entity ID: 3
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39S ribosomal protein L34, mitochondrialC [auth 2]92Homo sapiensMutation(s): 0 
Gene Names: MRPL34
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Entity ID: 4
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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
MoleculeChainsSequence LengthOrganismDetailsImage
5-methylcytosine rRNA methyltransferase NSUN4M [auth C]384Homo sapiensMutation(s): 0 
Gene Names: NSUN4
EC: 2.1.1
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Entity ID: 14
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39S ribosomal protein L2, mitochondrialN [auth D]305Homo sapiensMutation(s): 0 
Gene Names: MRPL2, CGI-22
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39S ribosomal protein L3, mitochondrialO [auth E]348Homo sapiensMutation(s): 0 
Gene Names: MRPL3, MRL3, RPML3
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Entity ID: 16
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39S ribosomal protein L4, mitochondrialP [auth F]311Homo sapiensMutation(s): 0 
Gene Names: MRPL4, CDABP0091, CGI-28
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Entity ID: 17
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Transcription termination factor 4, mitochondrialQ [auth G]381Homo sapiensMutation(s): 0 
Gene Names: MTERF4, MTERFD2, HSPC096
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Entity ID: 18
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39S ribosomal protein L9, mitochondrialR [auth H]267Homo sapiensMutation(s): 0 
Gene Names: MRPL9
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Entity ID: 19
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39S ribosomal protein L10, mitochondrialS [auth I]261Homo sapiensMutation(s): 0 
Gene Names: MRPL10, MRPL8, RPML8
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39S ribosomal protein L11, mitochondrialT [auth J]192Homo sapiensMutation(s): 0 
Gene Names: MRPL11, CGI-113
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39S ribosomal protein L13, mitochondrialU [auth K]178Homo sapiensMutation(s): 0 
Gene Names: MRPL13
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Entity ID: 22
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39S ribosomal protein L14, mitochondrialV [auth L]145Homo sapiensMutation(s): 0 
Gene Names: MRPL14, MRPL32, RPML32
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Entity ID: 23
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39S ribosomal protein L15, mitochondrialW [auth M]296Homo sapiensMutation(s): 0 
Gene Names: MRPL15, HSPC145
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39S ribosomal protein L16, mitochondrialX [auth N]251Homo sapiensMutation(s): 0 
Gene Names: MRPL16, PNAS-111
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39S ribosomal protein L17, mitochondrialY [auth O]175Homo sapiensMutation(s): 0 
Gene Names: MRPL17, LIP2
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39S ribosomal protein L18, mitochondrialZ [auth P]180Homo sapiensMutation(s): 0 
Gene Names: MRPL18, HSPC071
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39S ribosomal protein L19, mitochondrialAA [auth Q]292Homo sapiensMutation(s): 0 
Gene Names: MRPL19, KIAA0104, MRPL15
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Entity ID: 28
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39S ribosomal protein L20, mitochondrialBA [auth R]149Homo sapiensMutation(s): 0 
Gene Names: MRPL20
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39S ribosomal protein L21, mitochondrialCA [auth S]205Homo sapiensMutation(s): 0 
Gene Names: MRPL21
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39S ribosomal protein L22, mitochondrialDA [auth T]206Homo sapiensMutation(s): 0 
Gene Names: MRPL22, MRPL25, RPML25, HSPC158
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Entity ID: 31
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39S ribosomal protein L23, mitochondrialEA [auth U]153Homo sapiensMutation(s): 0 
Gene Names: MRPL23, L23MRP, RPL23L
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Entity ID: 32
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39S ribosomal protein L24, mitochondrialFA [auth V]216Homo sapiensMutation(s): 0 
Gene Names: MRPL24
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Entity ID: 33
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39S ribosomal protein L27, mitochondrialGA [auth W]148Homo sapiensMutation(s): 0 
Gene Names: MRPL27, HSPC250
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Entity ID: 34
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39S ribosomal protein L28, mitochondrialHA [auth X]256Homo sapiensMutation(s): 0 
Gene Names: MRPL28, MAAT1
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Entity ID: 35
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39S ribosomal protein L47, mitochondrialIA [auth Y]250Homo sapiensMutation(s): 0 
Gene Names: MRPL47, NCM1, CGI-204
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Entity ID: 36
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39S ribosomal protein L30, mitochondrialJA [auth Z]161Homo sapiensMutation(s): 0 
Gene Names: MRPL30, MRPL28, RPML28, HSPC249
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Entity ID: 37
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39S ribosomal protein L42, mitochondrialKA [auth a]142Homo sapiensMutation(s): 0 
Gene Names: MRPL42, MRPL31, MRPS32, RPML31, HSPC204, PTD007
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Entity ID: 38
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39S ribosomal protein L43, mitochondrialLA [auth b]215Homo sapiensMutation(s): 0 
Gene Names: MRPL43
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Entity ID: 39
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39S ribosomal protein L44, mitochondrialMA [auth c]332Homo sapiensMutation(s): 0 
Gene Names: MRPL44
EC: 3.1.26
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L45, mitochondrialNA [auth d]306Homo sapiensMutation(s): 0 
Gene Names: MRPL45
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Entity ID: 41
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39S ribosomal protein L46, mitochondrialOA [auth e]279Homo sapiensMutation(s): 0 
Gene Names: MRPL46, C15orf4, LIECG2
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Entity ID: 42
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39S ribosomal protein L48, mitochondrialPA [auth f]212Homo sapiensMutation(s): 0 
Gene Names: MRPL48, CGI-118, HSPC290
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Entity ID: 43
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39S ribosomal protein L49, mitochondrialQA [auth g]166Homo sapiensMutation(s): 0 
Gene Names: MRPL49, C11orf4, NOF1, OK/SW-cl.67
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Entity ID: 44
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39S ribosomal protein L50, mitochondrialRA [auth h]158Homo sapiensMutation(s): 0 
Gene Names: MRPL50
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Find proteins for Q8N5N7 (Homo sapiens)
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Entity ID: 45
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39S ribosomal protein L51, mitochondrialSA [auth i]128Homo sapiensMutation(s): 0 
Gene Names: MRPL51, MRP64, CDA09, HSPC241
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Entity ID: 46
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39S ribosomal protein L52, mitochondrialTA [auth j]123Homo sapiensMutation(s): 0 
Gene Names: MRPL52
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Entity ID: 47
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39S ribosomal protein L53, mitochondrialUA [auth k]112Homo sapiensMutation(s): 0 
Gene Names: MRPL53
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Entity ID: 48
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39S ribosomal protein L55, mitochondrialVA [auth m]128Homo sapiensMutation(s): 0 
Gene Names: MRPL55, UNQ5835/PRO19675
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Entity ID: 49
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Ribosomal protein 63, mitochondrialWA [auth o]102Homo sapiensMutation(s): 0 
Gene Names: MRPL57, MRP63
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Find proteins for Q9BQC6 (Homo sapiens)
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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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Find proteins for Q14197 (Homo sapiens)
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Entity ID: 51
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Growth arrest and DNA damage-inducible proteins-interacting protein 1YA [auth q]222Homo sapiensMutation(s): 0 
Gene Names: GADD45GIP1, MRPL59, PLINP1, PRG6
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Entity ID: 52
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39S ribosomal protein S18a, mitochondrialZA [auth r]196Homo sapiensMutation(s): 0 
Gene Names: MRPS18A
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Find proteins for Q9NVS2 (Homo sapiens)
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Entity ID: 53
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39S ribosomal protein S30, mitochondrialAB [auth s]439Homo sapiensMutation(s): 0 
Gene Names: MRPS30, PDCD9, BM-047
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Find proteins for Q9NP92 (Homo sapiens)
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Entity ID: 54
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Mitochondrial assembly of ribosomal large subunit protein 1BB [auth u]234Homo sapiensMutation(s): 0 
Gene Names: MALSU1, C7orf30
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Entity ID: 55
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MIEF1 upstream open reading frame proteinCB [auth v]70Homo sapiensMutation(s): 0 
Gene Names: MIEF1
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Entity ID: 56
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Acyl carrier protein, mitochondrialDB [auth w]156Homo sapiensMutation(s): 0 
Gene Names: NDUFAB1
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Entity ID: 11
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16S ribosomal RNAK [auth A]1,559Homo sapiens
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Entity ID: 12
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mitochondrial tRNAValL [auth B]69Homo sapiens
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Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download Ideal Coordinates CCD File 
EB [auth 0],
FB [auth 4],
PD [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]
BC [auth A]
BD [auth A]
CC [auth A]
AC [auth A],
AD [auth A],
BC [auth A],
BD [auth A],
CC [auth A],
CD [auth A],
DC [auth A],
DD [auth A],
EC [auth A],
ED [auth A],
FC [auth A],
FD [auth A],
GB [auth A],
GC [auth A],
GD [auth A],
HB [auth A],
HC [auth A],
HD [auth A],
IB [auth A],
IC [auth A],
ID [auth A],
JB [auth A],
JC [auth A],
JD [auth A],
KB [auth A],
KC [auth A],
KD [auth A],
LB [auth A],
LC [auth A],
LD [auth A],
MB [auth A],
MC [auth A],
MD [auth A],
NB [auth A],
NC [auth A],
ND [auth E],
OB [auth A],
OC [auth A],
OD [auth g],
PB [auth A],
PC [auth A],
QB [auth A],
QC [auth A],
RB [auth A],
RC [auth A],
SB [auth A],
SC [auth A],
TB [auth A],
TC [auth A],
UB [auth A],
UC [auth A],
VB [auth A],
VC [auth A],
WB [auth A],
WC [auth A],
XB [auth A],
XC [auth A],
YB [auth A],
YC [auth A],
ZB [auth A],
ZC [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



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

Deposition Data

Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyRI 2715/1-1
German Research Foundation (DFG)GermanyEXC 2067/1-390729940
German Research Foundation (DFG)GermanyFOR2848
German Research Foundation (DFG)GermanySFB860
German Research Foundation (DFG)GermanySFB1160

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-09
    Type: Initial release
  • Version 1.1: 2021-06-23
    Changes: Database references
  • Version 1.2: 2021-06-30
    Changes: Database references