5OOL

Structure of a native assembly intermediate of the human mitochondrial ribosome with unfolded interfacial rRNA

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.06 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history. 


Literature

Structures of the human mitochondrial ribosome in native states of assembly.

Brown, A., Rathore, S., Kimanius, D., Aibara, S., Bai, X.C., Rorbach, J., Amunts, A., Ramakrishnan, V.

(2017) Nat Struct Mol Biol 24: 866-869

  • DOI: 10.1038/nsmb.3464
  • Primary Citation of Related Structures:  
    5OOL, 5OOM

  • PubMed Abstract: 

    • Mammalian mitochondrial ribosomes (mitoribosomes) have less rRNA content and 36 additional proteins compared with the evolutionarily related bacterial ribosome. These differences make the assembly of mitoribosomes more complex than the assembly of bacterial ribosomes, but the molecular details of mitoribosomal biogenesis remain elusive ...

    Mammalian mitochondrial ribosomes (mitoribosomes) have less rRNA content and 36 additional proteins compared with the evolutionarily related bacterial ribosome. These differences make the assembly of mitoribosomes more complex than the assembly of bacterial ribosomes, but the molecular details of mitoribosomal biogenesis remain elusive. Here, we report the structures of two late-stage assembly intermediates of the human mitoribosomal large subunit (mt-LSU) isolated from a native pool within a human cell line and solved by cryo-EM to ∼3-Å resolution. Comparison of the structures reveals insights into the timing of rRNA folding and protein incorporation during the final steps of ribosomal maturation and the evolutionary adaptations that are required to preserve biogenesis after the structural diversification of mitoribosomes. Furthermore, the structures redefine the ribosome silencing factor (RsfS) family as multifunctional biogenesis factors and identify two new assembly factors (L0R8F8 and mt-ACP) not previously implicated in mitoribosomal biogenesis.

    Organizational Affiliation: 

    MRC Laboratory of Molecular Biology, Cambridge, UK.



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 L3, mitochondrialD [auth E]348Homo sapiensMutation(s): 0 
Gene Names: MRPL3, MRL3, RPML3
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Entity ID: 5
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39S ribosomal protein L4, mitochondrialE [auth F]311Homo sapiensMutation(s): 0 
Gene Names: MRPL4, CDABP0091, CGI-28
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Entity ID: 6
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39S ribosomal protein L9, mitochondrialF [auth H]267Homo sapiensMutation(s): 0 
Gene Names: MRPL9
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Entity ID: 7
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39S ribosomal protein L10, mitochondrialG [auth I]261Homo sapiensMutation(s): 0 
Gene Names: MRPL10, MRPL8, RPML8
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Entity ID: 8
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39S ribosomal protein L11, mitochondrialH [auth J]192Homo sapiensMutation(s): 0 
Gene Names: MRPL11, CGI-113
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39S ribosomal protein L13, mitochondrialI [auth K]178Homo sapiensMutation(s): 0 
Gene Names: MRPL13
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39S ribosomal protein L14, mitochondrialJ [auth L]145Homo sapiensMutation(s): 0 
Gene Names: MRPL14, MRPL32, RPML32
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39S ribosomal protein L15, mitochondrialK [auth M]296Homo sapiensMutation(s): 0 
Gene Names: MRPL15, HSPC145
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39S ribosomal protein L16, mitochondrialL [auth N]251Homo sapiensMutation(s): 0 
Gene Names: MRPL16, PNAS-111
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39S ribosomal protein L17, mitochondrialM [auth O]175Homo sapiensMutation(s): 0 
Gene Names: MRPL17, LIP2
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39S ribosomal protein L18, mitochondrialN [auth P]180Homo sapiensMutation(s): 0 
Gene Names: MRPL18, HSPC071
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Entity ID: 15
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39S ribosomal protein L19, mitochondrialO [auth Q]292Homo sapiensMutation(s): 0 
Gene Names: MRPL19, KIAA0104, MRPL15
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Entity ID: 16
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39S ribosomal protein L20, mitochondrialP [auth R]149Homo sapiensMutation(s): 0 
Gene Names: MRPL20
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Entity ID: 17
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39S ribosomal protein L21, mitochondrialQ [auth S]205Homo sapiensMutation(s): 0 
Gene Names: MRPL21
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Entity ID: 18
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39S ribosomal protein L22, mitochondrialR [auth T]206Homo sapiensMutation(s): 0 
Gene Names: MRPL22, MRPL25, RPML25, HSPC158
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Entity ID: 19
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39S ribosomal protein L23, mitochondrialS [auth U]153Homo sapiensMutation(s): 0 
Gene Names: MRPL23, L23MRP, RPL23L
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39S ribosomal protein L24, mitochondrialT [auth V]216Homo sapiensMutation(s): 0 
Gene Names: MRPL24
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39S ribosomal protein L27, mitochondrialU [auth W]148Homo sapiensMutation(s): 0 
Gene Names: MRPL27, HSPC250
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Entity ID: 22
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39S ribosomal protein L28, mitochondrialV [auth X]256Homo sapiensMutation(s): 0 
Gene Names: MRPL28, MAAT1
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Entity ID: 23
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39S ribosomal protein L47, mitochondrialW [auth Y]250Homo sapiensMutation(s): 0 
Gene Names: MRPL47, NCM1, CGI-204
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39S ribosomal protein L30, mitochondrialX [auth Z]161Homo sapiensMutation(s): 0 
Gene Names: MRPL30, MRPL28, RPML28, HSPC249
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39S ribosomal protein L32, mitochondrialY [auth 0]188Homo sapiensMutation(s): 0 
Gene Names: MRPL32, HSPC283
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39S ribosomal protein L33, mitochondrialZ [auth 1]65Homo sapiensMutation(s): 0 
Gene Names: MRPL33, C2orf1
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39S ribosomal protein L34, mitochondrialAA [auth 2]92Homo sapiensMutation(s): 0 
Gene Names: MRPL34
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39S ribosomal protein L35, mitochondrialBA [auth 3]188Homo sapiensMutation(s): 0 
Gene Names: MRPL35, BM-007
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Entity ID: 29
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39S ribosomal protein L36, mitochondrialCA [auth 4]103Homo sapiensMutation(s): 0 
Gene Names: MRPL36, BRIP1
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39S ribosomal protein L37, mitochondrialDA [auth 5]423Homo sapiensMutation(s): 0 
Gene Names: MRPL37, MRPL2, RPML2, HSPC235
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39S ribosomal protein L38, mitochondrialEA [auth 6]380Homo sapiensMutation(s): 0 
Gene Names: MRPL38, HSPC262
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39S ribosomal protein L39, mitochondrialFA [auth 7]338Homo sapiensMutation(s): 0 
Gene Names: MRPL39, C21orf92, MRPL5, RPML5, MSTP003, PRED22
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39S ribosomal protein L40, mitochondrialGA [auth 8]206Homo sapiensMutation(s): 0 
Gene Names: MRPL40, NLVCF, URIM
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39S ribosomal protein L41, mitochondrialHA [auth 9]137Homo sapiensMutation(s): 0 
Gene Names: MRPL41, BMRP, MRPL27, RPML27, PIG3
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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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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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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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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
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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
39S ribosomal protein L52, mitochondrialRA [auth j]123Homo sapiensMutation(s): 0 
Gene Names: MRPL52
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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
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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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Find proteins for Q9NP92 (Homo sapiens)
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Entity ID: 53
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Unknown protein or protein extensionAB [auth t]28Homo sapiensMutation(s): 0 
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetailsImage
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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Find proteins for L0R8F8 (Homo sapiens)
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetailsImage
Acyl carrier protein, mitochondrialDB [auth w]156Homo sapiensMutation(s): 0 
Gene Names: NDUFAB1
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Entity ID: 1
MoleculeChainsLengthOrganismImage
16S ribosomal RNAA 1559Homo sapiens
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Entity ID: 2
MoleculeChainsLengthOrganismImage
mitochondrial tRNAValB 69Homo sapiens
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PNS
Query on PNS
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VE [auth v]4'-PHOSPHOPANTETHEINE
C11 H23 N2 O7 P S
JDMUPRLRUUMCTL-VIFPVBQESA-N		 Ligand Interaction
ZN
Query on ZN
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OE [auth I],
SE [auth 0],
TE [auth 4]		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],
EB [auth A],
EC [auth A],
ED [auth A],
EE [auth A],
FB [auth A],
FC [auth A],
FD [auth A],
FE [auth A],
GB [auth A],
GC [auth A],
GD [auth A],
GE [auth A],
HB [auth A],
HC [auth A],
HD [auth A],
HE [auth A],
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 D],
OB [auth A],
OC [auth A],
OD [auth A],
PB [auth A],
PC [auth A],
PD [auth A],
PE [auth M],
QB [auth A],
QC [auth A],
QD [auth A],
QE [auth T],
RB [auth A],
RC [auth A],
RD [auth A],
RE [auth W],
SB [auth A],
SC [auth A],
SD [auth A],
TB [auth A],
TC [auth A],
TD [auth A],
UB [auth A],
UC [auth A],
UD [auth A],
UE [auth g],
VB [auth A],
VC [auth A],
VD [auth A],
WB [auth A],
WC [auth A],
WD [auth A],
XB [auth A],
XC [auth A],
XD [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
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.06 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-09-13
    Type: Initial release
  • Version 1.1: 2017-09-20
    Changes: Database references
  • Version 1.2: 2017-10-18
    Changes: Database references
  • Version 1.3: 2019-02-20
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.4: 2019-12-11
    Changes: Other