7OI9

Cryo-EM structure of late human 39S mitoribosome assembly intermediates, state 3B


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 1.0 of the entry. See complete history


Literature

A distinct assembly pathway of the human 39S late pre-mitoribosome.

Cheng, J.Berninghausen, O.Beckmann, R.

(2021) Nat Commun 12: 4544-4544

  • DOI: 10.1038/s41467-021-24818-x
  • Primary Citation of Related Structures:  
    7OIC, 7OID, 7OIA, 7OIB, 7OIE, 7OI9, 7OI7, 7OI8

  • PubMed Abstract: 
  • Assembly of the mitoribosome is largely enigmatic and involves numerous assembly factors. Little is known about their function and the architectural transitions of the pre-ribosomal intermediates. Here, we solve cryo-EM structures of the human 39S large subunit pre-ribosomes, representing five distinct late states ...

    Assembly of the mitoribosome is largely enigmatic and involves numerous assembly factors. Little is known about their function and the architectural transitions of the pre-ribosomal intermediates. Here, we solve cryo-EM structures of the human 39S large subunit pre-ribosomes, representing five distinct late states. Besides the MALSU1 complex used as bait for affinity purification, we identify several assembly factors, including the DDX28 helicase, MRM3, GTPBP10 and the NSUN4-mTERF4 complex, all of which keep the 16S rRNA in immature conformations. The late transitions mainly involve rRNA domains IV and V, which form the central protuberance, the intersubunit side and the peptidyltransferase center of the 39S subunit. Unexpectedly, we find deacylated tRNA in the ribosomal E-site, suggesting a role in 39S assembly. Taken together, our study provides an architectural inventory of the distinct late assembly phase of the human 39S mitoribosome.


    Organizational Affiliation

    Gene Center and Department for Biochemistry, LMU Munich, München, Germany. beckmann@genzentrum.lmu.de.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L2, mitochondrialA [auth D]305Homo sapiensMutation(s): 0 
Gene Names: MRPL2CGI-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: MRPL3MRL3RPML3
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L4, mitochondrialC [auth F]311Homo sapiensMutation(s): 0 
Gene Names: MRPL4CDABP0091CGI-28
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L9, mitochondrialD [auth H]267Homo sapiensMutation(s): 0 
Gene Names: MRPL9
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L10, mitochondrialE [auth I]261Homo sapiensMutation(s): 0 
Gene Names: MRPL10MRPL8RPML8
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Entity ID: 6
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39S ribosomal protein L11, mitochondrialF [auth J]192Homo sapiensMutation(s): 0 
Gene Names: MRPL11CGI-113
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
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: MRPL14MRPL32RPML32
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Entity ID: 9
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39S ribosomal protein L15, mitochondrialI [auth M]296Homo sapiensMutation(s): 0 
Gene Names: MRPL15HSPC145
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Entity ID: 10
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39S ribosomal protein L16, mitochondrialJ [auth N]251Homo sapiensMutation(s): 0 
Gene Names: MRPL16PNAS-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: MRPL17LIP2
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Entity ID: 12
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39S ribosomal protein L18, mitochondrialL [auth P]180Homo sapiensMutation(s): 0 
Gene Names: MRPL18HSPC071
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Entity ID: 13
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39S ribosomal protein L19, mitochondrialM [auth Q]292Homo sapiensMutation(s): 0 
Gene Names: MRPL19KIAA0104MRPL15
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Entity ID: 14
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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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Entity ID: 16
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39S ribosomal protein L22, mitochondrialP [auth T]206Homo sapiensMutation(s): 0 
Gene Names: MRPL22MRPL25RPML25HSPC158
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Entity ID: 17
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39S ribosomal protein L23, mitochondrialQ [auth U]153Homo sapiensMutation(s): 0 
Gene Names: MRPL23L23MRPRPL23L
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Entity ID: 18
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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: MRPL27HSPC250
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Entity ID: 20
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39S ribosomal protein L28, mitochondrialT [auth X]256Homo sapiensMutation(s): 0 
Gene Names: MRPL28MAAT1
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Entity ID: 21
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39S ribosomal protein L47, mitochondrialU [auth Y]250Homo sapiensMutation(s): 0 
Gene Names: MRPL47NCM1CGI-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: MRPL30MRPL28RPML28HSPC249
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Entity ID: 23
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39S ribosomal protein L32, mitochondrialW [auth 0]188Homo sapiensMutation(s): 0 
Gene Names: MRPL32HSPC283
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Entity ID: 24
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39S ribosomal protein L33, mitochondrialX [auth 1]65Homo sapiensMutation(s): 0 
Gene Names: MRPL33C2orf1
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Entity ID: 25
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39S ribosomal protein L34, mitochondrialY [auth 2]92Homo sapiensMutation(s): 0 
Gene Names: MRPL34
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Entity ID: 26
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39S ribosomal protein L35, mitochondrialZ [auth 3]188Homo sapiensMutation(s): 0 
Gene Names: MRPL35BM-007
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L37, mitochondrialAA [auth 5]423Homo sapiensMutation(s): 0 
Gene Names: MRPL37MRPL2RPML2HSPC235
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Entity ID: 28
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39S ribosomal protein L38, mitochondrialBA [auth 6]380Homo sapiensMutation(s): 0 
Gene Names: MRPL38HSPC262
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Entity ID: 29
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39S ribosomal protein L39, mitochondrialCA [auth 7]338Homo sapiensMutation(s): 0 
Gene Names: MRPL39C21orf92MRPL5RPML5MSTP003PRED22
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Entity ID: 30
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39S ribosomal protein L40, mitochondrialDA [auth 8]206Homo sapiensMutation(s): 0 
Gene Names: MRPL40NLVCFURIM
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Entity ID: 31
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39S ribosomal protein L41, mitochondrialEA [auth 9]137Homo sapiensMutation(s): 0 
Gene Names: MRPL41BMRPMRPL27RPML27PIG3
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Entity ID: 32
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39S ribosomal protein L42, mitochondrialFA [auth a]142Homo sapiensMutation(s): 0 
Gene Names: MRPL42MRPL31MRPS32RPML31HSPC204PTD007
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Entity ID: 33
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39S ribosomal protein L43, mitochondrialGA [auth b]215Homo 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: MRPL46C15orf4LIECG2
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Entity ID: 37
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39S ribosomal protein L48, mitochondrialKA [auth f]212Homo sapiensMutation(s): 0 
Gene Names: MRPL48CGI-118HSPC290
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Entity ID: 38
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39S ribosomal protein L49, mitochondrialLA [auth g]166Homo sapiensMutation(s): 0 
Gene Names: MRPL49C11orf4NOF1OK/SW-cl.67
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Entity ID: 39
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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: MRPL51MRP64CDA09HSPC241
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Entity ID: 41
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39S ribosomal protein L52, mitochondrialOA [auth j]123Homo sapiensMutation(s): 0 
Gene Names: MRPL52
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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: MRPL55UNQ5835/PRO19675
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Entity ID: 45
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Ribosomal protein 63, mitochondrialSA [auth o]102Homo sapiensMutation(s): 0 
Gene Names: MRPL57MRP63
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Entity ID: 46
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Peptidyl-tRNA hydrolase ICT1, mitochondrialTA [auth p]206Homo sapiensMutation(s): 0 
Gene Names: MRPL58DS1ICT1
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: GADD45GIP1MRPL59PLINP1PRG6
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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
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein S30, mitochondrialWA [auth s]439Homo sapiensMutation(s): 0 
Gene Names: MRPS30PDCD9BM-047
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial assembly of ribosomal large subunit protein 1XA [auth u]234Homo sapiensMutation(s): 0 
Gene Names: MALSU1C7orf30
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetailsImage
MIEF1 upstream open reading frame proteinYA [auth v]70Homo sapiensMutation(s): 0 
Gene Names: MIEF1
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetailsImage
Acyl carrier protein, mitochondrialZA [auth w]156Homo sapiensMutation(s): 0 
Gene Names: NDUFAB1
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Entity ID: 53
MoleculeChainsLengthOrganismImage
16S rRNAAB [auth A]1559Homo sapiens
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Entity ID: 54
MoleculeChainsLengthOrganismImage
mitochondrial Val tRNABB [auth B]69Homo sapiens
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PNS (Subject of Investigation/LOI)
Query on PNS

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GB [auth v]4'-PHOSPHOPANTETHEINE
C11 H23 N2 O7 P S
JDMUPRLRUUMCTL-VIFPVBQESA-N
 Ligand Interaction
ZN
Query on ZN

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DB [auth 0], FB [auth r]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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AC [auth A] , AD [auth A] , BC [auth A] , BD [auth A] , CB [auth W] , CC [auth A] , DC [auth A] , EB [auth g] , 
AC [auth A],  AD [auth A],  BC [auth A],  BD [auth A],  CB [auth W],  CC [auth A],  DC [auth A],  EB [auth g],  EC [auth A],  FC [auth A],  GC [auth A],  HB [auth A],  HC [auth A],  IB [auth A],  IC [auth A],  JB [auth A],  JC [auth A],  KB [auth A],  KC [auth A],  LB [auth A],  LC [auth A],  MB [auth A],  MC [auth A],  NB [auth A],  NC [auth A],  OB [auth A],  OC [auth A],  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: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-15
    Type: Initial release