3JCT

Cryo-em structure of eukaryotic pre-60S ribosomal subunits


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.08 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

Diverse roles of assembly factors revealed by structures of late nuclear pre-60S ribosomes

Wu, S.Tutuncuoglu, B.Yan, K.Brown, H.Zhang, Y.Tan, D.Gamalinda, M.Yuan, Y.Li, Z.Jakovljevic, J.Ma, C.Lei, J.Dong, M.Q.Woolford, J.L.Gao, N.

(2016) Nature 534: 133-137

  • DOI: 10.1038/nature17942
  • Primary Citation of Related Structures:  
    3JCT

  • PubMed Abstract: 
  • Ribosome biogenesis is a highly complex process in eukaryotes, involving temporally and spatially regulated ribosomal protein (r-protein) binding and ribosomal RNA remodelling events in the nucleolus, nucleoplasm and cytoplasm. Hundreds of assembly f ...

    Ribosome biogenesis is a highly complex process in eukaryotes, involving temporally and spatially regulated ribosomal protein (r-protein) binding and ribosomal RNA remodelling events in the nucleolus, nucleoplasm and cytoplasm. Hundreds of assembly factors, organized into sequential functional groups, facilitate and guide the maturation process into productive assembly branches in and across different cellular compartments. However, the precise mechanisms by which these assembly factors function are largely unknown. Here we use cryo-electron microscopy to characterize the structures of yeast nucleoplasmic pre-60S particles affinity-purified using the epitope-tagged assembly factor Nog2. Our data pinpoint the locations and determine the structures of over 20 assembly factors, which are enriched in two areas: an arc region extending from the central protuberance to the polypeptide tunnel exit, and the domain including the internal transcribed spacer 2 (ITS2) that separates 5.8S and 25S ribosomal RNAs. In particular, two regulatory GTPases, Nog2 and Nog1, act as hub proteins to interact with multiple, distant assembly factors and functional ribosomal RNA elements, manifesting their critical roles in structural remodelling checkpoints and nuclear export. Moreover, our snapshots of compositionally and structurally different pre-60S intermediates provide essential mechanistic details for three major remodelling events before nuclear export: rotation of the 5S ribonucleoprotein, construction of the active centre and ITS2 removal. The rich structural information in our structures provides a framework to dissect molecular roles of diverse assembly factors in eukaryotic ribosome assembly.


    Organizational Affiliation

    Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L2-AA254Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL2ARPL5BYFR031C-AYFR031BC
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L3B387Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL3MAK8TCM1YOR063WYOR29-14
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L4-AC362Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL4ARPL2RPL2AYBR031WYBR0315
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L5D297Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL5RPL1RPL1AYPL131WLPI14W
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L6-AE176Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL6ARPL17AYL16AYML073C
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L7-AF244Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL7ARPL6ARPL8AYL8AYGL076C
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L8-AG256Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL8AMAK7RPL4AYHL033C
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L9-AH191Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL9ARPL8ARPL9YGL147C
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Bud site selection protein 20I166Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: BUD20YLR074C
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L11-AJ174Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL11ARP39ARPL16AYPR102CP8283.14
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome-interacting protein CIC1K376Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CIC1NSA3YHR052W
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Entity ID: 12
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60S ribosomal protein L13-AL199Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL13AYDL082W
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L14-AM138Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL14AYKL006WYKL153
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L15-AN204Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL15ARPL10ARPL13AYL10AYLR029C
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L16-AO199Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL16ARPL13RPL21AYIL133C
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L17-AP184Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL17ARPL17RPL20AYKL180W
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Entity ID: 17
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60S ribosomal protein L18-AQ186Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL18ARP28AYOL120C
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L19-AR189Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL19ARPL23AYL14AYBR084C-AYBR084BC
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L20-AS172Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL20ARPL18ARPL18A2YMR242CYM9408.04C
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Entity ID: 20
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60S ribosomal protein L21-AT160Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL21AURP1YBR191WYBR1401
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L22-AU121Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL22AYLR061WL2168
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L23-AV137Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL23ARPL17ARPL17AAYBL087CYBL0713
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Entity ID: 23
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Ribosome assembly factor MRT4W236Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MRT4YKL009WYKL160
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L25X142Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL25YOL127W
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Entity ID: 25
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60S ribosomal protein L26-AY127Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL26ARPL26RPL33AYLR344WL8300.4
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L27-AZ136Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL27ARPL27YHR010W
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L28a149Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL28CYH2YGL103W
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleolar GTP-binding protein 1b647Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOG1YPL093WLPG15W
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L30c105Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL30RPL32YGL030W
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L31-Ad113Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL31ARPL34RPL34AYDL075WD2478
Find proteins for P0C2H8 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L32e130Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL32YBL092WYBL0838
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L33-Af107Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL33ARPL37AYPL143WLPI4WP2625
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Entity ID: 33
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60S ribosomal protein L34-Ag121Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL34AYER056C-AYER056BC
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Entity ID: 34
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60S ribosomal protein L35-Ah120Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL35ASOS1YDL191WD1249
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Entity ID: 35
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60S ribosomal protein L36-Ai100Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL36ARPL39AYMR194WYM9646.06
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Entity ID: 36
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60S ribosomal protein L37-Aj88Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL37ARPL35AYLR185WL9470.6
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Entity ID: 37
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60S ribosomal protein L38k78Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL38YLR325CL8543.2
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Entity ID: 38
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60S ribosomal protein L39l51Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL39RPL46SPB2YJL189WJ0360
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Entity ID: 39
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Nucleolar GTP-binding protein 2m486Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOG2YNR053CN3484
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Entity ID: 40
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Pescadillo homologn605Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOP7RRP13YPH1YGR103W
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Entity ID: 41
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Ribosome biogenesis protein 15o220Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOP15YNL110CN1954
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Entity ID: 42
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60S ribosomal protein L43-Ap92Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL43AYPR043WYP9499.02
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Entity ID: 43
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Ribosome biogenesis protein NOP53q455Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOP53YPL146CLPI2CP2610
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Entity ID: 44
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Ribosome biogenesis protein NSA2r261Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NSA2YER126CSYGP-ORF47
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Entity ID: 45
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Nuclear GTP-binding protein NUG1s520Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NUG1YER006W
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Entity ID: 46
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Ribosome biogenesis protein RLP7t322Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RLP7RPL7YNL002CN2014
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Entity ID: 47
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Ribosome biogenesis protein RLP24u199Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RLP24YLR009W
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Entity ID: 48
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Ribosome biogenesis protein RPF2v344Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPF2YKR081CYKR401
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Entity ID: 49
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Regulator of ribosome biosynthesisw203Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRS1YOR294W
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Entity ID: 50
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Ribosome assembly protein 4x515Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RSA4YCR072CYCR72C
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Entity ID: 51
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Eukaryotic translation initiation factor 6y245Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TIF6CDC95YPR016CLPZ15C
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Entity ID: 52
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UPF0642 protein YBL028Cz106Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: YBL028CYBL0423
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Entity ID: 56
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Probable metalloprotease ARX14593Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ARX1YDR101CYD8557.10c
EC: 3
Find proteins for Q03862 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 57
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rRNA-processing protein CGR15120Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CGR1YGL029W
Find proteins for P53188 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53188 
Go to UniProtKB:  P53188
Protein Feature View
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  • Reference Sequence
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Entity ID: 53
MoleculeChainsLengthOrganismImage
RDN25-1 rRNA13396Saccharomyces cerevisiae S288C
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Entity ID: 54
MoleculeChainsLengthOrganismImage
RDN58-1 rRNA2158Saccharomyces cerevisiae S288C
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Entity ID: 55
MoleculeChainsLengthOrganismImage
RDN5-2 rRNA3121Saccharomyces cerevisiae S288C
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Entity ID: 58
MoleculeChainsLengthOrganismImage
ITS2-1 miscRNA6232Saccharomyces cerevisiae S288C
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.08 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-06-01
    Type: Initial release
  • Version 1.1: 2017-02-01
    Changes: Database references
  • Version 1.2: 2019-12-18
    Changes: Advisory, Data collection, Database references, Derived calculations