6N8K

Cryo-EM structure of early cytoplasmic-immediate (ECI) pre-60S ribosomal subunit

  • Classification: RIBOSOME
  • Organism(s): Saccharomyces cerevisiae S288C
  • Mutation(s): No 

  • Deposited: 2018-11-29 Released: 2019-03-13 
  • Deposition Author(s): Zhou, Y., Musalgaonkar, S., Johnson, A.W., Taylor, D.W.
  • Funding Organization(s): Cancer Prevention and Research Institute of Texas (CPRIT), Robert A. Welch Foundation, Army Research Office, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Tightly-orchestrated rearrangements govern catalytic center assembly of the ribosome.

Zhou, Y.Musalgaonkar, S.Johnson, A.W.Taylor, D.W.

(2019) Nat Commun 10: 958-958

  • DOI: 10.1038/s41467-019-08880-0
  • Primary Citation of Related Structures:  
    6N8K, 6N8J, 6N8M, 6N8L, 6N8O, 6N8N

  • PubMed Abstract: 
  • The catalytic activity of the ribosome is mediated by RNA, yet proteins are essential for the function of the peptidyl transferase center (PTC). In eukaryotes, final assembly of the PTC occurs in the cytoplasm by insertion of the ribosomal protein Rpl10 (uL16) ...

    The catalytic activity of the ribosome is mediated by RNA, yet proteins are essential for the function of the peptidyl transferase center (PTC). In eukaryotes, final assembly of the PTC occurs in the cytoplasm by insertion of the ribosomal protein Rpl10 (uL16). We determine structures of six intermediates in late nuclear and cytoplasmic maturation of the large subunit that reveal a tightly-choreographed sequence of protein and RNA rearrangements controlling the insertion of Rpl10. We also determine the structure of the biogenesis factor Yvh1 and show how it promotes assembly of the P stalk, a critical element for recruitment of GTPases that drive translation. Together, our structures provide a blueprint for final assembly of a functional ribosome.


    Organizational Affiliation

    LIVESTRONG Cancer Institutes, Dell Medical School, Austin, TX, 78712, USA.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal Protein uL1A [auth s]217Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal export protein NMD3B [auth v]518Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NMD3YHR170W
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L2-AC [auth A]254Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL2ARPL5BYFR031C-AYFR031BC
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L28D [auth a]149Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL28CYH2YGL103W
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L3E [auth B]387Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL3MAK8TCM1YOR063WYOR29-14
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleolar GTP-binding protein 1F [auth b]647Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOG1YPL093WLPG15W
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L4-AG [auth C]362Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL4ARPL2RPL2AYBR031WYBR0315
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L30H [auth c]105Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL30RPL32YGL030W
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L31-AI [auth d]113Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL31ARPL34RPL34AYDL075WD2478
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L6-AJ [auth E]176Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL6ARPL17AYL16AYML073C
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L32K [auth e]130Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL32YBL092WYBL0838
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L7-AL [auth F]244Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL7ARPL6ARPL8AYL8AYGL076C
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L33-AM [auth f]107Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL33ARPL37AYPL143WLPI4WP2625
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L8-AN [auth G]256Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL8AMAK7RPL4AYHL033C
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L34-AO [auth g]121Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL34AYER056C-AYER056BC
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Entity ID: 16
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Bud site selection protein 20P [auth I]166Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: BUD20YLR074C
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Entity ID: 17
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60S ribosomal protein L9-AQ [auth H]191Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL9ARPL8ARPL9YGL147C
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L35-AR [auth h]120Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL35ASOS1YDL191WD1249
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L36-AS [auth i]100Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL36ARPL39AYMR194WYM9646.06
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Entity ID: 20
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60S ribosomal protein L37-AT [auth j]88Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL37ARPL35AYLR185WL9470.6
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L38U [auth k]78Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL38YLR325CL8543.2
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L13-AV [auth L]199Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL13AYDL082W
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L39W [auth l]51Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL39RPL46SPB2YJL189WJ0360
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L14-AX [auth M]138Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL14AYKL006WYKL153
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L43-AY [auth p]92Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL43AYPR043WYP9499.02
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L15-AZ [auth N]204Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL15ARPL10ARPL13AYL10AYLR029C
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosome biogenesis protein RLP24AA [auth u]199Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RLP24YLR009W
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L16-ABA [auth O]199Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL16ARPL13RPL21AYIL133C
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L17-ACA [auth P]184Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL17ARPL17RPL20AYKL180W
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L18-ADA [auth Q]186Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL18ARP28AYOL120C
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L19-AEA [auth R]189Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL19ARPL23AYL14AYBR084C-AYBR084BC
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L20-AFA [auth S]172Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL20ARPL18ARPL18A2YMR242CYM9408.04C
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Entity ID: 33
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60S ribosomal protein L21-AGA [auth T]160Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL21AURP1YBR191WYBR1401
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Entity ID: 34
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60S ribosomal protein L22-AHA [auth U]121Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL22AYLR061WL2168
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Entity ID: 35
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60S ribosomal protein L23-AIA [auth V]137Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL23ARPL17ARPL17AAYBL087CYBL0713
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosome assembly factor MRT4JA [auth W]236Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MRT4YKL009WYKL160
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Entity ID: 37
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60S ribosomal protein L25KA [auth X]142Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL25YOL127W
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L26-ALA [auth Y]127Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL26ARPL26RPL33AYLR344WL8300.4
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Entity ID: 39
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Eukaryotic translation initiation factor 6MA [auth y]245Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TIF6CDC95YPR016CLPZ15C
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Entity ID: 40
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60S ribosomal protein L27-ANA [auth Z]136Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL27ARPL27YHR010W
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
UPF0642 protein YBL028COA [auth z]106Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: YBL028CYBL0423
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L5PA [auth D]297Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL5RPL1RPL1AYPL131WLPI14W
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L11-AQA [auth J]174Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL11ARP39ARPL16AYPR102CP8283.14
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L42-ARA [auth q]106Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL42ARPL41ASCL41AYNL162WN1722
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L29SA [auth o]59Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL29YL43YFR032C-AYFR032BW
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Entity ID: 46
MoleculeChainsLengthOrganismImage
Saccharomyces cerevisiae S288C 35S pre-ribosomal RNA (RDN37-1), miscRNATA [auth 1]3396Saccharomyces cerevisiae S288C
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Entity ID: 47
MoleculeChainsLengthOrganismImage
5S rRNAUA [auth 2]121Saccharomyces cerevisiae S288C
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Entity ID: 48
MoleculeChainsLengthOrganismImage
5.8S rRNAVA [auth 3]158Saccharomyces cerevisiae S288C
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Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download Ideal Coordinates CCD File 
WA [auth b]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
XA [auth b]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cancer Prevention and Research Institute of Texas (CPRIT)United StatesRR160088
Robert A. Welch FoundationUnited StatesF-1938
Army Research OfficeUnited StatesW911NF-15-0120
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM53655
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM127127

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-13
    Type: Initial release
  • Version 1.1: 2020-01-08
    Changes: Author supporting evidence