6ELZ

State E (TAP-Flag-Ytm1 E80A) - Visualizing the assembly pathway of nucleolar pre-60S ribosmes


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 1.3 of the entry. See complete history


Literature

Visualizing the Assembly Pathway of Nucleolar Pre-60S Ribosomes.

Kater, L.Thoms, M.Barrio-Garcia, C.Cheng, J.Ismail, S.Ahmed, Y.L.Bange, G.Kressler, D.Berninghausen, O.Sinning, I.Hurt, E.Beckmann, R.

(2017) Cell 171: 1599-1610.e14

  • DOI: 10.1016/j.cell.2017.11.039
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Eukaryotic 60S ribosomal subunits are comprised of three rRNAs and ∼50 ribosomal proteins. The initial steps of their formation take place in the nucleolus, but, owing to a lack of structural information, this process is poorly understood. Using cryo ...

    Eukaryotic 60S ribosomal subunits are comprised of three rRNAs and ∼50 ribosomal proteins. The initial steps of their formation take place in the nucleolus, but, owing to a lack of structural information, this process is poorly understood. Using cryo-EM, we solved structures of early 60S biogenesis intermediates at 3.3 Å to 4.5 Å resolution, thereby providing insights into their sequential folding and assembly pathway. Besides revealing distinct immature rRNA conformations, we map 25 assembly factors in six different assembly states. Notably, the Nsa1-Rrp1-Rpf1-Mak16 module stabilizes the solvent side of the 60S subunit, and the Erb1-Ytm1-Nop7 complex organizes and connects through Erb1's meandering N-terminal extension, eight assembly factors, three ribosomal proteins, and three 25S rRNA domains. Our structural snapshots reveal the order of integration and compaction of the six major 60S domains within early nucleolar 60S particles developing stepwise from the solvent side around the exit tunnel to the central protuberance.


    Organizational Affiliation

    Gene Center Munich and Center of Integrated Protein Science-Munich (CiPS-M), Department of Biochemistry, Feodor-Lynen-Str. 25, University of Munich, 81377 Munich, Germany. Electronic address: beckmann@lmb.uni-muenchen.de.



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L13-AL199Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL13AYDL082W
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L15-AN204Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL15ARPL10ARPL13AYL10AYLR029C
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L18-AQ186Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL18ARP28AYOL120C
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L20-AS172Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL20ARPL18ARPL18A2YMR242CYM9408.04C
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L21-AT160Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL21AURP1YBR191WYBR1401
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L27-AZ136Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL27ARPL27YHR010W
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L30c105Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL30RPL32YGL030W
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L31-Ad113Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL31ARPL34RPL34AYDL075WD2478
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L32e130Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL32YBL092WYBL0838
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L33-Af107Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL33ARPL37AYPL143WLPI4WP2625
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L34-Ag121Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL34AYER056C-AYER056BC
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L36-Ai100Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL36ARPL39AYMR194WYM9646.06
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L37-Aj88Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL37ARPL35AYLR185WL9470.6
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L38k78Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL38YLR325CL8543.2
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L23-AV137Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL23ARPL17ARPL17AAYBL087CYBL0713
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L28a149Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL28CYH2YGL103W
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L17-AP184Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL17ARPL17RPL20AYKL180W
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L26-AY127Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL26ARPL26RPL33AYLR344WL8300.4
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L7-AF244Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL7ARPL6ARPL8AYL8AYGL076C
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L3B387Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL3MAK8TCM1YOR063WYOR29-14
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L4-AC362Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL4ARPL2RPL2AYBR031WYBR0315
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L9-AH191Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL9ARPL8ARPL9YGL147C
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
Ribosome biogenesis protein BRX1A291Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: BRX1YOL077C
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
Proteasome-interacting protein CIC1K376Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CIC1NSA3YHR052W
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
Ribosome biogenesis protein ERB1m807Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ERB1YMR049CYM9796.02C
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
ATP-dependent RNA helicase HAS1D505Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: HAS1YMR290C
EC: 3.6.4.13
Find proteins for Q03532 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
Ribosome assembly factor MRT4W236Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MRT4YKL009WYKL160
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
60S ribosome subunit biogenesis protein NIP7l181Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NIP7YPL211W
Find proteins for Q08962 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
Ribosome biogenesis protein 15o220Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOP15YNL110CN1954
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
Pescadillo homologn605Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOP7RRP13YPH1YGR103W
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
Ribosome biogenesis protein NSA2r261Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NSA2YER126CSYGP-ORF47
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
Ribosome biogenesis protein YTM1p460Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: YTM1YOR272W
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
25S rRNA (cytosine(2870)-C(5))-methyltransferaseq618Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOP2YNA1YNL061WN2428YNL2428W
EC: 2.1.1.310
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
Ribosome biogenesis protein RLP24u199Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RLP24YLR009W
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
Nucleolar protein 16v231Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOP16YER002W
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferasew841Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SPB1YCL054WYCL431YCL54W
EC: 2.1.1.167
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
Nucleolar complex-associated protein 3I663Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOC3YLR002C
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
rRNA-processing protein EBP2J427Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: EBP2YKL172WYKL636
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L6-AE176Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL6ARPL17AYL16AYML073C
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L8-AG256Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL8AMAK7RPL4AYHL033C
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L14-AM138Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL14AYKL006WYKL153
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L22-AU121Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL22AYLR061WL2168
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L16-AO199Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL16ARPL13RPL21AYIL133C
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L25X142Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL25YOL127W
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L35-Ah120Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL35ASOS1YDL191WD1249
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
Nucleolar GTP-binding protein 1b647Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOG1YPL093WLPG15W
Find proteins for Q02892 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
Nuclear GTP-binding protein NUG1s520Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NUG1YER006W
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
Ribosome biogenesis protein RLP7t322Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RLP7RPL7YNL002CN2014
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
Eukaryotic translation initiation factor 6y245Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TIF6CDC95YPR016CLPZ15C
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
UPF0642 protein YBL028Cz106Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: YBL028CYBL0423
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L19-AR189Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL19ARPL23AYL14AYBR084C-AYBR084BC
Find proteins for P0CX82 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 1
MoleculeChainsLengthOrganism
25S ribosomal RNA13396Saccharomyces cerevisiae S288C

Find similar nucleic acids by: Sequence   |  Structure

Entity ID: 2
MoleculeChainsLengthOrganism
5.8S ribosomal RNA2158Saccharomyces cerevisiae S288C

Find similar nucleic acids by: Sequence   |  Structure

Entity ID: 3
MoleculeChainsLengthOrganism
Internal transcribed spacer 26232Saccharomyces cerevisiae S288C
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
j
ZINC ION
Zn
PTFCDOFLOPIGGS-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

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-12-27
    Type: Initial release
  • Version 1.1: 2018-02-07
    Changes: Source and taxonomy, Structure summary
  • Version 1.2: 2018-11-21
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.3: 2020-01-22
    Changes: Database references