6EM5

State D architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.30 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

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: https://doi.org/10.1016/j.cell.2017.11.039
  • Primary Citation of Related Structures:  
    6ELZ, 6EM1, 6EM3, 6EM4, 6EM5, 6EMF, 6EMG, 6EN7

  • 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-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.


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13-AC [auth L]199Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14-AD [auth M]138Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L15-AE [auth N]204Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18-AF [auth Q]186Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L19-AG [auth R]189Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L20-AH [auth S]172Saccharomyces cerevisiae S288CMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L21-AI [auth T]160Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L22-AJ [auth U]121Saccharomyces cerevisiae S288CMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27-AK [auth Z]136Saccharomyces cerevisiae S288CMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L30L [auth c]105Saccharomyces cerevisiae S288CMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L31-AM [auth d]113Saccharomyces cerevisiae S288CMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L32N [auth e]130Saccharomyces cerevisiae S288CMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L33-AO [auth f]107Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L34-AP [auth g]121Saccharomyces cerevisiae S288CMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36-BQ [auth i]100Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37-AR [auth j]88Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L38S [auth k]78Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6-AT [auth E]176Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L8-AU [auth G]256Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L16-AV [auth O]199Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23-AW [auth V]137Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L25142Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L26-A127Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35-AZ [auth h]120Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L3AA [auth B]387Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4-ABA [auth C]362Saccharomyces cerevisiae S288CMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9-ACA [auth H]191Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein BRX1DA [auth A]291Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome-interacting protein CIC1EA [auth K]376Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein ERB1FA [auth m]807Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent RNA helicase HAS1GA [auth D]505Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.6.4.13
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome assembly factor MRT4HA [auth W]236Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosome subunit biogenesis protein NIP7IA [auth l]181Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar GTP-binding protein 1JA [auth b]647Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein 15KA [auth o]220Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Pescadillo homologLA [auth n]605Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein NSA2MA [auth r]261Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear GTP-binding protein NUG1NA [auth s]520Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein RLP7OA [auth t]322Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 6PA [auth y]245Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
UPF0642 protein YBL028CQA [auth z]106Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein YTM1RA [auth p]460Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
25S rRNA (cytosine(2870)-C(5))-methyltransferaseSA [auth q]618Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 2.1.1.310
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MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein RLP24TA [auth u]199Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar protein 16UA [auth v]231Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P40007 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferaseVA [auth w]841Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 2.1.1.167
UniProt
Find proteins for P25582 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar complex-associated protein 3WA [auth I]663Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q07896 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
rRNA-processing protein EBP2XA [auth J]427Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P36049 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome production factor 1YA [auth x]295Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P38805 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
Protein MAK16ZA [auth 3]306Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P10962 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal RNA-processing protein 1AB [auth 4]278Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P35178 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein NSA1BB [auth 5]463Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P53136 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7-ADB [auth F]244Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P05737 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L17-AEB [auth P]184Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 1
MoleculeChains LengthOrganismImage
5.8S ribosomal RNAA [auth 2]158Saccharomyces cerevisiae S288C
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Entity ID: 2
MoleculeChains LengthOrganismImage
Internal Transcribed Spacer 2B [auth 6]232Saccharomyces cerevisiae S288C
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Entity ID: 55
MoleculeChains LengthOrganismImage
25S ribosomal RNACB [auth 1]3,396Saccharomyces cerevisiae
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION2.0

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-27
    Type: Initial release