6YLG

Rix1-Rea1 pre-60S particle - 60S core, body 1 (rigid body refinement)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 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

Construction of the Central Protuberance and L1 Stalk during 60S Subunit Biogenesis.

Kater, L.Mitterer, V.Thoms, M.Cheng, J.Berninghausen, O.Beckmann, R.Hurt, E.

(2020) Mol Cell 79: 615-628.e5

  • DOI: 10.1016/j.molcel.2020.06.032
  • Primary Citation of Related Structures:  
    6YLF, 6YLE, 6YLH, 6YLG, 6YLY, 6YLX

  • PubMed Abstract: 
  • Ribosome assembly is driven by numerous assembly factors, including the Rix1 complex and the AAA ATPase Rea1. These two assembly factors catalyze 60S maturation at two distinct states, triggering poorly understood large-scale structural transitions t ...

    Ribosome assembly is driven by numerous assembly factors, including the Rix1 complex and the AAA ATPase Rea1. These two assembly factors catalyze 60S maturation at two distinct states, triggering poorly understood large-scale structural transitions that we analyzed by cryo-electron microscopy. Two nuclear pre-60S intermediates were discovered that represent previously unknown states after Rea1-mediated removal of the Ytm1-Erb1 complex and reveal how the L1 stalk develops from a pre-mature nucleolar to a mature-like nucleoplasmic state. A later pre-60S intermediate shows how the central protuberance arises, assisted by the nearby Rix1-Rea1 machinery, which was solved in its pre-ribosomal context to molecular resolution. This revealed a Rix1 2 -Ipi3 2 tetramer anchored to the pre-60S via Ipi1, strategically positioned to monitor this decisive remodeling. These results are consistent with a general underlying principle that temporarily stabilized immature RNA domains are successively remodeled by assembly factors, thereby ensuring failsafe assembly progression.


    Organizational Affiliation

    Biochemie-Zentrum der Universit├Ąt Heidelberg, 69120 Heidelberg, Germany. Electronic address: ed.hurt@bzh.uni-heidelberg.de.



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Probable metalloprotease ARX14593Saccharomyces cerevisiaeMutation(s): 0 
EC: 3
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Entity ID: 5
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rRNA-processing protein CGR15120Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 6
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60S ribosomal protein L2-AA254Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 8
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60S ribosomal protein L4-AC362Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L5D297Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 10
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60S ribosomal protein L6-AE176Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 11
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60S ribosomal protein L7-AF244Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 12
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60S ribosomal protein L8-AG256Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 13
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60S ribosomal protein L9-AH191Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 14
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Bud site selection protein 20I166Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 15
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60S ribosomal protein L11-AJ174Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 16
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Pre-rRNA-processing protein IPI1K334Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 17
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60S ribosomal protein L13-AL199Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 18
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60S ribosomal protein L14-AM138Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 19
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60S ribosomal protein L15-AN204Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 20
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60S ribosomal protein L16-AO199Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 21
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60S ribosomal protein L17-AP184Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 22
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60S ribosomal protein L18-AQ186Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 23
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60S ribosomal protein L19-AR189Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 24
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60S ribosomal protein L20-AS172Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 25
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60S ribosomal protein L21-AT160Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 26
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60S ribosomal protein L22-AU121Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 27
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60S ribosomal protein L23-AV137Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosome assembly factor MRT4W236Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 29
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60S ribosomal protein L25X142Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 30
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60S ribosomal protein L26-AY127Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 31
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60S ribosomal protein L27-AZ136Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 32
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60S ribosomal protein L28a149Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 33
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Nucleolar GTP-binding protein 1b647Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 34
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Ribosome biogenesis protein ALB1c175Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L31-Ad113Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 36
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60S ribosomal protein L32e130Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 37
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60S ribosomal protein L33-Af107Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 38
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60S ribosomal protein L34-Ag121Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 39
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60S ribosomal protein L35-Ah120Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 40
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60S ribosomal protein L36-Ai100Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 41
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60S ribosomal protein L37-Aj88Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 42
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60S ribosomal protein L38k78Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 43
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60S ribosomal protein L39l51Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleolar GTP-binding protein 2m486Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 45
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60S ribosomal protein L30n105Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 46
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60S ribosomal protein L1-Ao217Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 47
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60S ribosomal protein L43-Ap92Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 48
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60S ribosomal protein L12-Aq165Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosome biogenesis protein NSA2r261Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 50
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Nuclear GTP-binding protein NUG1s520Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 51
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Protein SDA1t767Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 52
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Ribosome biogenesis protein RLP24u199Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 53
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Ribosome assembly protein 4x515Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 6y245Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetailsImage
UPF0642 protein YBL028Cz106Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L3B387Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganismImage
25S rRNA13396Saccharomyces cerevisiae
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Entity ID: 2
MoleculeChainsLengthOrganismImage
5.8S rRNA2158Saccharomyces cerevisiae
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MoleculeChainsLengthOrganismImage
5S rRNA3121Saccharomyces cerevisiae
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download CCD File 
b, m
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
ZN
Query on ZN

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I, j, p, u
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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b, m
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-07-29
    Type: Initial release
  • Version 1.1: 2020-09-02
    Changes: Database references