5WLC

The complete structure of the small subunit processome

  • Classification: RIBOSOME
  • Organism(s): Saccharomyces cerevisiae BY4741
  • Mutation(s): No 

  • Deposited: 2017-07-26 Released: 2017-09-27 
  • Deposition Author(s): Barandun, J., Chaker-Margot, M., Hunziker, M., Klinge, S.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), European Molecular Biology Organization (EMBO), Swiss National Science Foundation, Natural Sciences and Engineering Research Council (NSERC, Canada), Human Frontier Science Program (HFSP)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

The complete structure of the small-subunit processome.

Barandun, J.Chaker-Margot, M.Hunziker, M.Molloy, K.R.Chait, B.T.Klinge, S.

(2017) Nat Struct Mol Biol 24: 944-953

  • DOI: 10.1038/nsmb.3472
  • Primary Citation of Related Structures:  
    5WLC

  • PubMed Abstract: 
  • The small-subunit processome represents the earliest stable precursor of the eukaryotic small ribosomal subunit. Here we present the cryo-EM structure of the Saccharomyces cerevisiae small-subunit processome at an overall resolution of 3.8 Å, which provides an essentially complete near-atomic model of this assembly ...

    The small-subunit processome represents the earliest stable precursor of the eukaryotic small ribosomal subunit. Here we present the cryo-EM structure of the Saccharomyces cerevisiae small-subunit processome at an overall resolution of 3.8 Å, which provides an essentially complete near-atomic model of this assembly. In this nucleolar superstructure, 51 ribosome-assembly factors and two RNAs encapsulate the 18S rRNA precursor and 15 ribosomal proteins in a state that precedes pre-rRNA cleavage at site A1. Extended flexible proteins are employed to connect distant sites in this particle. Molecular mimicry and steric hindrance, as well as protein- and RNA-mediated RNA remodeling, are used in a concerted fashion to prevent the premature formation of the central pseudoknot and its surrounding elements within the small ribosomal subunit.


    Organizational Affiliation

    Laboratory of Protein and Nucleic Acid Chemistry, The Rockefeller University, New York, New York, USA.



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
rpS18_uS13D [auth L3]146Saccharomyces cerevisiae BY4741Mutation(s): 0 
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rpS4_eS4E [auth L4]261Saccharomyces cerevisiae BY4741Mutation(s): 0 
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rpS5_uS7F [auth L5]225Saccharomyces cerevisiae BY4741Mutation(s): 0 
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rpS6_eS6G [auth L6]236Saccharomyces cerevisiae BY4741Mutation(s): 0 
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rpS7_eS7H [auth L7]190Saccharomyces cerevisiae BY4741Mutation(s): 0 
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rpS8_eS8I [auth L8]200Saccharomyces cerevisiae BY4741Mutation(s): 0 
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rpS9_uS4J [auth L9]197Saccharomyces cerevisiae BY4741Mutation(s): 0 
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rpS16_uS9K [auth LC]143Saccharomyces cerevisiae BY4741Mutation(s): 0 
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rpS11_uS17L [auth LD]156Saccharomyces cerevisiae BY4741Mutation(s): 0 
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rpS22_uS8M [auth LE]130Saccharomyces cerevisiae BY4741Mutation(s): 0 
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rpS24_eS24N [auth LF]135Saccharomyces cerevisiae BY4741Mutation(s): 0 
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rpS28_eS28O [auth LG]67Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Utp17P [auth LH]896Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Utp8Q [auth LI]713Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Utp15R [auth LJ]513Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Utp9S [auth LK]575Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Utp5T [auth LL]643Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Utp10U [auth LM]1769Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Utp4V [auth LN]776Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Utp1W [auth LO]923Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Utp6X [auth LP]440Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Utp12Y [auth LQ]943Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Utp13Z [auth LR]817Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Utp18AA [auth LS]594Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Utp21BA [auth LT]939Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Sof1CA [auth LU]489Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Enp2DA [auth LV]707Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Utp7EA [auth LW]554Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Kre33FA [auth LX], GA [auth LY]1056Saccharomyces cerevisiae BY4741Mutation(s): 0 
EC: 2.3.1
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Imp3HA [auth LZ]183Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Mpp10IA [auth NA]593Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Sas10JA [auth NB]610Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Lcp5KA [auth NC]357Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Bud21LA [auth ND]214Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Faf1MA [auth NE]346Saccharomyces cerevisiae BY4741Mutation(s): 0 
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rpS13_uS15NA [auth NF]151Saccharomyces cerevisiae BY4741Mutation(s): 0 
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rpS14_uS11OA [auth NG]137Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Utp22PA [auth NH]1237Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Rrp7QA [auth NI]297Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Rrp5RA [auth NJ]1729Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Krr1SA [auth NK]316Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Nop56TA [auth SA]504Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Nop58UA [auth SB]511Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Nop1VA [auth SC], WA [auth SD]327Saccharomyces cerevisiae BY4741Mutation(s): 0 
EC: 2.1.1
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Snu13XA [auth SE], YA [auth SF]126Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Rrp9ZA [auth SG]573Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Rcl1AB [auth SH]367Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Bms1BB [auth SI]1184Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Emg1CB [auth SJ], DB [auth SK]252Saccharomyces cerevisiae BY4741Mutation(s): 0 
EC: 2.1.1.260
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Utp24EB [auth SL]189Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Imp4FB [auth SM]290Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Utp30GB [auth SN]274Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Pno1HB [auth SO]274Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Utp20IB [auth SP]982Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Fcf2JB [auth SQ]217Saccharomyces cerevisiae BY4741Mutation(s): 0 
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rpS23_uS12KB [auth SR]145Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Utp14LB [auth SS]898Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Nop14MB [auth ST]792Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Noc4NB [auth SU]552Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Rrt14OB [auth SV]206Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Unassigned peptidesPB [auth SX]103Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 65
MoleculeChainsSequence LengthOrganismDetailsImage
Utp11QB [auth SY]250Saccharomyces cerevisiae BY4741Mutation(s): 0 
Find proteins for B5VM59 (Saccharomyces cerevisiae (strain AWRI1631))
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Go to UniProtKB:  B5VM59
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Entity ID: 66
MoleculeChainsSequence LengthOrganismDetailsImage
Enp1RB [auth SZ]483Saccharomyces cerevisiae BY4741Mutation(s): 0 
Find proteins for P38333 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 1
MoleculeChainsLengthOrganismImage
5' ETSA [auth L0]700Saccharomyces cerevisiae BY4741
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Entity ID: 2
MoleculeChainsLengthOrganismImage
18S pre-rRNAB [auth L1]1807Saccharomyces cerevisiae BY4741
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Entity ID: 3
MoleculeChainsLengthOrganismImage
U3 snoRNAC [auth L2]333Saccharomyces cerevisiae BY4741
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Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
SB [auth SL]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1DP2GM123459
European Molecular Biology Organization (EMBO)European UnionALTF 51-2014
Swiss National Science FoundationSwitzerland155515
Natural Sciences and Engineering Research Council (NSERC, Canada)CanadaPGS-D
Human Frontier Science Program (HFSP)France--

Revision History  (Full details and data files)

  • Version 1.0: 2017-09-27
    Type: Initial release
  • Version 1.1: 2017-10-11
    Changes: Database references
  • Version 1.2: 2017-10-18
    Changes: Author supporting evidence
  • Version 1.3: 2017-11-22
    Changes: Database references
  • Version 1.4: 2020-01-01
    Changes: Author supporting evidence