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
  • Structures With Same Primary Citation

  • 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 p ...

    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: 5
MoleculeChainsSequence LengthOrganismDetails
rpS4_eS4L4261Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
rpS5_uS7L5225Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
rpS6_eS6L6236Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
rpS7_eS7L7190Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
rpS8_eS8L8200Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
rpS9_uS4L9197Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
rpS16_uS9LC143Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
rpS11_uS17LD156Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
rpS28_eS28LG67Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Utp17LH896Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Utp8LI713Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
Utp10LM1769Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Utp4LN776Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
Utp1LO923Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
Utp6LP440Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
Utp13LR817Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
Utp18LS594Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
Utp21LT939Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
Utp7LW554Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
Kre33LX, LY1056Saccharomyces cerevisiae BY4741Mutation(s): 0 
EC: 2.3.1
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
Imp3LZ183Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
Mpp10NA593Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
Sas10NB610Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
Bud21ND214Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
Faf1NE346Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
rpS13_uS15NF151Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
rpS14_uS11NG137Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
Utp22NH1237Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
Rrp7NI297Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
Rrp5NJ1729Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
Krr1NK316Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
Nop56SA504Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
Nop1SC, SD327Saccharomyces cerevisiae BY4741Mutation(s): 0 
EC: 2.1.1
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
Snu13SE, SF126Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
Rrp9SG573Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
Bms1SI1184Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
Utp24SL189Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
Imp4SM290Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
Utp30SN274Saccharomyces cerevisiae BY4741Mutation(s): 0 
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MoleculeChainsSequence LengthOrganismDetails
Pno1SO274Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 59
MoleculeChainsSequence LengthOrganismDetails
rpS23_uS12SR145Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 60
MoleculeChainsSequence LengthOrganismDetails
Utp14SS898Saccharomyces cerevisiae BY4741Mutation(s): 0 
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MoleculeChainsSequence LengthOrganismDetails
Nop14ST792Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Noc4SU552Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Rrt14SV206Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Unassigned peptidesSX103Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Utp11SY250Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Enp1SZ483Saccharomyces cerevisiae BY4741Mutation(s): 0 
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rpS22_uS8LE130Saccharomyces cerevisiae BY4741Mutation(s): 0 
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MoleculeChainsSequence LengthOrganismDetails
rpS24_eS24LF135Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Utp15LJ513Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 19
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Utp9LK575Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
Utp5LL643Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
Utp12LQ943Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
Sof1LU489Saccharomyces cerevisiae BY4741Mutation(s): 0 
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MoleculeChainsSequence LengthOrganismDetails
Enp2LV707Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 36
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Lcp5NC357Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 4
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rpS18_uS13L3146Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Nop58SB511Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 50
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Rcl1SH367Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Go to UniProtKB:  Q08096
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  • Reference Sequence

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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
Emg1SJ, SK252Saccharomyces cerevisiae BY4741Mutation(s): 0 
EC: 2.1.1.260
Find proteins for Q06287 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  Q06287
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetails
Utp20SP982Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetails
Fcf2SQ217Saccharomyces cerevisiae BY4741Mutation(s): 0 
Find proteins for Q12035 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  Q12035
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Entity ID: 3
MoleculeChainsLengthOrganism
U3 snoRNAL2333Saccharomyces cerevisiae BY4741

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Entity ID: 1
MoleculeChainsLengthOrganism
5' ETSL0700Saccharomyces cerevisiae BY4741

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Entity ID: 2
MoleculeChainsLengthOrganism
18S pre-rRNAL11807Saccharomyces cerevisiae BY4741
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
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 

  • 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