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_eS4
L4
261Saccharomyces cerevisiae BY4741Mutation(s): 0 
Find proteins for P0CX35 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
rpS5_uS7
L5
225Saccharomyces cerevisiae BY4741Mutation(s): 0 
Find proteins for A0A1L4AA68 (Saccharomyces cerevisiae)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
rpS6_eS6
L6
236Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
rpS7_eS7
L7
190Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
rpS9_uS4
L9
197Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
rpS11_uS17
LD
156Saccharomyces cerevisiae BY4741Mutation(s): 0 
Find proteins for P0CX47 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Utp8
LI
713Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
Utp1
LO
923Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
Utp13
LR
817Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
Kre33
LX, LY
1056Saccharomyces cerevisiae BY4741Mutation(s): 0 
EC: 2.3.1
Find proteins for P53914 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
Mpp10
NA
593Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
Sas10
NB
610Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
Utp22
NH
1237Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
Rrp7
NI
297Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
Krr1
NK
316Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
Nop56
SA
504Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
Nop1
SC, SD
327Saccharomyces cerevisiae BY4741Mutation(s): 0 
EC: 2.1.1
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
Imp4
SM
290Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
Utp30
SN
274Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
Pno1
SO
274Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetails
Fcf2
SQ
217Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 59
MoleculeChainsSequence LengthOrganismDetails
rpS23_uS12
SR
145Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 61
MoleculeChainsSequence LengthOrganismDetails
Nop14
ST
792Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 63
MoleculeChainsSequence LengthOrganismDetails
Rrt14
SV
206Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
rpS16_uS9
LC
143Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
rpS22_uS8
LE
130Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
rpS24_eS24
LF
135Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
rpS28_eS28
LG
67Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Utp17
LH
896Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Utp15
LJ
513Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
Utp9
LK
575Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
Utp5
LL
643Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
Utp10
LM
1769Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Utp4
LN
776Saccharomyces cerevisiae BY4741Mutation(s): 0 
Find proteins for Q06679 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
Utp6
LP
440Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
Utp12
LQ
943Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
Utp18
LS
594Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
Utp21
LT
939Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
Sof1
LU
489Saccharomyces cerevisiae BY4741Mutation(s): 0 
Find proteins for P33750 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
Enp2
LV
707Saccharomyces cerevisiae BY4741Mutation(s): 0 
Find proteins for P48234 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
Utp7
LW
554Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
Imp3
LZ
183Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
Lcp5
NC
357Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
Bud21
ND
214Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
Faf1
NE
346Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
rpS13_uS15
NF
151Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
rpS18_uS13
L3
146Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
rpS14_uS11
NG
137Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
Rrp5
NJ
1729Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
Nop58
SB
511Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
Snu13
SE, SF
126Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
Rrp9
SG
573Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
Rcl1
SH
367Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
Bms1
SI
1184Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
Emg1
SJ, SK
252Saccharomyces cerevisiae BY4741Mutation(s): 0 
EC: 2.1.1.260
Find proteins for Q06287 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
Utp24
SL
189Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetails
Utp20
SP
982Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 60
MoleculeChainsSequence LengthOrganismDetails
Utp14
SS
898Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 62
MoleculeChainsSequence LengthOrganismDetails
Noc4
SU
552Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 64
MoleculeChainsSequence LengthOrganismDetails
Unassigned peptides
SX
103Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 65
MoleculeChainsSequence LengthOrganismDetails
Utp11
SY
250Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 66
MoleculeChainsSequence LengthOrganismDetails
Enp1
SZ
483Saccharomyces cerevisiae BY4741Mutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
rpS8_eS8
L8
200Saccharomyces cerevisiae BY4741Mutation(s): 0 
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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

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Entity ID: 3
MoleculeChainsLengthOrganism
U3 snoRNAL2333Saccharomyces 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

View Full Validation Report



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