5TZS

Architecture of the yeast small subunit processome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Architecture of the yeast small subunit processome.

Chaker-Margot, M.Barandun, J.Hunziker, M.Klinge, S.

(2017) Science 355

  • DOI: 10.1126/science.aal1880
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The small subunit (SSU) processome, a large ribonucleoprotein particle, organizes the assembly of the eukaryotic small ribosomal subunit by coordinating the folding, cleavage, and modification of nascent pre-ribosomal RNA (rRNA). Here, we present the ...

    The small subunit (SSU) processome, a large ribonucleoprotein particle, organizes the assembly of the eukaryotic small ribosomal subunit by coordinating the folding, cleavage, and modification of nascent pre-ribosomal RNA (rRNA). Here, we present the cryo-electron microscopy structure of the yeast SSU processome at 5.1-angstrom resolution. The structure reveals how large ribosome biogenesis complexes assist the 5' external transcribed spacer and U3 small nucleolar RNA in providing an intertwined RNA-protein assembly platform for the separate maturation of 18S rRNA domains. The strategic placement of a molecular motor at the center of the particle further suggests a mechanism for mediating conformational changes within this giant particle. This study provides a structural framework for a mechanistic understanding of eukaryotic ribosome assembly in the model organism Saccharomyces cerevisiae.


    Organizational Affiliation

    Laboratory of Protein and Nucleic Acid Chemistry, The Rockefeller University, New York, NY 10065, USA. klinge@rockefeller.edu.



Macromolecules

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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
rpS16_uS9
C
143Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS16ARP61RYMR143WYM9375.12
Find proteins for P0CX51 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX51

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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
rpS11_uS17
D
156Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS11ARPS18AYDR025WYD9813.03
Find proteins for P0CX47 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX47

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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
rpS22_uS8
E
130Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS22ARPS24RPS24AYJL190CJ0355
Find proteins for P0C0W1 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0C0W1

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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
rpS24_eS24
F
135Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS24ARPS24EAYER074W
Find proteins for P0CX31 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
rpS28_eS28
G
67Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS28ARPS33RPS33AYOR167CO3600
Find proteins for Q3E7X9 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q3E7X9

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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Utp4
H
544Saccharomyces cerevisiae S288CMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
UtpA_CTD1
I
176Saccharomyces cerevisiae S288CMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
UtpA_CTD2
J, K
107Saccharomyces cerevisiae S288CMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
Beta-propeller 2
M
258Saccharomyces cerevisiae S288CMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
Utp17
N
545Saccharomyces cerevisiae S288CMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Utp1
O
638Saccharomyces cerevisiae S288CMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
Utp6
P
306Saccharomyces cerevisiae S288CMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
Utp12
Q
710Saccharomyces cerevisiae S288CMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
Utp13
R
717Saccharomyces cerevisiae S288CMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
Utp18
S
250Saccharomyces cerevisiae S288CMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
Utp21
T
781Saccharomyces cerevisiae S288CMutation(s): 0 
Find proteins for Q06078 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
Beta-propeller 5
U
284Saccharomyces cerevisiae S288CMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
Enp2
V
263Saccharomyces cerevisiae S288CMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
UtpA_CTD4
W
104Saccharomyces cerevisiae S288CMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
Kre33
X
640Saccharomyces cerevisiae S288CMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
Kre33
Y
641Saccharomyces cerevisiae S288CMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
Imp3
Z
151Saccharomyces cerevisiae S288CMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
Nop56
a
312Saccharomyces cerevisiae S288CMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
Nop58
b
341Saccharomyces cerevisiae S288CMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
Nop1
c
221Saccharomyces cerevisiae S288CMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
Nop1
d
216Saccharomyces cerevisiae S288CMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
Snu13
e, f
126Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SNU13YEL026W
Find proteins for P39990 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
Ribosomal RNA-processing protein 9
g
573Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP9YPR137W
Find proteins for Q06506 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
rpS6_ES6
3
236Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS6ARPS101RPS10BYPL090CLPG18C
Find proteins for P0CX37 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
RNA 3'-terminal phosphate cyclase-like protein
h
367Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RCL1RTC1YOL010W
Find proteins for Q08096 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
Bms1,Ribosome biogenesis protein BMS1,Bms1
i
511Saccharomyces cerevisiae S288CMutation(s): 0 
Find proteins for Q08965 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
Ribosomal RNA small subunit methyltransferase NEP1
j, k
252Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: EMG1NEP1YLR186WL9470.5
EC: 2.1.1.260
Find proteins for Q06287 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
Utp24
l
124Saccharomyces cerevisiae S288CMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
Imp4
m
156Saccharomyces cerevisiae S288CMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
Utp30
n
160Saccharomyces cerevisiae S288CMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
Unassigned KH domain
o
175Saccharomyces cerevisiae S288CMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
Utp20
p
924Saccharomyces cerevisiae S288CMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
Repeat protein 2
q
372Saccharomyces cerevisiae S288CMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S23-A
r
145Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS23ARPS28AYGR118WG6178
Find proteins for P0CX29 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
rpS4_ES4
5
261Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS4ARPS7BYJR145CJ2186
Find proteins for P0CX35 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX35

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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
Beta-propeller 1
s, t, u
290Saccharomyces cerevisiae S288CMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
Repeat protein 1
v
580Saccharomyces cerevisiae S288CMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
Unassigned protein helices
y
507Saccharomyces cerevisiae S288CMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
rpS5_US7
6
225Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS5RPS2YJR123WJ2045
Find proteins for P26783 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P26783

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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
rpS7_eS7
7
190Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS7ARPS30YOR096WYOR3177W
Find proteins for P26786 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P26786

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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
rpS8_eS8
8
200Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS8ARPS14AYBL072CYBL06.05YBL0613
Find proteins for P0CX39 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX39

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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
rpS9_uS4
9
197Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS9ARPS13AYS11AYPL081W
Find proteins for O13516 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  O13516

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Entity ID: 1
MoleculeChainsLengthOrganism
5' external transcribed spacer0364Saccharomyces cerevisiae S288C

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Entity ID: 10
MoleculeChainsLengthOrganism
5' domain-associatedA39Saccharomyces cerevisiae S288C

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Entity ID: 11
MoleculeChainsLengthOrganism
3' domain-associatedB108Saccharomyces cerevisiae S288C

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Entity ID: 2
MoleculeChainsLengthOrganism
18S ribosomal RNA11800Saccharomyces cerevisiae S288C

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Entity ID: 3
MoleculeChainsLengthOrganism
U3 snoRNA2126Saccharomyces cerevisiae S288C

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Entity ID: 53
MoleculeChainsLengthOrganism
Unassigned RNA helicesz76Saccharomyces cerevisiae S288C
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-12-21
    Type: Initial release
  • Version 1.1: 2017-01-11
    Changes: Database references
  • Version 1.2: 2017-01-25
    Changes: Database references
  • Version 1.3: 2018-07-18
    Changes: Data collection