5TZS

Architecture of the yeast small subunit processome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.1 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

  • 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.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
rpS6_ES6
3
236Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS6A (RPS101, RPS10B)
Find proteins for P0CX37 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX37
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
rpS4_ES4
5
261Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS4A (RPS7B)
Find proteins for P0CX35 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX35
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
rpS5_US7
6
225Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS5 (RPS2)
Find proteins for P26783 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPS5
Go to UniProtKB:  P26783
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
rpS7_eS7
7
190Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS7A (RPS30)
Find proteins for P26786 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P26786
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
rpS8_eS8
8
200Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS8A (RPS14A)
Find proteins for P0CX39 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX39
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
rpS9_uS4
9
197Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS9A (RPS13A, YS11A)
Find proteins for O13516 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  O13516
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
rpS16_uS9
C
143Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS16A (RP61R)
Find proteins for P0CX51 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX51
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
rpS11_uS17
D
156Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS11A (RPS18A)
Find proteins for P0CX47 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX47
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
rpS22_uS8
E
130Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS22A (RPS24, RPS24A)
Find proteins for P0C0W1 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0C0W1
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
rpS24_eS24
F
135Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS24A (RPS24EA)
Find proteins for P0CX31 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX31
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
rpS28_eS28
G
67Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS28A (RPS33, RPS33A)
Find proteins for Q3E7X9 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q3E7X9
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Utp4
H
544N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
UtpA_CTD1
I
176N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
UtpA_CTD2
J, K
107N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
Beta-propeller 2
M
258N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
Utp17
N
545N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Utp1
O
638N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
Utp6
P
306N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
Utp12
Q
710N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
Utp13
R
717N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
Utp18
S
250N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
Utp21
T
781Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: UTP21
Find proteins for Q06078 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q06078
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
Beta-propeller 5
U
284N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
Enp2
V
263N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
UtpA_CTD4
W
104N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
Kre33
X
640N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
Kre33
Y
641N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
Imp3
Z
151N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
Nop56
a
312N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
Nop58
b
341N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
Nop1
c
221N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
Nop1
d
216N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
Snu13
e, f
126Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SNU13
Find proteins for P39990 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: SNU13
Go to UniProtKB:  P39990
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
Ribosomal RNA-processing protein 9
g
573Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RRP9
Find proteins for Q06506 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RRP9
Go to UniProtKB:  Q06506
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
RNA 3'-terminal phosphate cyclase-like protein
h
367Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RCL1 (RTC1)
Find proteins for Q08096 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RCL1
Go to UniProtKB:  Q08096
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
Bms1,Ribosome biogenesis protein BMS1,Bms1
i
511Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: BMS1
Find proteins for Q08965 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: BMS1
Go to UniProtKB:  Q08965
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
Ribosomal RNA small subunit methyltransferase NEP1
j, k
252Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: EMG1 (NEP1)
EC: 2.1.1.260
Find proteins for Q06287 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: EMG1
Go to UniProtKB:  Q06287
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
Utp24
l
124N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
Imp4
m
156N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
Utp30
n
160N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
Unassigned KH domain
o
175N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
Utp20
p
924N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
Repeat protein 2
q
372N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S23-A
r
145Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS23A (RPS28A)
Find proteins for P0CX29 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX29
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
Beta-propeller 1
s, t, u
290N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
Repeat protein 1
v
580N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
Unassigned protein helices
y
507N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 1
MoleculeChainsLengthOrganism
5' external transcribed spacer0364Saccharomyces cerevisiae S288C
Entity ID: 2
MoleculeChainsLengthOrganism
18S ribosomal RNA11800Saccharomyces cerevisiae S288C
Entity ID: 3
MoleculeChainsLengthOrganism
U3 snoRNA2126Saccharomyces cerevisiae S288C
Entity ID: 10
MoleculeChainsLengthOrganism
5' domain-associatedA39Saccharomyces cerevisiae S288C
Entity ID: 11
MoleculeChainsLengthOrganism
3' domain-associatedB108Saccharomyces cerevisiae S288C
Entity ID: 53
MoleculeChainsLengthOrganism
Unassigned RNA helicesz76Saccharomyces cerevisiae S288C
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
a, b, c, d, H, i, I, J, K, l, M, m, N, n, o, O, P, p, q, Q, R, s, S, T, t, U, u, v, V, W, X, y, Y, Z
L-PEPTIDE LINKINGC4 H9 N O2

--

N
Query on N
0, 2, A, B, z
RNA LINKINGC5 H11 O7 P

--

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.1 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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