6G51

Cryo-EM structure of a late human pre-40S ribosomal subunit - State D


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.1 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

Visualizing late states of human 40S ribosomal subunit maturation.

Ameismeier, M.Cheng, J.Berninghausen, O.Beckmann, R.

(2018) Nature 558: 249-253

  • DOI: 10.1038/s41586-018-0193-0
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The formation of eukaryotic ribosomal subunits extends from the nucleolus to the cytoplasm and entails hundreds of assembly factors. Despite differences in the pathways of ribosome formation, high-resolution structural information has been available ...

    The formation of eukaryotic ribosomal subunits extends from the nucleolus to the cytoplasm and entails hundreds of assembly factors. Despite differences in the pathways of ribosome formation, high-resolution structural information has been available only from fungi. Here we present cryo-electron microscopy structures of late-stage human 40S assembly intermediates, representing one state reconstituted in vitro and five native states that range from nuclear to late cytoplasmic. The earliest particles reveal the position of the biogenesis factor RRP12 and distinct immature rRNA conformations that accompany the formation of the 40S subunit head. Molecular models of the late-acting assembly factors TSR1, RIOK1, RIOK2, ENP1, LTV1, PNO1 and NOB1 provide mechanistic details that underlie their contribution to a sequential 40S subunit assembly. The NOB1 architecture displays an inactive nuclease conformation that requires rearrangement of the PNO1-bound 3' rRNA, thereby coordinating the final rRNA folding steps with site 3 cleavage.


    Organizational Affiliation

    Gene Center Munich and Center of Integrated Protein Science-Munich (CiPS-M), Department of Biochemistry, University of Munich, Munich, Germany. beckmann@genzentrum.lmu.de.,Gene Center Munich and Center of Integrated Protein Science-Munich (CiPS-M), Department of Biochemistry, University of Munich, Munich, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S17
R
135Homo sapiensMutation(s): 0 
Gene Names: RPS17 (RPS17L)
Find proteins for P08708 (Homo sapiens)
Go to Gene View: RPS17
Go to UniProtKB:  P08708
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein SA
A
295Homo sapiensMutation(s): 0 
Gene Names: RPSA (LAMBR, LAMR1)
Find proteins for P08865 (Homo sapiens)
Go to Gene View: RPSA
Go to UniProtKB:  P08865
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S3a
B
264Homo sapiensMutation(s): 0 
Gene Names: RPS3A (FTE1, MFTL)
Find proteins for P61247 (Homo sapiens)
Go to Gene View: RPS3A
Go to UniProtKB:  P61247
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S2
C
293Homo sapiensMutation(s): 0 
Gene Names: RPS2 (RPS4)
Find proteins for P15880 (Homo sapiens)
Go to Gene View: RPS2
Go to UniProtKB:  P15880
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S4, X isoform
E
263Homo sapiensMutation(s): 0 
Gene Names: RPS4X (CCG2, RPS4, SCAR)
Find proteins for P62701 (Homo sapiens)
Go to Gene View: RPS4X
Go to UniProtKB:  P62701
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S6
G
249Homo sapiensMutation(s): 0 
Gene Names: RPS6
Find proteins for P62753 (Homo sapiens)
Go to Gene View: RPS6
Go to UniProtKB:  P62753
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S7
H
194Homo sapiensMutation(s): 0 
Gene Names: RPS7
Find proteins for P62081 (Homo sapiens)
Go to Gene View: RPS7
Go to UniProtKB:  P62081
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S8
I
208Homo sapiensMutation(s): 0 
Gene Names: RPS8
Find proteins for P62241 (Homo sapiens)
Go to Gene View: RPS8
Go to UniProtKB:  P62241
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S9
J
194Homo sapiensMutation(s): 0 
Gene Names: RPS9
Find proteins for P46781 (Homo sapiens)
Go to Gene View: RPS9
Go to UniProtKB:  P46781
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S11
L
158Homo sapiensMutation(s): 0 
Gene Names: RPS11
Find proteins for P62280 (Homo sapiens)
Go to Gene View: RPS11
Go to UniProtKB:  P62280
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S13
N
151Homo sapiensMutation(s): 0 
Gene Names: RPS13
Find proteins for P62277 (Homo sapiens)
Go to Gene View: RPS13
Go to UniProtKB:  P62277
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S14
O
151Homo sapiensMutation(s): 0 
Gene Names: RPS14
Find proteins for P62263 (Homo sapiens)
Go to Gene View: RPS14
Go to UniProtKB:  P62263
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S21
V
83Homo sapiensMutation(s): 0 
Gene Names: RPS21
Find proteins for P63220 (Homo sapiens)
Go to Gene View: RPS21
Go to UniProtKB:  P63220
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S15a
W
130Homo sapiensMutation(s): 0 
Gene Names: RPS15A
Find proteins for P62244 (Homo sapiens)
Go to Gene View: RPS15A
Go to UniProtKB:  P62244
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S23
X
143Homo sapiensMutation(s): 0 
Gene Names: RPS23
Find proteins for P62266 (Homo sapiens)
Go to Gene View: RPS23
Go to UniProtKB:  P62266
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S24
Y
133Homo sapiensMutation(s): 0 
Gene Names: RPS24
Find proteins for P62847 (Homo sapiens)
Go to Gene View: RPS24
Go to UniProtKB:  P62847
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S27
b
84Homo sapiensMutation(s): 0 
Gene Names: RPS27 (MPS1)
Find proteins for P42677 (Homo sapiens)
Go to Gene View: RPS27
Go to UniProtKB:  P42677
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S30
e
59Homo sapiensMutation(s): 0 
Gene Names: FAU
Find proteins for P62861 (Homo sapiens)
Go to Gene View: FAU
Go to UniProtKB:  P62861
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
RNA-binding protein PNO1
x
252Homo sapiensMutation(s): 0 
Gene Names: PNO1
Find proteins for Q9NRX1 (Homo sapiens)
Go to Gene View: PNO1
Go to UniProtKB:  Q9NRX1
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
RNA-binding protein NOB1
y
412Homo sapiensMutation(s): 0 
Gene Names: NOB1 (ART4, NOB1P, PSMD8BP1)
Find proteins for Q9ULX3 (Homo sapiens)
Go to Gene View: NOB1
Go to UniProtKB:  Q9ULX3
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Pre-rRNA-processing protein TSR1 homolog
u
804Homo sapiensMutation(s): 0 
Gene Names: TSR1 (KIAA1401)
Find proteins for Q2NL82 (Homo sapiens)
Go to Gene View: TSR1
Go to UniProtKB:  Q2NL82
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein kinase RIO2
v
552Homo sapiensMutation(s): 0 
Gene Names: RIOK2 (RIO2)
EC: 2.7.11.1
Find proteins for Q9BVS4 (Homo sapiens)
Go to Gene View: RIOK2
Go to UniProtKB:  Q9BVS4
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
Protein LTV1 homolog
t
475Homo sapiensMutation(s): 0 
Gene Names: LTV1 (C6orf93)
Find proteins for Q96GA3 (Homo sapiens)
Go to Gene View: LTV1
Go to UniProtKB:  Q96GA3
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S29
d
56Homo sapiensMutation(s): 0 
Gene Names: RPS29
Find proteins for P62273 (Homo sapiens)
Go to Gene View: RPS29
Go to UniProtKB:  P62273
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S3
D
243Homo sapiensMutation(s): 0 
Gene Names: RPS3
EC: 4.2.99.18
Find proteins for P23396 (Homo sapiens)
Go to Gene View: RPS3
Go to UniProtKB:  P23396
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S5
F
204Homo sapiensMutation(s): 0 
Gene Names: RPS5
Find proteins for P46782 (Homo sapiens)
Go to Gene View: RPS5
Go to UniProtKB:  P46782
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S10
K
165Homo sapiensMutation(s): 0 
Gene Names: RPS10
Find proteins for P46783 (Homo sapiens)
Go to Gene View: RPS10
Go to UniProtKB:  P46783
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S12
M
132Homo sapiensMutation(s): 0 
Gene Names: RPS12
Find proteins for P25398 (Homo sapiens)
Go to Gene View: RPS12
Go to UniProtKB:  P25398
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S15
P
145Homo sapiensMutation(s): 0 
Gene Names: RPS15 (RIG)
Find proteins for P62841 (Homo sapiens)
Go to Gene View: RPS15
Go to UniProtKB:  P62841
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S16
Q
146Homo sapiensMutation(s): 0 
Gene Names: RPS16
Find proteins for P62249 (Homo sapiens)
Go to Gene View: RPS16
Go to UniProtKB:  P62249
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S18
S
152Homo sapiensMutation(s): 0 
Gene Names: RPS18 (D6S218E)
Find proteins for P62269 (Homo sapiens)
Go to Gene View: RPS18
Go to UniProtKB:  P62269
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S19
T
145Homo sapiensMutation(s): 0 
Gene Names: RPS19
Find proteins for P39019 (Homo sapiens)
Go to Gene View: RPS19
Go to UniProtKB:  P39019
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S20
U
119Homo sapiensMutation(s): 0 
Gene Names: RPS20
Find proteins for P60866 (Homo sapiens)
Go to Gene View: RPS20
Go to UniProtKB:  P60866
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S25
Z
125Homo sapiensMutation(s): 0 
Gene Names: RPS25
Find proteins for P62851 (Homo sapiens)
Go to Gene View: RPS25
Go to UniProtKB:  P62851
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S28
c
69Homo sapiensMutation(s): 0 
Gene Names: RPS28
Find proteins for P62857 (Homo sapiens)
Go to Gene View: RPS28
Go to UniProtKB:  P62857
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-40S ribosomal protein S27a
f
156Homo sapiensMutation(s): 0 
Gene Names: RPS27A (UBA80, UBCEP1)
Find proteins for P62979 (Homo sapiens)
Go to Gene View: RPS27A
Go to UniProtKB:  P62979
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
Receptor of activated protein C kinase 1
g
317Homo sapiensMutation(s): 0 
Gene Names: RACK1 (GNB2L1)
Find proteins for P63244 (Homo sapiens)
Go to Gene View: RACK1
Go to UniProtKB:  P63244
Entity ID: 1
MoleculeChainsLengthOrganism
18S ribosomal RNA21882Homo sapiens
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.1 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanySFB646
German Research FoundationGermanyGRK1721
German Research FoundationGermanyFOR1805
European Research CouncilGermanyCRYOTRANSLATION

Revision History 

  • Version 1.0: 2018-06-06
    Type: Initial release
  • Version 1.1: 2018-06-20
    Type: Data collection, Database references
  • Version 1.2: 2018-06-27
    Type: Data collection, Database references
  • Version 1.3: 2018-10-24
    Type: Advisory, Data collection, Derived calculations