6P4G

Structure of a mammalian small ribosomal subunit in complex with the Israeli Acute Paralysis Virus IRES (Class 1)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.1 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

The Israeli acute paralysis virus IRES captures host ribosomes by mimicking a ribosomal state with hybrid tRNAs.

Acosta-Reyes, F.Neupane, R.Frank, J.Fernandez, I.S.

(2019) Embo J. 38: e102226-e102226

  • DOI: 10.15252/embj.2019102226
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Colony collapse disorder (CCD) is a multi-faceted syndrome decimating bee populations worldwide, and a group of viruses of the widely distributed Dicistroviridae family have been identified as a causing agent of CCD. This family of viruses employs no ...

    Colony collapse disorder (CCD) is a multi-faceted syndrome decimating bee populations worldwide, and a group of viruses of the widely distributed Dicistroviridae family have been identified as a causing agent of CCD. This family of viruses employs non-coding RNA sequences, called internal ribosomal entry sites (IRESs), to precisely exploit the host machinery for viral protein production. Using single-particle cryo-electron microscopy (cryo-EM), we have characterized how the IRES of Israeli acute paralysis virus (IAPV) intergenic region captures and redirects translating ribosomes toward viral RNA messages. We reconstituted two in vitro reactions targeting a pre-translocation and a post-translocation state of the IAPV-IRES in the ribosome, allowing us to identify six structures using image processing classification methods. From these, we reconstructed the trajectory of IAPV-IRES from the early small subunit recruitment to the final post-translocated state in the ribosome. An early commitment of IRES/ribosome complexes for global pre-translocation mimicry explains the high efficiency observed for this IRES. Efforts directed toward fighting CCD by targeting the IAPV-IRES using RNA-interference technology are underway, and the structural framework presented here may assist in further refining these approaches.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.,Department of Biological Sciences, Columbia University, New York, NY, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
uS2
B
295Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPSA (LOC100340199)
Find proteins for G1TWL4 (Oryctolagus cuniculus)
Go to Gene View: RPSA
Go to UniProtKB:  G1TWL4
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
eS1
C
264Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS3A (LOC100342838, LOC100348981)
Find proteins for G1SS70 (Oryctolagus cuniculus)
Go to Gene View: RPS3A
Go to UniProtKB:  G1SS70
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
uS5
D
255Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SWM1 (Oryctolagus cuniculus)
Go to UniProtKB:  G1SWM1
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
uS3
E
281Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS3
Find proteins for G1TNM3 (Oryctolagus cuniculus)
Go to Gene View: RPS3
Go to UniProtKB:  G1TNM3
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
eS4
F
263Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100338112
Find proteins for G1TK17 (Oryctolagus cuniculus)
Go to UniProtKB:  G1TK17
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
uS7
G
204Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS5
Find proteins for G1TFM5 (Oryctolagus cuniculus)
Go to Gene View: RPS5
Go to UniProtKB:  G1TFM5
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
eS6
H
249Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TM55 (Oryctolagus cuniculus)
Go to UniProtKB:  G1TM55
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
eS7
I
194Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SVB0 (Oryctolagus cuniculus)
Go to UniProtKB:  G1SVB0
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
eS8
J
208Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100352057
Find proteins for G1TJW1 (Oryctolagus cuniculus)
Go to UniProtKB:  G1TJW1
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
uS4
K
194Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS9
Find proteins for B7NZS8 (Oryctolagus cuniculus)
Go to Gene View: RPS9
Go to UniProtKB:  B7NZS8
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
eS10
L
149Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100348511
Find proteins for G1TPV3 (Oryctolagus cuniculus)
Go to UniProtKB:  G1TPV3
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
uS17
M
158Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS11
Find proteins for G1TRM4 (Oryctolagus cuniculus)
Go to Gene View: RPS11
Go to UniProtKB:  G1TRM4
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
eS12
N
132Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS12
Find proteins for G1SFR8 (Oryctolagus cuniculus)
Go to Gene View: RPS12
Go to UniProtKB:  G1SFR8
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
uS15
O
151Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SP51 (Oryctolagus cuniculus)
Go to UniProtKB:  G1SP51
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
uS11
P
151Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS14
Find proteins for G1T1F0 (Oryctolagus cuniculus)
Go to Gene View: RPS14
Go to UniProtKB:  G1T1F0
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
uS19
Q
145Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS15
Find proteins for G1U0Q2 (Oryctolagus cuniculus)
Go to Gene View: RPS15
Go to UniProtKB:  G1U0Q2
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
uS9
R
172Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS16
Find proteins for G1SGX4 (Oryctolagus cuniculus)
Go to Gene View: RPS16
Go to UniProtKB:  G1SGX4
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
eS17
S
135Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100353606 (RPS17)
Find proteins for G1TU13 (Oryctolagus cuniculus)
Go to UniProtKB:  G1TU13
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
uS13
T
152Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS18
Find proteins for G1TPG3 (Oryctolagus cuniculus)
Go to Gene View: RPS18
Go to UniProtKB:  G1TPG3
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
eS19
U
145Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100345774
Find proteins for G1TN62 (Oryctolagus cuniculus)
Go to UniProtKB:  G1TN62
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
uS10
V
119Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS20 (LOC100341365, LOC100348955, LOC100354063)
Find proteins for G1SIZ2 (Oryctolagus cuniculus)
Go to Gene View: RPS20
Go to UniProtKB:  G1SIZ2
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
eS21
W
83Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS21
Find proteins for G1TM82 (Oryctolagus cuniculus)
Go to Gene View: RPS21
Go to UniProtKB:  G1TM82
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
uS8
X
130Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS15A
Find proteins for G1TG89 (Oryctolagus cuniculus)
Go to Gene View: RPS15A
Go to UniProtKB:  G1TG89
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
uS12
Y
143Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS23
Find proteins for G1SZ47 (Oryctolagus cuniculus)
Go to Gene View: RPS23
Go to UniProtKB:  G1SZ47
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
eS24
Z
134Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS24
Find proteins for G1T3D8 (Oryctolagus cuniculus)
Go to Gene View: RPS24
Go to UniProtKB:  G1T3D8
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
eS25
a
125Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TDB3 (Oryctolagus cuniculus)
Go to UniProtKB:  G1TDB3
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
eS26
b
115Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100346996
Find proteins for G1TFE8 (Oryctolagus cuniculus)
Go to UniProtKB:  G1TFE8
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
eS27
c
84Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100345694 (LOC100345044, LOC100348261, RPS27)
Find proteins for G1TZ76 (Oryctolagus cuniculus)
Go to UniProtKB:  G1TZ76
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
eS28
d
69Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS28
Find proteins for G1TIB4 (Oryctolagus cuniculus)
Go to Gene View: RPS28
Go to UniProtKB:  G1TIB4
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
eS29
e
56Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100337712
Find proteins for G1U7M4 (Oryctolagus cuniculus)
Go to UniProtKB:  G1U7M4
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
eS30
f
133Oryctolagus cuniculusMutation(s): 0 
Gene Names: FAU
Find proteins for G1T8A2 (Oryctolagus cuniculus)
Go to Gene View: FAU
Go to UniProtKB:  G1T8A2
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
eS31
g
156Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SK22 (Oryctolagus cuniculus)
Go to UniProtKB:  G1SK22
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
RACK1
h
317Oryctolagus cuniculusMutation(s): 0 
Gene Names: RACK1
Find proteins for G1SJB4 (Oryctolagus cuniculus)
Go to Gene View: RACK1
Go to UniProtKB:  G1SJB4
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
eL41
n
25Oryctolagus cuniculusMutation(s): 0 
Find proteins for A0A087WNH4 (Oryctolagus cuniculus)
Go to UniProtKB:  A0A087WNH4
Entity ID: 1
MoleculeChainsLengthOrganism
18S rRNA21869Oryctolagus cuniculus
Entity ID: 36
MoleculeChainsLengthOrganism
IAPV-IRES1253Israeli acute paralysis virus
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.1 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM29169

Revision History 

  • Version 1.0: 2019-09-18
    Type: Initial release
  • Version 1.1: 2019-10-30
    Type: Data collection, Database references
  • Version 1.2: 2019-11-13
    Type: Database references
  • Version 1.3: 2020-01-08
    Type: Author supporting evidence