8PPL

MERS-CoV Nsp1 bound to the human 43S pre-initiation complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.65 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Universal features of Nsp1-mediated translational shutdown by coronaviruses.

Schubert, K.Karousis, E.D.Ban, I.Lapointe, C.P.Leibundgut, M.Baumlin, E.Kummerant, E.Scaiola, A.Schonhut, T.Ziegelmuller, J.Puglisi, J.D.Muhlemann, O.Ban, N.

(2023) Mol Cell 83: 3546-3557.e8

  • DOI: https://doi.org/10.1016/j.molcel.2023.09.002
  • Primary Citation of Related Structures:  
    8PPK, 8PPL

  • PubMed Abstract: 

    Nonstructural protein 1 (Nsp1) produced by coronaviruses inhibits host protein synthesis. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Nsp1 C-terminal domain was shown to bind the ribosomal mRNA channel to inhibit translation, but it is unclear whether this mechanism is broadly used by coronaviruses, whether the Nsp1 N-terminal domain binds the ribosome, or how Nsp1 allows viral RNAs to be translated. Here, we investigated Nsp1 from SARS-CoV-2, Middle East respiratory syndrome coronavirus (MERS-CoV), and Bat-Hp-CoV coronaviruses using structural, biophysical, and biochemical experiments, revealing a conserved role for the C-terminal domain. Additionally, the N-terminal domain of Bat-Hp-CoV Nsp1 binds to the decoding center of the 40S subunit, where it would prevent mRNA and eIF1A accommodation. Structure-based experiments demonstrated the importance of decoding center interactions in all three coronaviruses and showed that the same regions of Nsp1 are necessary for the selective translation of viral RNAs. Our results provide a mechanistic framework to understand how Nsp1 controls preferential translation of viral RNAs.


  • Organizational Affiliation

    Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich 8049, Switzerland.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit KA [auth I3]218Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000178982 
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UniProt GroupQ9UBQ5
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit FB [auth I4]357Homo sapiensMutation(s): 0 
EC: 3.4.19.12
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GTEx:  ENSG00000175390 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit LC [auth I5]564Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100129 
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UniProt GroupQ9Y262
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit MD [auth I6]374Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000149100 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit HE [auth I8]352Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000147677 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit GF [auth Io]320Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000130811 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 1G [auth Ip]113Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000173812 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 1A, X-chromosomalH [auth Iq]144Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000173674 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 2 subunit 1I [auth Ir]315Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000134001 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 2 subunit 2J [auth Is]333Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125977 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 2 subunit 3K [auth It]472Homo sapiensMutation(s): 0 
EC: 3.6.5.3
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GTEx:  ENSG00000130741 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit AL [auth Iu]1,382Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000107581 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit EM [auth Iv]445Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000104408 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit DO [auth Ix]548Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100353 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit CP [auth Iy]913Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000184110 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein SAR [auth AA]295Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000168028 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3aS [auth AB]264Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000145425 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S2T [auth AC]293Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000140988 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3U [auth AD]243Homo sapiensMutation(s): 0 
EC: 4.2.99.18
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GTEx:  ENSG00000149273 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4, X isoformV [auth AE]263Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198034 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S5W [auth AF]204Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000083845 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6X [auth AG]249Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000137154 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7Y [auth AH]194Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171863 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8Z [auth AI]208Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142937 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S9AA [auth AJ]194Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000170889 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S10BA [auth AK]165Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000124614 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11CA [auth AL]158Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142534 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S12DA [auth AM]132Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000112306 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13EA [auth AN]151Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000110700 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14FA [auth AO]151Homo sapiensMutation(s): 1 
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GTEx:  ENSG00000164587 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15GA [auth AP]145Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000115268 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S16HA [auth AQ]146Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105193 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S17IA [auth AR]135Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182774 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS13JA [auth AS]152Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000231500 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS19KA [auth AT]145Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105372 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S20LA [auth AU]119Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000008988 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S21MA [auth AV]83Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171858 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15aNA [auth AW]130Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000134419 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23OA [auth AX]143Homo sapiensMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24PA [auth AY]133Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000138326 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S25QA [auth AZ]125Homo sapiensMutation(s): 0 
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PHAROS:  P62851
GTEx:  ENSG00000118181 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S26RA [auth Aa]115Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000197728 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27SA [auth Ab]84Homo sapiensMutation(s): 0 
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PHAROS:  P42677
GTEx:  ENSG00000177954 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S28TA [auth Ac]69Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000233927 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S29UA [auth Ad]56Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000213741 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-like FUBI-ribosomal protein eS30 fusion proteinVA [auth Ae]133Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000149806 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-40S ribosomal protein S27aWA [auth Af]156Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143947 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Receptor of activated protein C kinase 1XA [auth Ag]317Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000204628 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L41YA [auth Ah]25Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000229117 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
Host translation inhibitor nsp1ZA [auth Aj]216Middle East respiratory syndrome-related coronavirusMutation(s): 0 
Gene Names: rep1a-1b
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Find proteins for K9N7C7 (Middle East respiratory syndrome-related coronavirus (isolate United Kingdom/H123990006/2012))
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Entity ID: 14
MoleculeChains LengthOrganismImage
Met-tRNAi(Met)N [auth Iw]75Homo sapiens
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Entity ID: 17
MoleculeChains LengthOrganismImage
18S rRNAQ [auth A2]1,869Homo sapiens
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Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download Ideal Coordinates CCD File 
BB [auth It]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
MET
Query on MET

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DB [auth Iw]METHIONINE
C5 H11 N O2 S
FFEARJCKVFRZRR-BYPYZUCNSA-N
ZN
Query on ZN

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AB [auth Is],
NK [auth Aa],
PK [auth Ad],
QK [auth Af]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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AC [auth A2]
AD [auth A2]
AF [auth A2]
AG [auth A2]
BC [auth A2]
AC [auth A2],
AD [auth A2],
AF [auth A2],
AG [auth A2],
BC [auth A2],
BD [auth A2],
BF [auth A2],
BG [auth A2],
CB [auth It],
CC [auth A2],
CD [auth A2],
CE [auth A2],
CF [auth A2],
CH [auth A2],
DC [auth A2],
DE [auth A2],
DF [auth A2],
DG [auth A2],
DH [auth A2],
DK [auth A2],
EE [auth A2],
EG [auth A2],
EH [auth A2],
EK [auth AG],
FD [auth A2],
FE [auth A2],
FG [auth A2],
FH [auth A2],
GB [auth A2],
GC [auth A2],
GD [auth A2],
GG [auth A2],
HB [auth A2],
HC [auth A2],
HD [auth A2],
HF [auth A2],
HG [auth A2],
IB [auth A2],
IC [auth A2],
ID [auth A2],
IE [auth A2],
IF [auth A2],
IG [auth A2],
JB [auth A2],
JC [auth A2],
JE [auth A2],
JF [auth A2],
JG [auth A2],
JH [auth A2],
JK [auth AS],
KE [auth A2],
KF [auth A2],
KG [auth A2],
KH [auth A2],
KK [auth AS],
LD [auth A2],
LE [auth A2],
LG [auth A2],
LH [auth A2],
LK [auth AT],
MB [auth A2],
MD [auth A2],
MH [auth A2],
MK [auth AX],
NB [auth A2],
NC [auth A2],
ND [auth A2],
NF [auth A2],
NH [auth A2],
OB [auth A2],
OC [auth A2],
OD [auth A2],
OE [auth A2],
OF [auth A2],
OH [auth A2],
PB [auth A2],
PC [auth A2],
PE [auth A2],
PF [auth A2],
PG [auth A2],
QC [auth A2],
QE [auth A2],
QF [auth A2],
QG [auth A2],
RD [auth A2],
RE [auth A2],
RF [auth A2],
RG [auth A2],
SD [auth A2],
SG [auth A2],
TB [auth A2],
TC [auth A2],
TD [auth A2],
UB [auth A2],
UC [auth A2],
UD [auth A2],
UE [auth A2],
UF [auth A2],
VB [auth A2],
VC [auth A2],
VE [auth A2],
VF [auth A2],
WB [auth A2],
WC [auth A2],
WE [auth A2],
WF [auth A2],
WG [auth A2],
XD [auth A2],
XE [auth A2],
XG [auth A2],
YD [auth A2],
YG [auth A2],
ZC [auth A2],
ZD [auth A2],
ZF [auth A2],
ZG [auth A2]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
UNX
Query on UNX

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AE [auth A2]
AH [auth A2]
AI [auth A2]
AJ [auth A2]
AK [auth A2]
AE [auth A2],
AH [auth A2],
AI [auth A2],
AJ [auth A2],
AK [auth A2],
BE [auth A2],
BH [auth A2],
BI [auth A2],
BJ [auth A2],
BK [auth A2],
CG [auth A2],
CI [auth A2],
CJ [auth A2],
CK [auth A2],
DD [auth A2],
DI [auth A2],
DJ [auth A2],
EB [auth Iw],
EC [auth A2],
ED [auth A2],
EF [auth A2],
EI [auth A2],
EJ [auth A2],
FB [auth Iw],
FC [auth A2],
FF [auth A2],
FI [auth A2],
FJ [auth A2],
FK [auth AJ],
GE [auth A2],
GF [auth A2],
GH [auth A2],
GI [auth A2],
GJ [auth A2],
GK [auth AN],
HE [auth A2],
HH [auth A2],
HI [auth A2],
HJ [auth A2],
HK [auth AO],
IH [auth A2],
II [auth A2],
IJ [auth A2],
IK [auth AO],
JD [auth A2],
JI [auth A2],
JJ [auth A2],
KB [auth A2],
KC [auth A2],
KD [auth A2],
KI [auth A2],
KJ [auth A2],
LB [auth A2],
LC [auth A2],
LF [auth A2],
LI [auth A2],
LJ [auth A2],
MC [auth A2],
ME [auth A2],
MF [auth A2],
MG [auth A2],
MI [auth A2],
MJ [auth A2],
NE [auth A2],
NG [auth A2],
NI [auth A2],
NJ [auth A2],
OG [auth A2],
OI [auth A2],
OJ [auth A2],
OK [auth Ad],
PD [auth A2],
PH [auth A2],
PI [auth A2],
PJ [auth A2],
QB [auth A2],
QD [auth A2],
QH [auth A2],
QI [auth A2],
QJ [auth A2],
RB [auth A2],
RC [auth A2],
RH [auth A2],
RI [auth A2],
RJ [auth A2],
SB [auth A2],
SC [auth A2],
SE [auth A2],
SF [auth A2],
SH [auth A2],
SI [auth A2],
SJ [auth A2],
TE [auth A2],
TF [auth A2],
TG [auth A2],
TH [auth A2],
TI [auth A2],
TJ [auth A2],
UG [auth A2],
UH [auth A2],
UI [auth A2],
UJ [auth A2],
VD [auth A2],
VG [auth A2],
VH [auth A2],
VI [auth A2],
VJ [auth A2],
WD [auth A2],
WH [auth A2],
WI [auth A2],
WJ [auth A2],
XB [auth A2],
XC [auth A2],
XF [auth A2],
XH [auth A2],
XI [auth A2],
XJ [auth A2],
YB [auth A2],
YC [auth A2],
YE [auth A2],
YF [auth A2],
YH [auth A2],
YI [auth A2],
YJ [auth A2],
ZB [auth A2],
ZE [auth A2],
ZH [auth A2],
ZI [auth A2],
ZJ [auth A2]
UNKNOWN ATOM OR ION
X
Modified Residues  3 Unique
IDChains TypeFormula2D DiagramParent
SAC
Query on SAC
R [auth AA]L-PEPTIDE LINKINGC5 H9 N O4SER
NMM
Query on NMM
KA [auth AT]L-PEPTIDE LINKINGC7 H16 N4 O2ARG
HY3
Query on HY3
OA [auth AX]L-PEPTIDE LINKINGC5 H9 N O3PRO
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.65 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland182341
Swiss National Science FoundationSwitzerland182831
Swiss National Science FoundationSwitzerland204161
Swiss National Science FoundationSwitzerland51NF40-182880
Swiss National Science FoundationSwitzerland51NF40--205601
Other governmentSwitzerlandETH-23 18-2
Other governmentSwitzerland--
Other privateSwitzerland--
Other privateSwitzerland--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM011378
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM145306
National Institutes of Health/National Institute on Aging (NIH/NIA)United StatesAG064690
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesK99GM144678

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-18
    Type: Initial release
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Derived calculations
  • Version 2.1: 2024-04-24
    Changes: Data collection