8PPK

Bat-Hp-CoV Nsp1 and eIF1 bound to the human 40S small ribosomal subunit


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.98 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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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 1A [auth p]113Homo sapiensMutation(s): 0 
Gene Names: EIF1SUI1
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GTEx:  ENSG00000173812 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein SAC [auth A]295Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000168028 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3aD [auth B]264Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000145425 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S2E [auth C]293Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000140988 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3F [auth D]243Homo sapiensMutation(s): 0 
EC: 4.2.99.18
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GTEx:  ENSG00000149273 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4, X isoformG [auth E]263Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198034 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S5H [auth F]204Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000083845 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6I [auth G]249Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000137154 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7J [auth H]194Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171863 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8K [auth I]208Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142937 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S9L [auth J]194Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000170889 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S10M [auth K]165Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000124614 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11N [auth L]158Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142534 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S12O [auth M]132Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000112306 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13P [auth N]151Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000110700 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14Q [auth O]151Homo sapiensMutation(s): 1 
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GTEx:  ENSG00000164587 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15R [auth P]145Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000115268 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S16S [auth Q]146Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105193 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S17T [auth R]135Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182774 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS13U [auth S]152Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000231500 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS19V [auth T]145Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105372 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S20W [auth U]119Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000008988 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S21X [auth V]83Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171858 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15aY [auth W]130Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000134419 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23Z [auth X]143Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000186468 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24AA [auth Y]133Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000138326 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S25BA [auth Z]125Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000118181 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S26CA [auth a]115Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000197728 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27DA [auth b]84Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000177954 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S28EA [auth c]69Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000233927 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S29FA [auth d]56Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000213741 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS30GA [auth e]133Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000149806 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-40S ribosomal protein S27aHA [auth f]156Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143947 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Receptor of activated protein C kinase 1IA [auth g]317Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000204628 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L41JA [auth h]25Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000229117 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Nsp1KA [auth j]188Bat Hp-betacoronavirus/Zhejiang2013Mutation(s): 0 
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Entity ID: 2
MoleculeChains LengthOrganismImage
18S rRNAB [auth 2]1,869Homo sapiens
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
FJ [auth a],
GJ [auth d],
HJ [auth f]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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AB [auth 2]
AC [auth 2]
AD [auth 2]
AH [auth 2]
BB [auth 2]
AB [auth 2],
AC [auth 2],
AD [auth 2],
AH [auth 2],
BB [auth 2],
BC [auth 2],
BD [auth 2],
BH [auth 2],
CB [auth 2],
CC [auth 2],
CD [auth 2],
CH [auth 2],
DB [auth 2],
DC [auth 2],
DD [auth 2],
DH [auth 2],
DJ [auth X],
EB [auth 2],
EC [auth 2],
ED [auth 2],
EG [auth 2],
EH [auth 2],
FB [auth 2],
FC [auth 2],
FD [auth 2],
FG [auth 2],
GB [auth 2],
GC [auth 2],
GD [auth 2],
GG [auth 2],
HB [auth 2],
HC [auth 2],
HD [auth 2],
HG [auth 2],
IB [auth 2],
IC [auth 2],
ID [auth 2],
IG [auth 2],
JB [auth 2],
JC [auth 2],
JD [auth 2],
JG [auth 2],
KB [auth 2],
KC [auth 2],
KD [auth 2],
KG [auth 2],
KH [auth 2],
LB [auth 2],
LC [auth 2],
LD [auth 2],
LG [auth 2],
LH [auth 2],
MB [auth 2],
MC [auth 2],
MD [auth 2],
MG [auth 2],
NB [auth 2],
NC [auth 2],
ND [auth 2],
NG [auth 2],
OB [auth 2],
OC [auth 2],
OD [auth 2],
OG [auth 2],
PB [auth 2],
PC [auth 2],
PD [auth 2],
PG [auth 2],
PI [auth 2],
QB [auth 2],
QC [auth 2],
QD [auth 2],
QG [auth 2],
QI [auth 2],
RB [auth 2],
RC [auth 2],
RD [auth 2],
RG [auth 2],
RI [auth 2],
SB [auth 2],
SC [auth 2],
SD [auth 2],
SG [auth 2],
SI [auth 2],
TB [auth 2],
TC [auth 2],
TD [auth 2],
TG [auth 2],
TI [auth 2],
UB [auth 2],
UC [auth 2],
UD [auth 2],
UG [auth 2],
UI [auth 2],
VB [auth 2],
VC [auth 2],
VD [auth 2],
VG [auth 2],
WB [auth 2],
WC [auth 2],
WD [auth 2],
WG [auth 2],
XB [auth 2],
XC [auth 2],
XG [auth 2],
YB [auth 2],
YC [auth 2],
YG [auth 2],
ZB [auth 2],
ZC [auth 2],
ZG [auth 2]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
UNX
Query on UNX

Download Ideal Coordinates CCD File 
AE [auth 2]
AF [auth 2]
AG [auth 2]
AI [auth 2]
AJ [auth N]
AE [auth 2],
AF [auth 2],
AG [auth 2],
AI [auth 2],
AJ [auth N],
BE [auth 2],
BF [auth 2],
BG [auth 2],
BI [auth 2],
BJ [auth O],
CE [auth 2],
CF [auth 2],
CG [auth 2],
CI [auth 2],
CJ [auth O],
DE [auth 2],
DF [auth 2],
DG [auth 2],
DI [auth 2],
EE [auth 2],
EF [auth 2],
EI [auth 2],
EJ [auth X],
FE [auth 2],
FF [auth 2],
FH [auth 2],
FI [auth 2],
GE [auth 2],
GF [auth 2],
GH [auth 2],
GI [auth 2],
HE [auth 2],
HF [auth 2],
HH [auth 2],
HI [auth 2],
IE [auth 2],
IF [auth 2],
IH [auth 2],
II [auth 2],
JE [auth 2],
JF [auth 2],
JH [auth 2],
JI [auth 2],
KE [auth 2],
KF [auth 2],
KI [auth 2],
LA [auth 2],
LE [auth 2],
LF [auth 2],
LI [auth 2],
MA [auth 2],
ME [auth 2],
MF [auth 2],
MH [auth 2],
MI [auth 2],
NA [auth 2],
NE [auth 2],
NF [auth 2],
NH [auth 2],
NI [auth 2],
OA [auth 2],
OE [auth 2],
OF [auth 2],
OH [auth 2],
OI [auth 2],
PA [auth 2],
PE [auth 2],
PF [auth 2],
PH [auth 2],
QA [auth 2],
QE [auth 2],
QF [auth 2],
QH [auth 2],
RA [auth 2],
RE [auth 2],
RF [auth 2],
RH [auth 2],
SA [auth 2],
SE [auth 2],
SF [auth 2],
SH [auth 2],
TA [auth 2],
TE [auth 2],
TF [auth 2],
TH [auth 2],
UA [auth 2],
UE [auth 2],
UF [auth 2],
UH [auth 2],
VA [auth 2],
VE [auth 2],
VF [auth 2],
VH [auth 2],
VI [auth G],
WA [auth 2],
WE [auth 2],
WF [auth 2],
WH [auth 2],
WI [auth H],
XA [auth 2],
XD [auth 2],
XE [auth 2],
XF [auth 2],
XH [auth 2],
XI [auth I],
YA [auth 2],
YD [auth 2],
YE [auth 2],
YF [auth 2],
YH [auth 2],
YI [auth J],
ZA [auth 2],
ZD [auth 2],
ZE [auth 2],
ZF [auth 2],
ZH [auth 2],
ZI [auth L]
UNKNOWN ATOM OR ION
X
Modified Residues  3 Unique
IDChains TypeFormula2D DiagramParent
SAC
Query on SAC
C [auth A]L-PEPTIDE LINKINGC5 H9 N O4SER
NMM
Query on NMM
V [auth T]L-PEPTIDE LINKINGC7 H16 N4 O2ARG
HY3
Query on HY3
Z [auth X]L-PEPTIDE LINKINGC5 H9 N O3PRO
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.98 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1

Structure Validation

View Full Validation Report

Currently 8PPK does not have a validation slider image.



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