6ZLW

SARS-CoV-2 Nsp1 bound to the human 40S ribosomal subunit

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2.

Thoms, M., Buschauer, R., Ameismeier, M., Koepke, L., Denk, T., Hirschenberger, M., Kratzat, H., Hayn, M., Mackens-Kiani, T., Cheng, J., Straub, J.H., Sturzel, C.M., Frohlich, T., Berninghausen, O., Becker, T., Kirchhoff, F., Sparrer, K.M.J., Beckmann, R.

(2020) Science 369: 1249-1255

  • DOI: 10.1126/science.abc8665
  • Primary Citation of Related Structures:  
    6ZME, 6ZLW, 6ZM7, 6ZMT, 6ZN5, 6ZMI, 6ZMO, 6ZP4, 6ZON

  • PubMed Abstract: 

    • Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the current coronavirus disease 2019 (COVID-19) pandemic. A major virulence factor of SARS-CoVs is the nonstructural protein 1 (Nsp1), which suppresses host gene e ...

    Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the current coronavirus disease 2019 (COVID-19) pandemic. A major virulence factor of SARS-CoVs is the nonstructural protein 1 (Nsp1), which suppresses host gene expression by ribosome association. Here, we show that Nsp1 from SARS-CoV-2 binds to the 40 S ribosomal subunit, resulting in shutdown of messenger RNA (mRNA) translation both in vitro and in cells. Structural analysis by cryo-electron microscopy of in vitro-reconstituted Nsp1-40 S and various native Nsp1-40 S and -80 S complexes revealed that the Nsp1 C terminus binds to and obstructs the mRNA entry tunnel. Thereby, Nsp1 effectively blocks retinoic acid-inducible gene I-dependent innate immune responses that would otherwise facilitate clearance of the infection. Thus, the structural characterization of the inhibitory mechanism of Nsp1 may aid structure-based drug design against SARS-CoV-2.

    Organizational Affiliation: 

    Gene Center Munich, Department of Biochemistry, University of Munich, Munich, Germany. beckmann@genzentrum.lmu.de konstantin.sparrer@uni-ulm.de.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein SAB295Homo sapiensMutation(s): 0 
Gene Names: RPSA, LAMBR, LAMR1
Find proteins for P08865 (Homo sapiens)
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PHAROS  P08865
GTEx  ENSG00000168028
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S3aC264Homo sapiensMutation(s): 0 
Gene Names: RPS3A, FTE1, MFTL
Find proteins for P61247 (Homo sapiens)
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PHAROS  P61247
GTEx  ENSG00000145425
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S2D293Homo sapiensMutation(s): 0 
Gene Names: RPS2, RPS4
Find proteins for P15880 (Homo sapiens)
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PHAROS  P15880
GTEx  ENSG00000140988
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S4, X isoformE263Homo sapiensMutation(s): 0 
Gene Names: RPS4X, CCG2, RPS4, SCAR
Find proteins for P62701 (Homo sapiens)
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PHAROS  P62701
GTEx  ENSG00000198034
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S3F243Homo sapiensMutation(s): 0 
Gene Names: RPS3, OK/SW-cl.26
EC: 4.2.99.18
Find proteins for P23396 (Homo sapiens)
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PHAROS  P23396
GTEx  ENSG00000149273
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S6G249Homo sapiensMutation(s): 0 
Gene Names: RPS6, OK/SW-cl.2
Find proteins for P62753 (Homo sapiens)
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PHAROS  P62753
GTEx  ENSG00000137154
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S7H194Homo sapiensMutation(s): 0 
Gene Names: RPS7
Find proteins for P62081 (Homo sapiens)
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PHAROS  P62081
GTEx  ENSG00000171863
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S8I208Homo sapiensMutation(s): 0 
Gene Names: RPS8, OK/SW-cl.83
Find proteins for P62241 (Homo sapiens)
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PHAROS  P62241
GTEx  ENSG00000142937
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S9J194Homo sapiensMutation(s): 0 
Gene Names: RPS9
Find proteins for P46781 (Homo sapiens)
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PHAROS  P46781
GTEx  ENSG00000170889
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S5K204Homo sapiensMutation(s): 0 
Gene Names: RPS5
Find proteins for P46782 (Homo sapiens)
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PHAROS  P46782
GTEx  ENSG00000083845
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S11L158Homo sapiensMutation(s): 0 
Gene Names: RPS11
Find proteins for P62280 (Homo sapiens)
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PHAROS  P62280
GTEx  ENSG00000142534
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S10M165Homo sapiensMutation(s): 0 
Gene Names: RPS10
Find proteins for P46783 (Homo sapiens)
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PHAROS  P46783
GTEx  ENSG00000124614
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S13N151Homo sapiensMutation(s): 0 
Gene Names: RPS13
Find proteins for P62277 (Homo sapiens)
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PHAROS  P62277
GTEx  ENSG00000110700
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S12O132Homo sapiensMutation(s): 0 
Gene Names: RPS12
Find proteins for P25398 (Homo sapiens)
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PHAROS  P25398
GTEx  ENSG00000112306
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S14P151Homo sapiensMutation(s): 0 
Gene Names: RPS14, PRO2640
Find proteins for P62263 (Homo sapiens)
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Entity ID: 16
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40S ribosomal protein S15Q145Homo sapiensMutation(s): 0 
Gene Names: RPS15, RIG
Find proteins for P62841 (Homo sapiens)
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PHAROS  P62841
GTEx  ENSG00000115268
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Entity ID: 17
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40S ribosomal protein S16R146Homo sapiensMutation(s): 0 
Gene Names: RPS16
Find proteins for P62249 (Homo sapiens)
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PHAROS  P62249
GTEx  ENSG00000105193
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Entity ID: 18
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40S ribosomal protein S17S135Homo sapiensMutation(s): 0 
Gene Names: RPS17, RPS17L
Find proteins for P08708 (Homo sapiens)
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PHAROS  P08708
GTEx  ENSG00000182774
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S18T152Homo sapiensMutation(s): 0 
Gene Names: RPS18, D6S218E
Find proteins for P62269 (Homo sapiens)
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PHAROS  P62269
GTEx  ENSG00000231500
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S19U145Homo sapiensMutation(s): 0 
Gene Names: RPS19
Find proteins for P39019 (Homo sapiens)
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PHAROS  P39019
GTEx  ENSG00000105372
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Entity ID: 21
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40S ribosomal protein S20V119Homo sapiensMutation(s): 0 
Gene Names: RPS20
Find proteins for P60866 (Homo sapiens)
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PHAROS  P60866
GTEx  ENSG00000008988
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S15aW130Homo sapiensMutation(s): 0 
Gene Names: RPS15A, OK/SW-cl.82
Find proteins for P62244 (Homo sapiens)
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PHAROS  P62244
GTEx  ENSG00000134419
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Entity ID: 23
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40S ribosomal protein S23X143Homo sapiensMutation(s): 0 
Gene Names: RPS23
Find proteins for P62266 (Homo sapiens)
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PHAROS  P62266
GTEx  ENSG00000186468
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S24Y133Homo sapiensMutation(s): 0 
Gene Names: RPS24
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PHAROS  P62847
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S21Z83Homo sapiensMutation(s): 0 
Gene Names: RPS21
Find proteins for P63220 (Homo sapiens)
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PHAROS  P63220
GTEx  ENSG00000171858
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S25a125Homo sapiensMutation(s): 0 
Gene Names: RPS25
Find proteins for P62851 (Homo sapiens)
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PHAROS  P62851
GTEx  ENSG00000118181
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S27b84Homo sapiensMutation(s): 0 
Gene Names: RPS27, MPS1
Find proteins for P42677 (Homo sapiens)
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PHAROS  P42677
GTEx  ENSG00000177954
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S26c115Homo sapiensMutation(s): 0 
Gene Names: RPS26
Find proteins for P62854 (Homo sapiens)
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PHAROS  P62854
GTEx  ENSG00000197728
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Entity ID: 29
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40S ribosomal protein S28d69Homo sapiensMutation(s): 0 
Gene Names: RPS28
Find proteins for P62857 (Homo sapiens)
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PHAROS  P62857
GTEx  ENSG00000233927
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S30e59Homo sapiensMutation(s): 0 
Gene Names: FAU
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PHAROS  P62861
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Entity ID: 31
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40S ribosomal protein S29f56Homo sapiensMutation(s): 0 
Gene Names: RPS29
Find proteins for P62273 (Homo sapiens)
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PHAROS  P62273
GTEx  ENSG00000213741
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Entity ID: 32
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Ubiquitin-40S ribosomal protein S27ag156Homo sapiensMutation(s): 0 
Gene Names: RPS27A, UBA80, UBCEP1
Find proteins for P62979 (Homo sapiens)
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PHAROS  P62979
GTEx  ENSG00000143947
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L41h25Homo sapiensMutation(s): 0 
Gene Names: RPL41
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PHAROS  P62945
GTEx  ENSG00000229117
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
Receptor of activated protein C kinase 1j317Homo sapiensMutation(s): 0 
Gene Names: RACK1, GNB2L1, HLC7, PIG21
Find proteins for P63244 (Homo sapiens)
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PHAROS  P63244
GTEx  ENSG00000204628
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
Non-structural protein 1i180Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep, 1a-1b
EC: 3.4.19.12 (PDB Primary Data), 3.4.22 (PDB Primary Data), 3.4.22.69 (PDB Primary Data), 2.7.7.48 (PDB Primary Data), 3.6.4.12 (PDB Primary Data), 3.6.4.13 (PDB Primary Data), 3.1.13 (PDB Primary Data), 3.1 (PDB Primary Data), 2.1.1 (PDB Primary Data)
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Entity ID: 35
MoleculeChainsLengthOrganismImage
18S ribosomal RNA21868Homo sapiens
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download Ideal Coordinates CCD File 
c, f, g
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanySFB/TRR-174
German Research Foundation (DFG)GermanyBE1814/15-1
German Research Foundation (DFG)GermanyBE1814/1-1

Revision History 

  • Version 1.0: 2020-07-29
    Type: Initial release
  • Version 1.1: 2020-09-16
    Changes: Database references