6ZMT

SARS-CoV-2 Nsp1 bound to a pre-40S-like ribosome complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 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 expression by ribosome association ...

    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 SA B295Homo sapiensMutation(s): 0 
Gene Names: RPSALAMBRLAMR1
Find proteins for P08865 (Homo sapiens)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S3a C264Homo sapiensMutation(s): 0 
Gene Names: RPS3AFTE1MFTL
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S2 D293Homo sapiensMutation(s): 0 
Gene Names: RPS2RPS4
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S4, X isoform E263Homo sapiensMutation(s): 0 
Gene Names: RPS4XCCG2RPS4SCAR
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S3 F243Homo sapiensMutation(s): 0 
Gene Names: RPS3OK/SW-cl.26
EC: 4.2.99.18
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S6 G249Homo sapiensMutation(s): 0 
Gene Names: RPS6OK/SW-cl.2
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S7 H194Homo sapiensMutation(s): 0 
Gene Names: RPS7
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S8 I208Homo sapiensMutation(s): 0 
Gene Names: RPS8OK/SW-cl.83
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Entity ID: 9
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40S ribosomal protein S9 J194Homo sapiensMutation(s): 0 
Gene Names: RPS9
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S5 K204Homo sapiensMutation(s): 0 
Gene Names: RPS5
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S11 L158Homo sapiensMutation(s): 0 
Gene Names: RPS11
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Entity ID: 12
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40S ribosomal protein S10 M165Homo sapiensMutation(s): 0 
Gene Names: RPS10
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S13 N151Homo sapiensMutation(s): 0 
Gene Names: RPS13
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S12 O132Homo sapiensMutation(s): 0 
Gene Names: RPS12
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S14 P151Homo sapiensMutation(s): 0 
Gene Names: RPS14PRO2640
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S15 Q145Homo sapiensMutation(s): 0 
Gene Names: RPS15RIG
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Entity ID: 17
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40S ribosomal protein S16 R146Homo sapiensMutation(s): 0 
Gene Names: RPS16
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Entity ID: 18
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40S ribosomal protein S17 S135Homo sapiensMutation(s): 0 
Gene Names: RPS17RPS17L
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Entity ID: 19
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40S ribosomal protein S18 T152Homo sapiensMutation(s): 0 
Gene Names: RPS18D6S218E
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Entity ID: 20
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40S ribosomal protein S19 U145Homo sapiensMutation(s): 0 
Gene Names: RPS19
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Entity ID: 21
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40S ribosomal protein S20 V119Homo sapiensMutation(s): 0 
Gene Names: RPS20
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S15a W130Homo sapiensMutation(s): 0 
Gene Names: RPS15AOK/SW-cl.82
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Entity ID: 23
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40S ribosomal protein S23 X143Homo sapiensMutation(s): 0 
Gene Names: RPS23
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Entity ID: 24
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40S ribosomal protein S24 Y133Homo sapiensMutation(s): 0 
Gene Names: RPS24
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Entity ID: 25
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40S ribosomal protein S21 Z83Homo sapiensMutation(s): 0 
Gene Names: RPS21
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S25 a125Homo sapiensMutation(s): 0 
Gene Names: RPS25
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S27 b84Homo sapiensMutation(s): 0 
Gene Names: RPS27MPS1
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S28 d69Homo sapiensMutation(s): 0 
Gene Names: RPS28
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S30 e59Homo sapiensMutation(s): 0 
Gene Names: FAU
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S29 f56Homo sapiensMutation(s): 0 
Gene Names: RPS29
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-40S ribosomal protein S27a g156Homo sapiensMutation(s): 0 
Gene Names: RPS27AUBA80UBCEP1
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
Receptor of activated protein C kinase 1 j317Homo sapiensMutation(s): 0 
Gene Names: RACK1GNB2L1HLC7PIG21
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
Non-structural protein 1 i180Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-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
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-rRNA-processing protein TSR1 homolog u804Homo sapiensMutation(s): 0 
Gene Names: TSR1KIAA1401
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Entity ID: 33
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 
f, g
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 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  (Full details and data files)

  • Version 1.0: 2020-08-19
    Type: Initial release
  • Version 1.1: 2020-09-16
    Changes: Database references