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:  
    6ZP4, 6ZON, 6ZME, 6ZLW, 6ZM7, 6ZMT, 6ZN5, 6ZMI, 6ZMO

  • 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 SAA [auth B]295Homo sapiensMutation(s): 0 
Gene Names: RPSALAMBRLAMR1
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Entity ID: 2
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40S ribosomal protein S3aB [auth C]264Homo sapiensMutation(s): 0 
Gene Names: RPS3AFTE1MFTL
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S2C [auth D]293Homo sapiensMutation(s): 0 
Gene Names: RPS2RPS4
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S4, X isoformD [auth E]263Homo sapiensMutation(s): 0 
Gene Names: RPS4XCCG2RPS4SCAR
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S3E [auth F]243Homo 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 S6F [auth G]249Homo sapiensMutation(s): 0 
Gene Names: RPS6OK/SW-cl.2
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Entity ID: 7
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40S ribosomal protein S7G [auth H]194Homo sapiensMutation(s): 0 
Gene Names: RPS7
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Entity ID: 8
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40S ribosomal protein S8H [auth I]208Homo sapiensMutation(s): 0 
Gene Names: RPS8OK/SW-cl.83
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Entity ID: 9
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40S ribosomal protein S9I [auth J]194Homo sapiensMutation(s): 0 
Gene Names: RPS9
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Entity ID: 10
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40S ribosomal protein S5J [auth K]204Homo sapiensMutation(s): 0 
Gene Names: RPS5
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Entity ID: 11
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40S ribosomal protein S11K [auth L]158Homo sapiensMutation(s): 0 
Gene Names: RPS11
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Entity ID: 12
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40S ribosomal protein S10L [auth M]165Homo sapiensMutation(s): 0 
Gene Names: RPS10
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Entity ID: 13
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40S ribosomal protein S13M [auth N]151Homo sapiensMutation(s): 0 
Gene Names: RPS13
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Entity ID: 14
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40S ribosomal protein S12N [auth O]132Homo sapiensMutation(s): 0 
Gene Names: RPS12
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Entity ID: 15
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40S ribosomal protein S14O [auth P]151Homo sapiensMutation(s): 0 
Gene Names: RPS14PRO2640
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Entity ID: 16
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40S ribosomal protein S15P [auth Q]145Homo sapiensMutation(s): 0 
Gene Names: RPS15RIG
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Entity ID: 17
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40S ribosomal protein S16Q [auth R]146Homo sapiensMutation(s): 0 
Gene Names: RPS16
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Entity ID: 18
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40S ribosomal protein S17R [auth S]135Homo sapiensMutation(s): 0 
Gene Names: RPS17RPS17L
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Entity ID: 19
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40S ribosomal protein S18S [auth T]152Homo sapiensMutation(s): 0 
Gene Names: RPS18D6S218E
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Entity ID: 20
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40S ribosomal protein S19T [auth U]145Homo sapiensMutation(s): 0 
Gene Names: RPS19
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Entity ID: 21
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40S ribosomal protein S20U [auth V]119Homo sapiensMutation(s): 0 
Gene Names: RPS20
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Entity ID: 22
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40S ribosomal protein S15aV [auth W]130Homo sapiensMutation(s): 0 
Gene Names: RPS15AOK/SW-cl.82
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Entity ID: 23
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40S ribosomal protein S23W [auth X]143Homo sapiensMutation(s): 0 
Gene Names: RPS23
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Entity ID: 24
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40S ribosomal protein S24X [auth Y]133Homo sapiensMutation(s): 0 
Gene Names: RPS24
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Entity ID: 25
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40S ribosomal protein S21Y [auth Z]83Homo sapiensMutation(s): 0 
Gene Names: RPS21
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Entity ID: 26
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40S ribosomal protein S25Z [auth a]125Homo sapiensMutation(s): 0 
Gene Names: RPS25
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Entity ID: 27
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40S ribosomal protein S27AA [auth b]84Homo sapiensMutation(s): 0 
Gene Names: RPS27MPS1
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Entity ID: 28
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40S ribosomal protein S28BA [auth d]69Homo sapiensMutation(s): 0 
Gene Names: RPS28
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Entity ID: 29
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40S ribosomal protein S30CA [auth e]59Homo sapiensMutation(s): 0 
Gene Names: FAU
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Entity ID: 30
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40S ribosomal protein S29DA [auth f]56Homo sapiensMutation(s): 0 
Gene Names: RPS29
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Entity ID: 31
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Ubiquitin-40S ribosomal protein S27aEA [auth g]156Homo sapiensMutation(s): 0 
Gene Names: RPS27AUBA80UBCEP1
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Entity ID: 32
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Receptor of activated protein C kinase 1FA [auth j]317Homo sapiensMutation(s): 0 
Gene Names: RACK1GNB2L1HLC7PIG21
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Entity ID: 34
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Non-structural protein 1HA [auth i]180Severe 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
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Pre-rRNA-processing protein TSR1 homologIA [auth u]804Homo sapiensMutation(s): 0 
Gene Names: TSR1KIAA1401
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Entity ID: 33
MoleculeChainsLengthOrganismImage
18S ribosomal RNAGA [auth 2]1868Homo sapiens
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Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
JA [auth f], KA [auth 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