7K5I

SARS-COV-2 nsp1 in complex with human 40S ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report



Literature

SARS-CoV-2 Nsp1 suppresses host but not viral translation through a bipartite mechanism.

Shi, M.Wang, L.Fontana, P.Vora, S.Zhang, Y.Fu, T.M.Lieberman, J.Wu, H.

(2020) Biorxiv 

  • DOI: 10.1101/2020.09.18.302901
  • Primary Citation of Related Structures:  
    7K5I

  • PubMed Abstract: 
  • The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a highly contagious virus that underlies the current COVID-19 pandemic. SARS-CoV-2 is thought to disable various features of host immunity and cellular defense. The SARS-CoV-2 nonstr ...

    The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a highly contagious virus that underlies the current COVID-19 pandemic. SARS-CoV-2 is thought to disable various features of host immunity and cellular defense. The SARS-CoV-2 nonstructural protein 1 (Nsp1) is known to inhibit host protein translation and could be a target for antiviral therapy against COVID-19. However, how SARS-CoV-2 circumvents this translational blockage for the production of its own proteins is an open question. Here, we report a bipartite mechanism of SARS-CoV-2 Nsp1 which operates by: (1) hijacking the host ribosome via direct interaction of its C-terminal domain (CT) with the 40S ribosomal subunit and (2) specifically lifting this inhibition for SARS-CoV-2 via a direct interaction of its N-terminal domain (NT) with the 5' untranslated region (5' UTR) of SARS-CoV-2 mRNA. We show that while Nsp1-CT is sufficient for binding to 40S and inhibition of host protein translation, the 5' UTR of SARS-CoV-2 mRNA removes this inhibition by binding to Nsp1-NT, suggesting that the Nsp1-NT-UTR interaction is incompatible with the Nsp1-CT-40S interaction. Indeed, lengthening the linker between Nsp1-NT and Nsp1-CT of Nsp1 progressively reduced the ability of SARS-CoV-2 5' UTR to escape the translational inhibition, supporting that the incompatibility is likely steric in nature. The short SL1 region of the 5' UTR is required for viral mRNA translation in the presence of Nsp1. Thus, our data provide a comprehensive view on how Nsp1 switches infected cells from host mRNA translation to SARS-CoV-2 mRNA translation, and that Nsp1 and 5' UTR may be targeted for anti-COVID-19 therapeutics.


    Organizational Affiliation

    School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu, 41566, Republic of Korea; KNU Institute for Microorganisms, Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu, 41566, Republic of Korea. Electronic address: kkim@knu.ac.kr.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S17R135Homo sapiensMutation(s): 0 
Gene Names: RPS17RPS17L
Find proteins for P08708 (Homo sapiens)
Explore P08708 
Go to UniProtKB:  P08708
NIH Common Fund Data Resources
PHAROS  P08708
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S29d56Homo sapiensMutation(s): 0 
Gene Names: RPS29
Find proteins for P62273 (Homo sapiens)
Explore P62273 
Go to UniProtKB:  P62273
NIH Common Fund Data Resources
PHAROS  P62273
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S3D243Homo sapiensMutation(s): 0 
Gene Names: RPS3OK/SW-cl.26
EC: 4.2.99.18
Find proteins for P23396 (Homo sapiens)
Explore P23396 
Go to UniProtKB:  P23396
NIH Common Fund Data Resources
PHAROS  P23396
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S5F204Homo sapiensMutation(s): 0 
Gene Names: RPS5
Find proteins for P46782 (Homo sapiens)
Explore P46782 
Go to UniProtKB:  P46782
NIH Common Fund Data Resources
PHAROS  P46782
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S10K165Homo sapiensMutation(s): 0 
Gene Names: RPS10
Find proteins for P46783 (Homo sapiens)
Explore P46783 
Go to UniProtKB:  P46783
NIH Common Fund Data Resources
PHAROS  P46783
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S12M132Homo sapiensMutation(s): 0 
Gene Names: RPS12
Find proteins for P25398 (Homo sapiens)
Explore P25398 
Go to UniProtKB:  P25398
NIH Common Fund Data Resources
PHAROS  P25398
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S15P145Homo sapiensMutation(s): 0 
Gene Names: RPS15RIG
Find proteins for P62841 (Homo sapiens)
Explore P62841 
Go to UniProtKB:  P62841
NIH Common Fund Data Resources
PHAROS  P62841
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S16Q146Homo sapiensMutation(s): 0 
Gene Names: RPS16
Find proteins for P62249 (Homo sapiens)
Explore P62249 
Go to UniProtKB:  P62249
NIH Common Fund Data Resources
PHAROS  P62249
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S18S152Homo sapiensMutation(s): 0 
Gene Names: RPS18D6S218E
Find proteins for P62269 (Homo sapiens)
Explore P62269 
Go to UniProtKB:  P62269
NIH Common Fund Data Resources
PHAROS  P62269
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S19T145Homo sapiensMutation(s): 0 
Gene Names: RPS19
Find proteins for P39019 (Homo sapiens)
Explore P39019 
Go to UniProtKB:  P39019
NIH Common Fund Data Resources
PHAROS  P39019
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S20U119Homo sapiensMutation(s): 0 
Gene Names: RPS20
Find proteins for P60866 (Homo sapiens)
Explore P60866 
Go to UniProtKB:  P60866
NIH Common Fund Data Resources
PHAROS  P60866
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S25Z125Homo sapiensMutation(s): 0 
Gene Names: RPS25
Find proteins for P62851 (Homo sapiens)
Explore P62851 
Go to UniProtKB:  P62851
NIH Common Fund Data Resources
PHAROS  P62851
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S28c69Homo sapiensMutation(s): 0 
Gene Names: RPS28
Find proteins for P62857 (Homo sapiens)
Explore P62857 
Go to UniProtKB:  P62857
NIH Common Fund Data Resources
PHAROS  P62857
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S27af149Homo sapiensMutation(s): 0 
Gene Names: RPS27A
Find proteins for Q5RKT7 (Homo sapiens)
Explore Q5RKT7 
Go to UniProtKB:  Q5RKT7
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Receptor of activated protein C kinase 1g317Homo sapiensMutation(s): 0 
Gene Names: RACK1GNB2L1HLC7PIG21
Find proteins for P63244 (Homo sapiens)
Explore P63244 
Go to UniProtKB:  P63244
NIH Common Fund Data Resources
PHAROS  P63244
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein SAA295Homo sapiensMutation(s): 0 
Gene Names: RPSALAMBRLAMR1
Find proteins for P08865 (Homo sapiens)
Explore P08865 
Go to UniProtKB:  P08865
NIH Common Fund Data Resources
PHAROS  P08865
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S3aB264Homo sapiensMutation(s): 0 
Gene Names: RPS3AFTE1MFTL
Find proteins for P61247 (Homo sapiens)
Explore P61247 
Go to UniProtKB:  P61247
NIH Common Fund Data Resources
PHAROS  P61247
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S2C293Homo sapiensMutation(s): 0 
Gene Names: RPS2RPS4
Find proteins for P15880 (Homo sapiens)
Explore P15880 
Go to UniProtKB:  P15880
NIH Common Fund Data Resources
PHAROS  P15880
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S4, X isoformE263Homo sapiensMutation(s): 0 
Gene Names: RPS4XCCG2RPS4SCAR
Find proteins for P62701 (Homo sapiens)
Explore P62701 
Go to UniProtKB:  P62701
NIH Common Fund Data Resources
PHAROS  P62701
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S6G249Homo sapiensMutation(s): 0 
Gene Names: RPS6OK/SW-cl.2
Find proteins for P62753 (Homo sapiens)
Explore P62753 
Go to UniProtKB:  P62753
NIH Common Fund Data Resources
PHAROS  P62753
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S7H194Homo sapiensMutation(s): 0 
Gene Names: RPS7
Find proteins for P62081 (Homo sapiens)
Explore P62081 
Go to UniProtKB:  P62081
NIH Common Fund Data Resources
PHAROS  P62081
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S8I208Homo sapiensMutation(s): 0 
Gene Names: RPS8OK/SW-cl.83
Find proteins for P62241 (Homo sapiens)
Explore P62241 
Go to UniProtKB:  P62241
NIH Common Fund Data Resources
PHAROS  P62241
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S9J194Homo sapiensMutation(s): 0 
Gene Names: RPS9
Find proteins for P46781 (Homo sapiens)
Explore P46781 
Go to UniProtKB:  P46781
NIH Common Fund Data Resources
PHAROS  P46781
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S11L158Homo sapiensMutation(s): 0 
Gene Names: RPS11
Find proteins for P62280 (Homo sapiens)
Explore P62280 
Go to UniProtKB:  P62280
NIH Common Fund Data Resources
PHAROS  P62280
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S13N151Homo sapiensMutation(s): 0 
Gene Names: RPS13
Find proteins for P62277 (Homo sapiens)
Explore P62277 
Go to UniProtKB:  P62277
NIH Common Fund Data Resources
PHAROS  P62277
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S14O151Homo sapiensMutation(s): 0 
Gene Names: RPS14PRO2640
Find proteins for P62263 (Homo sapiens)
Explore P62263 
Go to UniProtKB:  P62263
NIH Common Fund Data Resources
PHAROS  P62263
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S21V83Homo sapiensMutation(s): 0 
Gene Names: RPS21
Find proteins for P63220 (Homo sapiens)
Explore P63220 
Go to UniProtKB:  P63220
NIH Common Fund Data Resources
PHAROS  P63220
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S15aW130Homo sapiensMutation(s): 0 
Gene Names: RPS15AOK/SW-cl.82
Find proteins for P62244 (Homo sapiens)
Explore P62244 
Go to UniProtKB:  P62244
NIH Common Fund Data Resources
PHAROS  P62244
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S23X143Homo sapiensMutation(s): 0 
Gene Names: RPS23
Find proteins for P62266 (Homo sapiens)
Explore P62266 
Go to UniProtKB:  P62266
NIH Common Fund Data Resources
PHAROS  P62266
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S24Y133Homo sapiensMutation(s): 0 
Gene Names: RPS24
Find proteins for P62847 (Homo sapiens)
Explore P62847 
Go to UniProtKB:  P62847
NIH Common Fund Data Resources
PHAROS  P62847
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S26a102Homo sapiensMutation(s): 0 
Gene Names: RPS26
Find proteins for P62854 (Homo sapiens)
Explore P62854 
Go to UniProtKB:  P62854
NIH Common Fund Data Resources
PHAROS  P62854
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S27b84Homo sapiensMutation(s): 0 
Gene Names: RPS27MPS1
Find proteins for P42677 (Homo sapiens)
Explore P42677 
Go to UniProtKB:  P42677
NIH Common Fund Data Resources
PHAROS  P42677
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S30e59Homo sapiensMutation(s): 0 
Gene Names: FAU
Find proteins for P62861 (Homo sapiens)
Explore P62861 
Go to UniProtKB:  P62861
NIH Common Fund Data Resources
PHAROS  P62861
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L41h25Homo sapiensMutation(s): 0 
Gene Names: RPL41
Find proteins for P62945 (Homo sapiens)
Explore P62945 
Go to UniProtKB:  P62945
NIH Common Fund Data Resources
PHAROS  P62945
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
SARS-COV-2 Nsp11180Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
EC: 3.4.19.12 (UniProt), 3.4.22 (UniProt), 3.4.22.69 (UniProt), 2.7.7.48 (UniProt), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt), 3.1.13 (UniProt), 3.1 (UniProt), 2.1.1 (UniProt)
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTD1 
Go to UniProtKB:  P0DTD1
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
40S ribosomal rRNA18S21868Homo sapiens
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
a, d, f
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
2
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2020-09-16 
  • Released Date: 2020-10-14 
  • Deposition Author(s): Wang, L., Shi, M., Wu, H.

Revision History 

  • Version 1.0: 2020-10-14
    Type: Initial release