EMDB-11276: SARS-CoV-2 Nsp1 bound to the human 40S ribosomal subunit

Basic information

• Entry: Database: EMDB / ID: EMD-11276
• Title: SARS-CoV-2 Nsp1 bound to the human 40S ribosomal subunit

Sample

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

• Human 40S ribosomal subunit
• SARS-CoV-2 Nsp1
• (40S ribosomal protein ...) x 31
• Ubiquitin-40S ribosomal protein S27a
• 60S ribosomal protein L41
• Receptor of activated protein C kinase 1
• nucleic-acidNucleic acid
• Non-structural protein 1
• ligand

Function / homology

Function:

positive regulation of base-excision repair / positive regulation of DNA N-glycosylase activity / positive regulation of respiratory burst involved in inflammatory response / oxidized pyrimidine DNA binding / negative regulation of DNA repair / response to TNF agonist / nucleolus organization / protein tyrosine kinase inhibitor activity / positive regulation of gastrulation / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of Golgi to plasma membrane protein transport / NF-kappaB complex / negative regulation of RNA splicing / response to extracellular stimulus / IRE1-RACK1-PP2A complex / ubiquitin ligase inhibitor activity / laminin receptor activity / cytoplasmic side of rough endoplasmic reticulum membrane / regulation of cell division / positive regulation of endodeoxyribonuclease activity / oxidized purine DNA binding / negative regulation of endoplasmic reticulum unfolded protein response / protein kinase A binding / negative regulation of hydrogen peroxide-induced neuron death / supercoiled DNA binding / negative regulation of ubiquitin protein ligase activity / erythrocyte homeostasis / positive regulation of ceramide biosynthetic process / mammalian oogenesis stage / negative regulation of phagocytosis / ubiquitin-like protein conjugating enzyme binding / translation regulator activity / regulation of establishment of cell polarity / signaling adaptor activity / cysteine-type endopeptidase activator activity involved in apoptotic process / negative regulation of Wnt signaling pathway / activation-induced cell death of T cells / positive regulation of T cell receptor signaling pathway / positive regulation of mitochondrial depolarization / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / negative regulation of smoothened signaling pathway / phagocytic cup / ion channel inhibitor activity / iron-sulfur cluster binding / positive regulation of activated T cell proliferation / positive regulation of cellular component movement / fibroblast growth factor binding / rescue of stalled ribosome / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / positive regulation of apoptotic signaling pathway / stress granule assembly / poly(U) RNA binding / monocyte chemotaxis / DNA-(apurinic or apyrimidinic site) lyase / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / positive regulation of ubiquitin-protein transferase activity / BH3 domain binding / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / erythrocyte development / positive regulation of cyclic-nucleotide phosphodiesterase activity / spindle assembly / TOR signaling / ribosomal small subunit export from nucleus / positive regulation of JUN kinase activity / regulation of tumor necrosis factor-mediated signaling pathway / maturation of SSU-rRNA / SRP-dependent cotranslational protein targeting to membrane / regulation of translational fidelity / negative regulation of ubiquitin-dependent protein catabolic process / T cell proliferation involved in immune response / negative regulation of respiratory burst involved in inflammatory response / negative regulation of protein kinase B signaling / small-subunit processome / positive regulation of microtubule polymerization / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / translation initiation factor binding / ribosomal small subunit biogenesis / molecular adaptor activity / gastrulation / positive regulation of DNA repair / polysome / laminin binding / Hsp70 protein binding / positive regulation of cell cycle / erythrocyte differentiation / tubulin binding / translational initiation / negative regulation of peptidyl-serine phosphorylation / positive regulation of intrinsic apoptotic signaling pathway / negative regulation of protein ubiquitination / innate immune response in mucosa / endodeoxyribonuclease activity / polysomal ribosome / MyD88-independent toll-like receptor signaling pathway / mRNA 3'-UTR binding / DNA-(apurinic or apyrimidinic site) endonuclease activity / nucleotide-binding oligomerization domain containing signaling pathway / positive regulation of interleukin-2 production / cyclin binding

Domain/homology:

Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S7, conserved site / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S19, superfamily / Ribosomal protein S15P / Ribosomal protein S4/S9 / DPUP/SUD, C-terminal, betacoronavirus / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Non-structural protein NSP1, betacoronavirus / Ribosomal protein S19 conserved site / Ribosomal protein S9, conserved site / Non-structural protein NSP3, N-terminal, betacoronavirus / Ribosomal protein S5 domain 2-type fold / G-protein beta WD-40 repeat / Ribosomal protein S17, conserved site / Ubiquitin domain / Ubiquitin conserved site / WD40 repeat, conserved site / RNA synthesis protein NSP10, coronavirus / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S8e, conserved site / Ribosomal protein S7 domain / Non-structural protein NSP3, SUD-M domain, betacoronavirus / Ribosomal protein S5/S7, eukaryotic/archaeal / 50S ribosomal protein L30e-like / Ribosomal protein S8 superfamily / Ribosomal protein S17/S11 / Ribosomal protein S5/S7 / Non-structural protein NSP3, nucleic acid-binding (NAR) domain, betacoronavirus / Non-structural protein NSP4, C-terminal, coronavirus / 40S ribosomal protein S11, N-terminal / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein S4, C-terminal domain / Ubiquitin-like domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase / (+) RNA virus helicase core domain / Ribosomal protein S28e conserved site / Ribosomal protein S17, archaeal/eukaryotic / 40S ribosomal protein SA / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S2, eukaryotic / Ribosomal protein S10 domain / 30s ribosomal protein S13, C-terminal / P-loop containing nucleoside triphosphate hydrolase / Ribosomal protein S4/S9, eukaryotic/archaeal / Ribosomal protein S19A/S15e / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S28e / Non-structural protein NSP8, coronavirus-like / Zinc-binding ribosomal protein / Nucleic acid-binding, OB-fold / Ribosomal S11, conserved site / Ribosomal S24e conserved site / Ribosomal protein S4, conserved site / WD40-repeat-containing domain / K homology domain-like, alpha/beta / WD40/YVTN repeat-like-containing domain superfamily / Non-structural protein NSP7, coronavirus / Ribosomal protein S13-like, H2TH / Non-structural protein NSP9, coronavirus / Ribosomal protein L2, domain 2 / Ribosomal protein S13/S15, N-terminal / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein L23/L15e core domain superfamily / Peptidase C16, coronavirus / Ribosomal protein S5, N-terminal / Ribosomal protein S6, eukaryotic / Ribosomal protein S4e, central region / Ribosomal protein S2, conserved site / RNA polymerase, N-terminal, coronaviral / Ribosomal protein S6e, conserved site / Ribosomal protein S30 / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3, conserved site / KOW / Ribosomal protein S21e, conserved site / Ribosomal protein S12/S23 / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S19e, conserved site / Ribosomal protein S17e, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein L41 / Non-structural protein 14, coronavirus / Peptidase C30, coronavirus / Ribosomal protein S13, conserved site / Ribosomal protein S10, conserved site / Ribosomal protein S4e, N-terminal, conserved site / Peptidase S1, PA clan / K homology domain superfamily, prokaryotic type / S15/NS1, RNA-binding / Non-structural protein NSP16, coronavirus-like / Ribosomal protein S5, N-terminal, conserved site / WD40-repeat-containing domain superfamily / Ribosomal protein S4e, N-terminal / RNA synthesis protein NSP10 superfamily, coronavirus / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S24e / Ribosomal protein S19/S15 / Ribosomal protein S19e / Ribosomal protein S17e

Component:

40S ribosomal protein S23 / 40S ribosomal protein S15 / 40S ribosomal protein S29 / 40S ribosomal protein S13 / 40S ribosomal protein S11 / 40S ribosomal protein S4, X isoform / 40S ribosomal protein S6 / 40S ribosomal protein S26 / 40S ribosomal protein S24 / 40S ribosomal protein S25 / 40S ribosomal protein S28 / 40S ribosomal protein S30 / 60S ribosomal protein L41 / Ubiquitin-40S ribosomal protein S27a / 40S ribosomal protein S21 / 40S ribosomal protein S18 / 40S ribosomal protein S12 / 40S ribosomal protein S14 / 40S ribosomal protein S27 / 40S ribosomal protein S17 / 40S ribosomal protein SA / Replicase polyprotein 1ab / 40S ribosomal protein S2 / 40S ribosomal protein S3 / 40S ribosomal protein S19 / 40S ribosomal protein S9 / 40S ribosomal protein S16 / 40S ribosomal protein S5 / 40S ribosomal protein S10 / 40S ribosomal protein S20 / 40S ribosomal protein S3a / 40S ribosomal protein S7 / 40S ribosomal protein S8 / 40S ribosomal protein S15a / Receptor of activated protein C kinase 1

• Biological species: Homo sapiens (human) / Severe acute respiratory syndrome coronavirus 2 / Human (human)
• Method: single particle reconstruction / cryo EM / Resolution: 2.6 Å
• Authors: Thoms M / Buschauer R / Ameismeier M / Denk T / Kratzat H / Mackens-Kiani T / Cheng J / Berninghausen O / Becker T / Beckmann R

Funding support

Germany, 3 items

Organization	Grant number	Country
German Research Foundation (DFG)	SFB/TRR-174	Germany
German Research Foundation (DFG)	BE1814/1-1	Germany
German Research Foundation (DFG)	BE1814/15-1	Germany

• Citation: Journal: Science / Year: 2020; Title: Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2.; Authors: Matthias Thoms / Robert Buschauer / Michael Ameismeier / Lennart Koepke / Timo Denk / Maximilian Hirschenberger / Hanna Kratzat / Manuel Hayn / Timur Mackens-Kiani / Jingdong Cheng / Jan H Straub / Christina M Stürzel / Thomas Fröhlich / Otto Berninghausen / Thomas Becker / Frank Kirchhoff / Konstantin M J Sparrer / Roland Beckmann / ; 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. Here, we show that Nsp1 from SARS-CoV-2 binds to the 40 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 and various native Nsp1-40 and -80 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.
• Validation Report: Summary, Full report, XML, About validation report

History

Deposition	Jul 1, 2020	-
Header (metadata) release	Jul 29, 2020	-
Map release	Jul 29, 2020	-
Update	Sep 16, 2020	-
Current status	Sep 16, 2020	Processing site: PDBe / Status: Released

Map

• File: Download / File: emd_11276.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Voxel size: X=Y=Z: 1.059 Å

Density

Contour Level	By AUTHOR: 0.6 / Movie #1: 1.2
Minimum - Maximum	-25.766035 - 43.87194
Average (Standard dev.)	0.0000912184 (±0.7160544)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order Z Y X Origin 0 0 0 Dimensions 400 400 400 Spacing 400 400 400
Cell	A=B=C: 423.6 Å α=β=γ: 90.0 °

CCP4 map header:

mode	Image stored as Reals
Å/pix. X/Y/Z	1.059	1.059	1.059
M x/y/z	400	400	400
origin x/y/z	0.000	0.000	0.000
length x/y/z	423.600	423.600	423.600
α/β/γ	90.000	90.000	90.000
start NX/NY/NZ	0	0	0
NX/NY/NZ	400	400	400
MAP C/R/S	3	2	1
start NC/NR/NS	0	0	0
NC/NR/NS	400	400	400
D min/max/mean	-25.766	43.872	0.000

Supplemental data

Additional map: In vitro reconstituted Nsp1-40S complex. Focused refined map...

• File: emd_11276_additional_1.map
• Annotation: In vitro reconstituted Nsp1-40S complex. Focused refined map of 40S body.

Additional map: Native Nsp1-40S complex.

• File: emd_11276_additional_2.map
• Annotation: Native Nsp1-40S complex.

Additional map: Native Nsp1-40S complex.

• File: emd_11276_additional_3.map
• Annotation: Native Nsp1-40S complex.

Sample components

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

• Entire: Name: SARS-CoV-2 Nsp1 bound to the human 40S ribosomal subunit; Number of components: 40

Component #1: protein, SARS-CoV-2 Nsp1 bound to the human 40S ribosomal subunit

• Protein: Name: SARS-CoV-2 Nsp1 bound to the human 40S ribosomal subunit; Recombinant expression: No

Component #2: protein, Human 40S ribosomal subunit

• Protein: Name: Human 40S ribosomal subunit / Recombinant expression: No
• Source: Species: Homo sapiens (human)

Component #3: protein, SARS-CoV-2 Nsp1

• Protein: Name: SARS-CoV-2 Nsp1 / Recombinant expression: No
• Source: Species: Severe acute respiratory syndrome coronavirus 2
• Source (engineered): Expression System: Escherichia coli K-12 (bacteria)

Component #4: protein, 40S ribosomal protein SA

• Protein: Name: 40S ribosomal protein SA / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 32.883938 kDa
• Source: Species: Human (human)

Component #5: protein, 40S ribosomal protein S3a

• Protein: Name: 40S ribosomal protein S3a / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 30.002061 kDa
• Source: Species: Human (human)

Component #6: protein, 40S ribosomal protein S2

• Protein: Name: 40S ribosomal protein S2 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 31.376516 kDa
• Source: Species: Human (human)

Component #7: protein, 40S ribosomal protein S4, X isoform

• Protein: Name: 40S ribosomal protein S4, X isoformRibosome / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 29.654869 kDa
• Source: Species: Human (human)

Component #8: protein, 40S ribosomal protein S3

• Protein: Name: 40S ribosomal protein S3 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 26.729369 kDa
• Source: Species: Human (human)

Component #9: protein, 40S ribosomal protein S6

• Protein: Name: 40S ribosomal protein S6 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 28.751906 kDa
• Source: Species: Human (human)

Component #10: protein, 40S ribosomal protein S7

• Protein: Name: 40S ribosomal protein S7 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 22.168914 kDa
• Source: Species: Human (human)

Component #11: protein, 40S ribosomal protein S8

• Protein: Name: 40S ribosomal protein S8 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 24.263387 kDa
• Source: Species: Human (human)

Component #12: protein, 40S ribosomal protein S9

• Protein: Name: 40S ribosomal protein S9 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 22.641564 kDa
• Source: Species: Human (human)

Component #13: protein, 40S ribosomal protein S5

• Protein: Name: 40S ribosomal protein S5 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 22.913453 kDa
• Source: Species: Human (human)

Component #14: protein, 40S ribosomal protein S11

• Protein: Name: 40S ribosomal protein S11 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 18.468826 kDa
• Source: Species: Human (human)

Component #15: protein, 40S ribosomal protein S10

• Protein: Name: 40S ribosomal protein S10 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 18.933846 kDa
• Source: Species: Human (human)

Component #16: protein, 40S ribosomal protein S13

• Protein: Name: 40S ribosomal protein S13 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 17.259389 kDa
• Source: Species: Human (human)

Component #17: protein, 40S ribosomal protein S12

• Protein: Name: 40S ribosomal protein S12 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 14.538987 kDa
• Source: Species: Human (human)

Component #18: protein, 40S ribosomal protein S14

• Protein: Name: 40S ribosomal protein S14 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 16.302772 kDa
• Source: Species: Human (human)

Component #19: protein, 40S ribosomal protein S15

• Protein: Name: 40S ribosomal protein S15 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 17.076207 kDa
• Source: Species: Human (human)

Component #20: protein, 40S ribosomal protein S16

• Protein: Name: 40S ribosomal protein S16 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 16.477377 kDa
• Source: Species: Human (human)

Component #21: protein, 40S ribosomal protein S17

• Protein: Name: 40S ribosomal protein S17 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 15.578156 kDa
• Source: Species: Human (human)

Component #22: protein, 40S ribosomal protein S18

• Protein: Name: 40S ribosomal protein S18 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 17.759777 kDa
• Source: Species: Human (human)

Component #23: protein, 40S ribosomal protein S19

• Protein: Name: 40S ribosomal protein S19 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 16.091562 kDa
• Source: Species: Human (human)

Component #24: protein, 40S ribosomal protein S20

• Protein: Name: 40S ribosomal protein S20 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 13.398763 kDa
• Source: Species: Human (human)

Component #25: protein, 40S ribosomal protein S15a

• Protein: Name: 40S ribosomal protein S15a / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 14.865555 kDa
• Source: Species: Human (human)

Component #26: protein, 40S ribosomal protein S23

• Protein: Name: 40S ribosomal protein S23 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 15.844666 kDa
• Source: Species: Human (human)

Component #27: protein, 40S ribosomal protein S24

• Protein: Name: 40S ribosomal protein S24 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 15.463333 kDa
• Source: Species: Human (human)

Component #28: protein, 40S ribosomal protein S21

• Protein: Name: 40S ribosomal protein S21 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 9.124389 kDa
• Source: Species: Human (human)

Component #29: protein, 40S ribosomal protein S25

• Protein: Name: 40S ribosomal protein S25 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 13.776224 kDa
• Source: Species: Human (human)

Component #30: protein, 40S ribosomal protein S27

• Protein: Name: 40S ribosomal protein S27 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 9.480186 kDa
• Source: Species: Human (human)

Component #31: protein, 40S ribosomal protein S26

• Protein: Name: 40S ribosomal protein S26 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 13.047532 kDa
• Source: Species: Human (human)

Component #32: protein, 40S ribosomal protein S28

• Protein: Name: 40S ribosomal protein S28 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 7.855052 kDa
• Source: Species: Human (human)

Component #33: protein, 40S ribosomal protein S30

• Protein: Name: 40S ribosomal protein S30 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 6.668938 kDa
• Source: Species: Human (human)

Component #34: protein, 40S ribosomal protein S29

• Protein: Name: 40S ribosomal protein S29 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 6.690821 kDa
• Source: Species: Human (human)

Component #35: protein, Ubiquitin-40S ribosomal protein S27a

• Protein: Name: Ubiquitin-40S ribosomal protein S27a / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 18.004041 kDa
• Source: Species: Human (human)

Component #36: protein, 60S ribosomal protein L41

• Protein: Name: 60S ribosomal protein L41 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 3.473451 kDa
• Source: Species: Human (human)

Component #37: protein, Receptor of activated protein C kinase 1

• Protein: Name: Receptor of activated protein C kinase 1 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 35.115652 kDa
• Source: Species: Human (human)

Component #38: nucleic-acid, 18S ribosomal RNA

nucleic acid

Name: 18S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:

UACCUGGUUG AUCCUGCCAG UAGCAUAUGC UUGUCUCAAA GAUUAAGCCA UGCAUGUCUA AGUACGCACG GCCGGUACAG UGAAACUGCG AAUGGCUCAU UAAAUCAGUU AUGGUUCCUU UGGUCGCUCG CUCCUCUCCU ACUUGGAUAA CUGUGGUAAU UCUAGAGCUA AUACAUGCCG ACGGGCGCUG ACCCCCUUCG CGGGGGGGAU GCGUGCAUUU AUCAGAUCAA AACCAACCCG GUCAGCCCCU CUCCGGCCCC GGCCGGGGGG CGGGCCGCGG CGGCUUUGGU GACUCUAGAU AACCUCGGGC CGAUCGCACG CCCCCCGUGG CGGCGACGAC CCAUUCGAAC GUCUGCCCUA UCAACUUUCG AUGGUAGUCG CCGUGCCUAC CAUGGUGACC ACGGGUGACG GGGAAUCAGG GUUCGAUUCC GGAGAGGGAG CCUGAGAAAC GGCUACCACA UCCAAGGAAG GCAGCAGGCG CGCAAAUUAC CCACUCCCGA CCCGGGGAGG UAGUGACGAA AAAUAACAAU ACAGGACUCU UUCGAGGCCC UGUAAUUGGA AUGAGUCCAC UUUAAAUCCU UUAACGAGGA UCCAUUGGAG GGCAAGUCUG GUGCCAGCAG CCGCGGUAAU UCCAGCUCCA AUAGCGUAUA UUAAAGUUGC UGCAGUUAAA AAGCUCGUAG UUGGAUCUUG GGAGCGGGCG GGCGGUCCGC CGCGAGGCGA GCCACCGCCC GUCCCCGCCC CUUGCCUCUC GGCGCCCCCU CGAUGCUCUU AGCUGAGUGU CCCGCGGGGC CCGAAGCGUU UACUUUGAAA AAAUUAGAGU GUUCAAAGCA GGCCCGAGCC GCCUGGAUAC CGCAGCUAGG AAUAAUGGAA UAGGACCGCG GUUCUAUUUU GUUGGUUUUC GGAACUGAGG CCAUGAUUAA GAGGGACGGC CGGGGGCAUU CGUAUUGCGC CGCUAGAGGU GAAAUUCUUG GACCGGCGCA AGACGGACCA GAGCGAAAGC AUUUGCCAAG AAUGUUUUCA UUAAUCAAGA ACGAAAGUCG GAGGUUCGAA GACGAUCAGA UACCGUCGUA GUUCCGACCA UAAACGAUGC CGACCGGCGA UGCGGCGGCG UUAUUCCCAU GACCCGCCGG GCAGCUUCCG GGAAACCAAA GUCUUUGGGU UCCGGGGGGA GUAUGGUUGC AAAGCUGAAA CUUAAAGGAA UUGACGGAAG GGCACCACCA GGAGUGGAGC CUGCGGCUUA AUUUGACUCA ACACGGGAAA CCUCACCCGG CCCGGACACG GACAGGAUUG ACAGAUUGAU AGCUCUUUCU CGAUUCCGUG GGUGGUGGUG CAUGGCCGUU CUUAGUUGGU GGAGCGAUUU GUCUGGUUAA UUCCGAUAAC GAACGAGACU CUGGCAUGCU AACUAGUUAC GCGACCCCCG AGCGGUCGGC GUCCCCCAAC UUCUUAGAGG GACAAGUGGC GUUCAGCCAC CCGAGAUUGA GCAAUAACAG GUCUGUGAUG CCCUUAGAUG UCCGGGGCUG CACGCGCGCU ACACUGACUG GCUCAGCGUG UGCCUACCCU ACGCCGGCAG GCGCGGGUAA CCCGUUGAAC CCCAUUCGUG AUGGGGAUCG GGGAUUGCAA UUAUUCCCCA UGAACGAGGA AUUCCCAGUA AGUGCGGGUC AUAAGCUUGC GUUGAUUAAG UCCCUGCCCU UUGUACACAC CGCCCGUCGC UACUACCGAU UGGAUGGUUU AGUGAGGCCC UCGGAUCGGC CCCGCCGGGG UCGGCCCACG CCCUGGCGGA GCGCUGAGAA GACGGUCGAA CUUGACUAUC UAGAGGAAGU AAAAGUCGUA ACAAGGUUUC CGUAGGUGAA CCUGCGGAAG GAUCAUUA

• Mass: Theoretical: 602.432625 kDa
• Source: Species: Human (human)

Component #39: protein, Non-structural protein 1

• Protein: Name: Non-structural protein 1 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 19.801287 kDa
• Source: Species: Severe acute respiratory syndrome coronavirus 2
• Source (engineered): Expression System: Escherichia coli K-12 (bacteria)

Component #40: ligand, ZINC ION

• Ligand: Name: ZINC ION / Number of Copies: 3 / Recombinant expression: No
• Mass: Theoretical: 6.540905 MDa

Experimental details

Sample preparation

• Specimen: Specimen state: Particle / Method: cryo EM
• Sample solution: pH: 7.5
• Vitrification: Cryogen name: ETHANE

Electron microscopy imaging

• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company
• Imaging: Microscope: FEI TITAN KRIOS
• Electron gun: Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 44.8 e/Ų / Illumination mode: FLOOD BEAM
• Lens: Imaging mode: BRIGHT FIELD
• Specimen Holder: Model: OTHER
• Camera: Detector: GATAN K2 SUMMIT (4k x 4k)

Image processing

• Processing: Method: single particle reconstruction / Number of projections: 173060
• 3D reconstruction: Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF

Atomic model buiding

Output model

6zlw