6ZP4 image
Deposition Date 2020-07-08
Release Date 2020-07-29
Last Version Date 2024-05-01
Entry Detail
PDB ID:
6ZP4
Keywords:
VIRAL PROTEIN
Title:
SARS-CoV-2 Nsp1 bound to a human 43S preinitiation ribosome complex - state 2
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Severe acute respiratory syndrome coronavirus 2 (Taxon ID: 2697049)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
2.90 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
6ZP4 validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:tRNA
Chain IDs:WA (auth: 1)
Chain Length:75
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Molecule:18S ribosomal RNA
Chain IDs:R (auth: 2)
Chain Length:1868
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 2 subunit 2
Gene (Uniprot):EIF2S2
Chain IDs:XA (auth: 4)
Chain Length:333
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P20042 Pfam ID:PF01873 EC:3.6.5.3
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 3 subunit A
Gene (Uniprot):EIF3A
Chain IDs:MA (auth: A)
Chain Length:1382
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q14152 Pfam ID:PF01399, PF22591
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 3 subunit B
Gene (Uniprot):EIF3B
Chain IDs:LA (auth: B)
Chain Length:814
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P55884 Pfam ID:PF00076, PF08662
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 3 subunit C
Gene (Uniprot):EIF3C
Chain IDs:NA (auth: C)
Chain Length:913
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q99613 Pfam ID:PF05470, PF01399
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S15a
Gene (Uniprot):RPS15A
Chain IDs:N (auth: D)
Chain Length:130
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62244 Pfam ID:PF00410
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 3 subunit E
Gene (Uniprot):EIF3E
Chain IDs:OA (auth: E)
Chain Length:204
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P60228 Pfam ID:PF09440, PF01399, PF21357
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 3 subunit F
Gene (Uniprot):EIF3F
Chain IDs:PA (auth: F)
Chain Length:357
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O00303 Pfam ID:PF01398, PF13012
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 1A, X-chromosomal
Gene (Uniprot):EIF1AX
Chain IDs:JA (auth: G)
Chain Length:144
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P47813 Pfam ID:PF01176
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 3 subunit H
Gene (Uniprot):EIF3H
Chain IDs:QA (auth: H)
Chain Length:352
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O15372 Pfam ID:PF01398, PF19445
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 3 subunit I
Gene (Uniprot):EIF3I
Chain IDs:KA (auth: I)
Chain Length:325
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q13347 Pfam ID:PF00400, PF12894
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Non-structural protein 1
Gene (Uniprot):rep
Chain IDs:BB (auth: J)
Chain Length:180
Number of Molecules:1
Biological Source:Severe acute respiratory syndrome coronavirus 2
UniProt ID:P0DTD1 Pfam ID:PF11501 EC:2.7.7.48
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 3 subunit K
Gene (Uniprot):EIF3K
Chain IDs:RA (auth: K)
Chain Length:218
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9UBQ5 Pfam ID:PF10075
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 3 subunit L
Gene (Uniprot):EIF3L
Chain IDs:SA (auth: L)
Chain Length:56
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9Y262 Pfam ID:PF10255
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 3 subunit M
Gene (Uniprot):EIF3M
Chain IDs:TA (auth: M)
Chain Length:151
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q7L2H7 Pfam ID:PF01399, PF18005
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 3 subunit D
Gene (Uniprot):EIF3D
Chain IDs:UA (auth: N)
Chain Length:158
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O15371 Pfam ID:PF05091
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 2 subunit 1
Gene (Uniprot):EIF2S1
Chain IDs:YA (auth: O)
Chain Length:315
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P05198 Pfam ID:PF00575, PF07541 EC:3.6.5.3
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S25
Gene (Uniprot):RPS25
Chain IDs:CA (auth: P)
Chain Length:125
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62851 Pfam ID:PF03297
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S26
Gene (Uniprot):RPS26
Chain IDs:D (auth: Q)
Chain Length:115
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62854 Pfam ID:PF01283
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S27
Gene (Uniprot):RPS27
Chain IDs:P (auth: R)
Chain Length:84
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P42677 Pfam ID:PF01667
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S28
Gene (Uniprot):RPS28
Chain IDs:DA (auth: S)
Chain Length:69
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62857 Pfam ID:PF01200
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S30
Gene (Uniprot):FAU
Chain IDs:Q (auth: T)
Chain Length:59
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62861 Pfam ID:PF04758
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ubiquitin-40S ribosomal protein S27a
Gene (Uniprot):RPS27A
Chain IDs:FA (auth: U)
Chain Length:165
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62979 Pfam ID:PF00240, PF01599
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Receptor of activated protein C kinase 1
Gene (Uniprot):RACK1
Chain IDs:GA (auth: V)
Chain Length:317
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P63244 Pfam ID:PF00400
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L41
Gene (Uniprot):RPL41
Chain IDs:F (auth: W)
Chain Length:25
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62945 Pfam ID:PF05162
Polymer Type:polypeptide(L)
Molecule:Unknown factor
Chain IDs:VA (auth: X)
Chain Length:78
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 2 subunit 3
Gene (Uniprot):EIF2S3
Chain IDs:ZA (auth: Y)
Chain Length:472
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P41091 Pfam ID:PF03144, PF09173, PF00009 EC:3.6.5.3
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 1
Gene (Uniprot):EIF1
Chain IDs:AB (auth: Z)
Chain Length:113
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P41567 Pfam ID:PF01253
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein SA
Gene (Uniprot):RPSA
Chain IDs:A (auth: a)
Chain Length:1382
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P08865 Pfam ID:PF00318, PF16122
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S3
Gene (Uniprot):RPS3
Chain IDs:T (auth: b)
Chain Length:814
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P23396 Pfam ID:PF07650, PF00189
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S9
Gene (Uniprot):RPS9
Chain IDs:J (auth: c)
Chain Length:913
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P46781 Pfam ID:PF00163, PF01479
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S2
Gene (Uniprot):RPS2
Chain IDs:C (auth: d)
Chain Length:130
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P15880 Pfam ID:PF00333, PF03719
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S5
Gene (Uniprot):RPS5
Chain IDs:U (auth: e)
Chain Length:204
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P46782 Pfam ID:PF00177
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S16
Gene (Uniprot):RPS16
Chain IDs:Y (auth: g)
Chain Length:144
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62249 Pfam ID:PF00380
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S20
Gene (Uniprot):RPS20
Chain IDs:BA (auth: h)
Chain Length:352
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P60866 Pfam ID:PF00338
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S14
Gene (Uniprot):RPS14
Chain IDs:HA (auth: i)
Chain Length:325
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62263 Pfam ID:PF00411
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S23
Gene (Uniprot):RPS23
Chain IDs:IA (auth: j)
Chain Length:180
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62266 Pfam ID:PF00164
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S18
Gene (Uniprot):RPS18
Chain IDs:Z (auth: k)
Chain Length:218
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62269 Pfam ID:PF00416
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S29
Gene (Uniprot):RPS29
Chain IDs:EA (auth: l)
Chain Length:56
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62273 Pfam ID:PF00253
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S13
Gene (Uniprot):RPS13
Chain IDs:L (auth: m)
Chain Length:151
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62277 Pfam ID:PF08069, PF00312
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S11
Gene (Uniprot):RPS11
Chain IDs:K (auth: n)
Chain Length:158
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62280 Pfam ID:PF16205, PF00366
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S15
Gene (Uniprot):RPS15
Chain IDs:X (auth: o)
Chain Length:315
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62841 Pfam ID:PF00203
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S3a
Gene (Uniprot):RPS3A
Chain IDs:B (auth: p)
Chain Length:125
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P61247 Pfam ID:PF01015
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S4, X isoform
Gene (Uniprot):RPS4X
Chain IDs:E (auth: q)
Chain Length:115
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62701 Pfam ID:PF08071, PF00900, PF00467, PF16121
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S6
Gene (Uniprot):RPS6
Chain IDs:G (auth: r)
Chain Length:84
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62753 Pfam ID:PF01092
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S7
Gene (Uniprot):RPS7
Chain IDs:H (auth: s)
Chain Length:69
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62081 Pfam ID:PF01251
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S8
Gene (Uniprot):RPS8
Chain IDs:I (auth: t)
Chain Length:59
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62241 Pfam ID:PF01201
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S10
Gene (Uniprot):RPS10
Chain IDs:V (auth: u)
Chain Length:165
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P46783 Pfam ID:PF03501
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S12
Gene (Uniprot):RPS12
Chain IDs:W (auth: v)
Chain Length:317
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P25398 Pfam ID:PF01248
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S17
Gene (Uniprot):RPS17
Chain IDs:S (auth: w)
Chain Length:25
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P08708 Pfam ID:PF00833
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S19
Gene (Uniprot):RPS19
Chain IDs:AA (auth: x)
Chain Length:78
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P39019 Pfam ID:PF01090
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S21
Gene (Uniprot):RPS21
Chain IDs:M (auth: y)
Chain Length:472
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P63220 Pfam ID:PF01249
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S24
Gene (Uniprot):RPS24
Chain IDs:O (auth: z)
Chain Length:113
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62847 Pfam ID:PF01282
Ligand Molecules
GTP
MG
ZN
Primary Citation
Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2.
Science 369 1249 1255 (2020)
PMID: 32680882 DOI: 10.1126/science.abc8665

Abstact

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 40S 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 Nsp1-40S and various native Nsp1-40S and -80S 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.

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Protein

Chemical

Disease

Primary Citation of related structures
6ZP4