› 6zn5

Electron Microscopy
3.2Å resolution

Function and Biology Details

Reactions catalysed: 
The C-O-P bond 3' to the apurinic or apyrimidinic site in DNA is broken by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate
S-adenosyl-L-methionine + a 5'-(5'-triphosphoguanosine)-[mRNA] = S-adenosyl-L-homocysteine + a 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA]
S-adenosyl-L-methionine + a 5'-(N(7)-methyl 5'-triphosphoguanosine)-(ribonucleotide)-[mRNA] = S-adenosyl-L-homocysteine + a 5'-(N(7)-methyl 5'-triphosphoguanosine)-(2'-O-methyl-ribonucleotide)-[mRNA]
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
GTP + a 5'-diphospho-[mRNA] = diphosphate + a 5'-(5'-triphosphoguanosine)-[mRNA]
Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).
TSAVLQ-|-SGFRK-NH(2) and SGVTFQ-|-GKFKK the two peptides corresponding to the two self-cleavage sites of the SARS 3C-like proteinase are the two most reactive peptide substrates. The enzyme exhibits a strong preference for substrates containing Gln at P1 position and Leu at P2 position.
ATP + H(2)O = ADP + phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 36-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-140309 (preferred)
Entry contents:
35 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (36 distinct):
Small ribosomal subunit protein uS2 Chain: B
Molecule details ›
Chain: B
Length: 206 amino acids
Theoretical weight: 23.1 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P08865 (Residues: 2-207; Coverage: 70%)
Gene names: LAMBR, LAMR1, RPSA
Sequence domains: Ribosomal protein S2
Small ribosomal subunit protein eS1 Chain: C
Molecule details ›
Chain: C
Length: 213 amino acids
Theoretical weight: 24.76 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P61247 (Residues: 21-233; Coverage: 81%)
Gene names: FTE1, MFTL, RPS3A
Sequence domains: Ribosomal S3Ae family
Small ribosomal subunit protein uS5 Chain: D
Molecule details ›
Chain: D
Length: 218 amino acids
Theoretical weight: 24.09 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P15880 (Residues: 59-276; Coverage: 74%)
Gene names: RPS2, RPS4
Sequence domains:
Small ribosomal subunit protein eS4, X isoform Chain: E
Molecule details ›
Chain: E
Length: 262 amino acids
Theoretical weight: 29.52 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62701 (Residues: 2-263; Coverage: 100%)
Gene names: CCG2, RPS4, RPS4X, SCAR
Sequence domains:
Small ribosomal subunit protein uS3 Chain: F
Molecule details ›
Chain: F
Length: 225 amino acids
Theoretical weight: 24.97 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P23396 (Residues: 3-227; Coverage: 93%)
Gene names: OK/SW-cl.26, RPS3
Sequence domains:
Small ribosomal subunit protein eS6 Chain: G
Molecule details ›
Chain: G
Length: 230 amino acids
Theoretical weight: 26.6 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62753 (Residues: 1-230; Coverage: 92%)
Gene names: OK/SW-cl.2, RPS6
Sequence domains: Ribosomal protein S6e
Small ribosomal subunit protein eS7 Chain: H
Molecule details ›
Chain: H
Length: 186 amino acids
Theoretical weight: 21.32 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62081 (Residues: 8-193; Coverage: 96%)
Gene name: RPS7
Sequence domains: Ribosomal protein S7e
Small ribosomal subunit protein eS8 Chain: I
Molecule details ›
Chain: I
Length: 205 amino acids
Theoretical weight: 23.95 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62241 (Residues: 2-206; Coverage: 99%)
Gene names: OK/SW-cl.83, RPS8
Sequence domains: Ribosomal protein S8e
Small ribosomal subunit protein uS4 Chain: J
Molecule details ›
Chain: J
Length: 180 amino acids
Theoretical weight: 21.28 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P46781 (Residues: 2-181; Coverage: 93%)
Gene name: RPS9
Sequence domains:
Small ribosomal subunit protein uS7 Chain: K
Molecule details ›
Chain: K
Length: 189 amino acids
Theoretical weight: 21.33 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P46782 (Residues: 16-204; Coverage: 93%)
Gene name: RPS5
Sequence domains: Ribosomal protein S7p/S5e
Small ribosomal subunit protein uS17 Chain: L
Molecule details ›
Chain: L
Length: 151 amino acids
Theoretical weight: 17.53 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62280 (Residues: 2-152; Coverage: 96%)
Gene name: RPS11
Sequence domains:
Small ribosomal subunit protein eS10 Chain: M
Molecule details ›
Chain: M
Length: 95 amino acids
Theoretical weight: 11.37 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P46783 (Residues: 3-97; Coverage: 58%)
Gene name: RPS10
Sequence domains: Plectin/S10 domain
Small ribosomal subunit protein uS15 Chain: N
Molecule details ›
Chain: N
Length: 149 amino acids
Theoretical weight: 17.06 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62277 (Residues: 2-150; Coverage: 99%)
Gene name: RPS13
Sequence domains:
Small ribosomal subunit protein eS12 Chain: O
Molecule details ›
Chain: O
Length: 123 amino acids
Theoretical weight: 13.71 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P25398 (Residues: 10-132; Coverage: 93%)
Gene name: RPS12
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Small ribosomal subunit protein uS11 Chain: P
Molecule details ›
Chain: P
Length: 135 amino acids
Theoretical weight: 14.46 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62263 (Residues: 17-151; Coverage: 89%)
Gene names: PRO2640, RPS14
Sequence domains: Ribosomal protein S11
Small ribosomal subunit protein uS19 Chain: Q
Molecule details ›
Chain: Q
Length: 120 amino acids
Theoretical weight: 14.07 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62841 (Residues: 15-134; Coverage: 83%)
Gene names: RIG, RPS15
Sequence domains: Ribosomal protein S19
Small ribosomal subunit protein uS9 Chain: R
Molecule details ›
Chain: R
Length: 139 amino acids
Theoretical weight: 15.77 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62249 (Residues: 8-146; Coverage: 95%)
Gene name: RPS16
Sequence domains: Ribosomal protein S9/S16
Small ribosomal subunit protein eS17 Chain: S
Molecule details ›
Chain: S
Length: 132 amino acids
Theoretical weight: 15.25 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P08708 (Residues: 2-133; Coverage: 98%)
Gene names: RPS17, RPS17L
Sequence domains: Ribosomal S17
Small ribosomal subunit protein uS13 Chain: T
Molecule details ›
Chain: T
Length: 143 amino acids
Theoretical weight: 16.81 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62269 (Residues: 3-145; Coverage: 94%)
Gene names: D6S218E, RPS18
Sequence domains: Ribosomal protein S13/S18
Small ribosomal subunit protein eS19 Chain: U
Molecule details ›
Chain: U
Length: 144 amino acids
Theoretical weight: 15.96 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P39019 (Residues: 2-145; Coverage: 99%)
Gene name: RPS19
Sequence domains: Ribosomal protein S19e
Small ribosomal subunit protein uS10 Chain: V
Molecule details ›
Chain: V
Length: 101 amino acids
Theoretical weight: 11.51 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P60866 (Residues: 17-117; Coverage: 85%)
Gene name: RPS20
Sequence domains: Ribosomal protein S10p/S20e
Small ribosomal subunit protein uS8 Chain: W
Molecule details ›
Chain: W
Length: 129 amino acids
Theoretical weight: 14.73 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62244 (Residues: 2-130; Coverage: 99%)
Gene names: OK/SW-cl.82, RPS15A
Sequence domains: Ribosomal protein S8
Small ribosomal subunit protein uS12 Chain: X
Molecule details ›
Chain: X
Length: 141 amino acids
Theoretical weight: 15.63 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62266 (Residues: 2-142; Coverage: 99%)
Gene name: RPS23
Sequence domains: Ribosomal protein S12/S23
Small ribosomal subunit protein eS24 Chain: Y
Molecule details ›
Chain: Y
Length: 124 amino acids
Theoretical weight: 14.48 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62847 (Residues: 3-126; Coverage: 93%)
Gene name: RPS24
Sequence domains: Ribosomal protein S24e
Small ribosomal subunit protein eS21 Chain: Z
Molecule details ›
Chain: Z
Length: 82 amino acids
Theoretical weight: 8.98 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P63220 (Residues: 1-82; Coverage: 99%)
Gene name: RPS21
Sequence domains: Ribosomal protein S21e
Small ribosomal subunit protein eS25 Chain: a
Molecule details ›
Chain: a
Length: 72 amino acids
Theoretical weight: 8.18 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62851 (Residues: 42-113; Coverage: 58%)
Gene name: RPS25
Sequence domains: S25 ribosomal protein
Small ribosomal subunit protein eS27 Chain: b
Molecule details ›
Chain: b
Length: 82 amino acids
Theoretical weight: 9.21 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P42677 (Residues: 2-83; Coverage: 98%)
Gene names: MPS1, RPS27
Sequence domains: Ribosomal protein S27
Small ribosomal subunit protein eS26 Chain: c
Molecule details ›
Chain: c
Length: 101 amino acids
Theoretical weight: 11.65 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62854 (Residues: 2-102; Coverage: 88%)
Gene name: RPS26
Sequence domains: Ribosomal protein S26e
Small ribosomal subunit protein eS28 Chain: d
Molecule details ›
Chain: d
Length: 61 amino acids
Theoretical weight: 6.88 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62857 (Residues: 8-68; Coverage: 88%)
Gene name: RPS28
Sequence domains: Ribosomal protein S28e
Small ribosomal subunit protein eS30 Chain: e
Molecule details ›
Chain: e
Length: 56 amino acids
Theoretical weight: 6.3 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62861 (Residues: 78-133; Coverage: 42%)
Gene name: FAU
Sequence domains: Ribosomal protein S30
Small ribosomal subunit protein uS14 Chain: f
Molecule details ›
Chain: f
Length: 54 amino acids
Theoretical weight: 6.5 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62273 (Residues: 3-56; Coverage: 96%)
Gene name: RPS29
Sequence domains: Ribosomal protein S14p/S29e
Small ribosomal subunit protein eS31 Chain: g
Molecule details ›
Chain: g
Length: 72 amino acids
Theoretical weight: 8.45 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62979 (Residues: 78-149; Coverage: 46%)
Gene names: RPS27A, UBA80, UBCEP1
Sequence domains: Ribosomal protein S27a
Small ribosomal subunit protein RACK1 Chain: j
Molecule details ›
Chain: j
Length: 314 amino acids
Theoretical weight: 34.73 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P63244 (Residues: 2-315; Coverage: 99%)
Gene names: GNB2L1, HLC7, PIG21, RACK1
Sequence domains: WD domain, G-beta repeat
Host translation inhibitor nsp1 Chain: i
Molecule details ›
Chain: i
Length: 180 amino acids
Theoretical weight: 19.8 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
UniProt:
  • Canonical: P0DTD1 (Residues: 1-180; Coverage: 3%)
Gene names: 1a-1b, rep
Sequence domains: Betacoronavirus replicase NSP1
Pre-rRNA-processing protein TSR1 homolog Chain: u
Molecule details ›
Chain: u
Length: 804 amino acids
Theoretical weight: 91.95 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q2NL82 (Residues: 1-804; Coverage: 100%)
Gene names: KIAA1401, TSR1
Sequence domains:
18S Ribosomal RNA Chain: 2
Molecule details ›
Chain: 2
Length: 1868 nucleotides
Theoretical weight: 602.43 KDa
Sequence domains: Eukaryotic small subunit ribosomal RNA

Ligands and Environments

1 bound ligand:
Ligand ZN 3 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.2Å
Relevant EMDB volumes: EMD-11310

Quick links

Citations

173 review citations

The COVID-19 puzzle: deciphering pathophysiology and phenotypes of a new disease entity.
Osuchowski et al. (2021)
172 more

4 mentions without citation

Structural Characterization of SARS-CoV-2: Where We Are, and Where We Need to Be.
Mariano et al. (2020)
3 more