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

Electron Microscopy
2.6Å resolution
PDB entry 6zlw coloured by chain, front view.
PDB entry 6zlw coloured by chain, side view.
PDB entry 6zlw coloured by chain, top view.
Source organisms:
Assembly composition:
hetero 36-mer (preferred)
Entry contents: 35 distinct polypeptide molecules
1 distinct RNA molecule

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Assemblies

Assembly 1 (preferred)
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Assembly Name: SARS-CoV-2 NSP10-NSP16 2'-O-methyltransferase complex and RNA
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Multimeric state: hetero 36-mer
Accessible surface area: 390418.61 Å2
Buried surface area: 191375.34 Å2
Dissociation area: 1,751.19 Å2
Dissociation energy (ΔGdiss): 10.55 kcal/mol
Dissociation entropy (TΔSdiss): 14.85 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-530809

Macromolecules

Small ribosomal subunit protein uS2
Chain: B
Length: 295 amino acids
Theoretical weight: 32.88 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P08865 (Residues: 1-295; Coverage: 100%)
Gene names: LAMBR, LAMR1, RPSA
Pfam:
InterPro:
Small ribosomal subunit protein uS2 in PDB entry 6zlw, assembly 1, front view.
Small ribosomal subunit protein uS2 in PDB entry 6zlw, assembly 1, side view.
Small ribosomal subunit protein uS2 in PDB entry 6zlw, assembly 1, top view.
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Small ribosomal subunit protein eS1
Chain: C
Length: 264 amino acids
Theoretical weight: 30 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P61247 (Residues: 1-264; Coverage: 100%)
Gene names: FTE1, MFTL, RPS3A
Pfam: Ribosomal S3Ae family
InterPro:
Small ribosomal subunit protein eS1 in PDB entry 6zlw, assembly 1, front view.
Small ribosomal subunit protein eS1 in PDB entry 6zlw, assembly 1, side view.
Small ribosomal subunit protein eS1 in PDB entry 6zlw, assembly 1, top view.
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Small ribosomal subunit protein uS5
Chain: D
Length: 293 amino acids
Theoretical weight: 31.38 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P15880 (Residues: 1-293; Coverage: 100%)
Gene names: RPS2, RPS4
Pfam:
InterPro:
Small ribosomal subunit protein uS5 in PDB entry 6zlw, assembly 1, front view.
Small ribosomal subunit protein uS5 in PDB entry 6zlw, assembly 1, side view.
Small ribosomal subunit protein uS5 in PDB entry 6zlw, assembly 1, top view.
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Small ribosomal subunit protein eS4, X isoform
Chain: E
Length: 263 amino acids
Theoretical weight: 29.65 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62701 (Residues: 1-263; Coverage: 100%)
Gene names: CCG2, RPS4, RPS4X, SCAR
Pfam:
InterPro:
Small ribosomal subunit protein eS4, X isoform in PDB entry 6zlw, assembly 1, front view.
Small ribosomal subunit protein eS4, X isoform in PDB entry 6zlw, assembly 1, side view.
Small ribosomal subunit protein eS4, X isoform in PDB entry 6zlw, assembly 1, top view.
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Small ribosomal subunit protein uS3
Chain: F
Length: 243 amino acids
Theoretical weight: 26.73 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P23396 (Residues: 1-243; Coverage: 100%)
Gene names: OK/SW-cl.26, RPS3
Pfam:
InterPro:
Small ribosomal subunit protein uS3 in PDB entry 6zlw, assembly 1, front view.
Small ribosomal subunit protein uS3 in PDB entry 6zlw, assembly 1, side view.
Small ribosomal subunit protein uS3 in PDB entry 6zlw, assembly 1, top view.
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Small ribosomal subunit protein eS6
Chain: G
Length: 249 amino acids
Theoretical weight: 28.75 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62753 (Residues: 1-249; Coverage: 100%)
Gene names: OK/SW-cl.2, RPS6
Pfam: Ribosomal protein S6e
InterPro:
Small ribosomal subunit protein eS6 in PDB entry 6zlw, assembly 1, front view.
Small ribosomal subunit protein eS6 in PDB entry 6zlw, assembly 1, side view.
Small ribosomal subunit protein eS6 in PDB entry 6zlw, assembly 1, top view.
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Small ribosomal subunit protein eS7
Chain: H
Length: 194 amino acids
Theoretical weight: 22.17 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62081 (Residues: 1-194; Coverage: 100%)
Gene name: RPS7
Pfam: Ribosomal protein S7e
InterPro:
Small ribosomal subunit protein eS7 in PDB entry 6zlw, assembly 1, front view.
Small ribosomal subunit protein eS7 in PDB entry 6zlw, assembly 1, side view.
Small ribosomal subunit protein eS7 in PDB entry 6zlw, assembly 1, top view.
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Small ribosomal subunit protein eS8
Chain: I
Length: 208 amino acids
Theoretical weight: 24.26 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62241 (Residues: 1-208; Coverage: 100%)
Gene names: OK/SW-cl.83, RPS8
Pfam: Ribosomal protein S8e
InterPro:
Small ribosomal subunit protein eS8 in PDB entry 6zlw, assembly 1, front view.
Small ribosomal subunit protein eS8 in PDB entry 6zlw, assembly 1, side view.
Small ribosomal subunit protein eS8 in PDB entry 6zlw, assembly 1, top view.
Molecule details ›

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Small ribosomal subunit protein uS4
Chain: J
Length: 194 amino acids
Theoretical weight: 22.64 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P46781 (Residues: 1-194; Coverage: 100%)
Gene name: RPS9
Pfam:
InterPro:
Small ribosomal subunit protein uS4 in PDB entry 6zlw, assembly 1, front view.
Small ribosomal subunit protein uS4 in PDB entry 6zlw, assembly 1, side view.
Small ribosomal subunit protein uS4 in PDB entry 6zlw, assembly 1, top view.
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Small ribosomal subunit protein uS7
Chain: K
Length: 204 amino acids
Theoretical weight: 22.91 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P46782 (Residues: 1-204; Coverage: 100%)
Gene name: RPS5
Pfam: Ribosomal protein S7p/S5e
InterPro:
Small ribosomal subunit protein uS7 in PDB entry 6zlw, assembly 1, front view.
Small ribosomal subunit protein uS7 in PDB entry 6zlw, assembly 1, side view.
Small ribosomal subunit protein uS7 in PDB entry 6zlw, assembly 1, top view.
Molecule details ›

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Small ribosomal subunit protein uS17
Chain: L
Length: 158 amino acids
Theoretical weight: 18.47 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62280 (Residues: 1-158; Coverage: 100%)
Gene name: RPS11
Pfam:
InterPro:
Small ribosomal subunit protein uS17 in PDB entry 6zlw, assembly 1, front view.
Small ribosomal subunit protein uS17 in PDB entry 6zlw, assembly 1, side view.
Small ribosomal subunit protein uS17 in PDB entry 6zlw, assembly 1, top view.
Molecule details ›

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Small ribosomal subunit protein eS10
Chain: M
Length: 165 amino acids
Theoretical weight: 18.93 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P46783 (Residues: 1-165; Coverage: 100%)
Gene name: RPS10
Pfam: Plectin/S10 domain
InterPro:
Small ribosomal subunit protein eS10 in PDB entry 6zlw, assembly 1, front view.
Small ribosomal subunit protein eS10 in PDB entry 6zlw, assembly 1, side view.
Small ribosomal subunit protein eS10 in PDB entry 6zlw, assembly 1, top view.
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Small ribosomal subunit protein uS15
Chain: N
Length: 151 amino acids
Theoretical weight: 17.26 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62277 (Residues: 1-151; Coverage: 100%)
Gene name: RPS13
Pfam:
InterPro:
Small ribosomal subunit protein uS15 in PDB entry 6zlw, assembly 1, front view.
Small ribosomal subunit protein uS15 in PDB entry 6zlw, assembly 1, side view.
Small ribosomal subunit protein uS15 in PDB entry 6zlw, assembly 1, top view.
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Small ribosomal subunit protein eS12
Chain: O
Length: 132 amino acids
Theoretical weight: 14.54 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P25398 (Residues: 1-132; Coverage: 100%)
Gene name: RPS12
Pfam: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
InterPro:
Small ribosomal subunit protein eS12 in PDB entry 6zlw, assembly 1, front view.
Small ribosomal subunit protein eS12 in PDB entry 6zlw, assembly 1, side view.
Small ribosomal subunit protein eS12 in PDB entry 6zlw, assembly 1, top view.
Molecule details ›

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Small ribosomal subunit protein uS11
Chain: P
Length: 151 amino acids
Theoretical weight: 16.3 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62263 (Residues: 1-151; Coverage: 100%)
Gene names: PRO2640, RPS14
Pfam: Ribosomal protein S11
InterPro:
Small ribosomal subunit protein uS11 in PDB entry 6zlw, assembly 1, front view.
Small ribosomal subunit protein uS11 in PDB entry 6zlw, assembly 1, side view.
Small ribosomal subunit protein uS11 in PDB entry 6zlw, assembly 1, top view.
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Small ribosomal subunit protein uS19
Chain: Q
Length: 145 amino acids
Theoretical weight: 17.08 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62841 (Residues: 1-145; Coverage: 100%)
Gene names: RIG, RPS15
Pfam: Ribosomal protein S19
InterPro:
Small ribosomal subunit protein uS19 in PDB entry 6zlw, assembly 1, front view.
Small ribosomal subunit protein uS19 in PDB entry 6zlw, assembly 1, side view.
Small ribosomal subunit protein uS19 in PDB entry 6zlw, assembly 1, top view.
Molecule details ›

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Small ribosomal subunit protein uS9
Chain: R
Length: 146 amino acids
Theoretical weight: 16.48 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62249 (Residues: 1-146; Coverage: 100%)
Gene name: RPS16
Pfam: Ribosomal protein S9/S16
InterPro:
Small ribosomal subunit protein uS9 in PDB entry 6zlw, assembly 1, front view.
Small ribosomal subunit protein uS9 in PDB entry 6zlw, assembly 1, side view.
Small ribosomal subunit protein uS9 in PDB entry 6zlw, assembly 1, top view.
Molecule details ›

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Small ribosomal subunit protein eS17
Chain: S
Length: 135 amino acids
Theoretical weight: 15.58 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P08708 (Residues: 1-135; Coverage: 100%)
Gene names: RPS17, RPS17L
Pfam: Ribosomal S17
InterPro:
Small ribosomal subunit protein eS17 in PDB entry 6zlw, assembly 1, front view.
Small ribosomal subunit protein eS17 in PDB entry 6zlw, assembly 1, side view.
Small ribosomal subunit protein eS17 in PDB entry 6zlw, assembly 1, top view.
Molecule details ›

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Small ribosomal subunit protein uS13
Chain: T
Length: 152 amino acids
Theoretical weight: 17.76 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62269 (Residues: 1-152; Coverage: 100%)
Gene names: D6S218E, RPS18
Pfam: Ribosomal protein S13/S18
InterPro:
Small ribosomal subunit protein uS13 in PDB entry 6zlw, assembly 1, front view.
Small ribosomal subunit protein uS13 in PDB entry 6zlw, assembly 1, side view.
Small ribosomal subunit protein uS13 in PDB entry 6zlw, assembly 1, top view.
Molecule details ›

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Small ribosomal subunit protein eS19
Chain: U
Length: 145 amino acids
Theoretical weight: 16.09 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P39019 (Residues: 1-145; Coverage: 100%)
Gene name: RPS19
Pfam: Ribosomal protein S19e
InterPro:
Small ribosomal subunit protein eS19 in PDB entry 6zlw, assembly 1, front view.
Small ribosomal subunit protein eS19 in PDB entry 6zlw, assembly 1, side view.
Small ribosomal subunit protein eS19 in PDB entry 6zlw, assembly 1, top view.
Molecule details ›

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Small ribosomal subunit protein uS10
Chain: V
Length: 119 amino acids
Theoretical weight: 13.4 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P60866 (Residues: 1-119; Coverage: 100%)
Gene name: RPS20
Pfam: Ribosomal protein S10p/S20e
InterPro:
Small ribosomal subunit protein uS10 in PDB entry 6zlw, assembly 1, front view.
Small ribosomal subunit protein uS10 in PDB entry 6zlw, assembly 1, side view.
Small ribosomal subunit protein uS10 in PDB entry 6zlw, assembly 1, top view.
Molecule details ›

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Small ribosomal subunit protein uS8
Chain: W
Length: 130 amino acids
Theoretical weight: 14.87 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62244 (Residues: 1-130; Coverage: 100%)
Gene names: OK/SW-cl.82, RPS15A
Pfam: Ribosomal protein S8
InterPro:
Small ribosomal subunit protein uS8 in PDB entry 6zlw, assembly 1, front view.
Small ribosomal subunit protein uS8 in PDB entry 6zlw, assembly 1, side view.
Small ribosomal subunit protein uS8 in PDB entry 6zlw, assembly 1, top view.
Molecule details ›

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Small ribosomal subunit protein uS12
Chain: X
Length: 143 amino acids
Theoretical weight: 15.84 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62266 (Residues: 1-143; Coverage: 100%)
Gene name: RPS23
Pfam: Ribosomal protein S12/S23
InterPro:
Small ribosomal subunit protein uS12 in PDB entry 6zlw, assembly 1, front view.
Small ribosomal subunit protein uS12 in PDB entry 6zlw, assembly 1, side view.
Small ribosomal subunit protein uS12 in PDB entry 6zlw, assembly 1, top view.
Molecule details ›

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Small ribosomal subunit protein eS24
Chain: Y
Length: 133 amino acids
Theoretical weight: 15.46 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62847 (Residues: 1-133; Coverage: 100%)
Gene name: RPS24
Pfam: Ribosomal protein S24e
InterPro:
Small ribosomal subunit protein eS24 in PDB entry 6zlw, assembly 1, front view.
Small ribosomal subunit protein eS24 in PDB entry 6zlw, assembly 1, side view.
Small ribosomal subunit protein eS24 in PDB entry 6zlw, assembly 1, top view.
Molecule details ›

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Small ribosomal subunit protein eS21
Chain: Z
Length: 83 amino acids
Theoretical weight: 9.12 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P63220 (Residues: 1-83; Coverage: 100%)
Gene name: RPS21
Pfam: Ribosomal protein S21e
InterPro:
Small ribosomal subunit protein eS21 in PDB entry 6zlw, assembly 1, front view.
Small ribosomal subunit protein eS21 in PDB entry 6zlw, assembly 1, side view.
Small ribosomal subunit protein eS21 in PDB entry 6zlw, assembly 1, top view.
Molecule details ›

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Small ribosomal subunit protein eS25
Chain: a
Length: 125 amino acids
Theoretical weight: 13.78 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62851 (Residues: 1-125; Coverage: 100%)
Gene name: RPS25
Pfam: S25 ribosomal protein
InterPro:
Small ribosomal subunit protein eS25 in PDB entry 6zlw, assembly 1, front view.
Small ribosomal subunit protein eS25 in PDB entry 6zlw, assembly 1, side view.
Small ribosomal subunit protein eS25 in PDB entry 6zlw, assembly 1, top view.
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Small ribosomal subunit protein eS27
Chain: b
Length: 84 amino acids
Theoretical weight: 9.48 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P42677 (Residues: 1-84; Coverage: 100%)
Gene names: MPS1, RPS27
Pfam: Ribosomal protein S27
InterPro:
Small ribosomal subunit protein eS27 in PDB entry 6zlw, assembly 1, front view.
Small ribosomal subunit protein eS27 in PDB entry 6zlw, assembly 1, side view.
Small ribosomal subunit protein eS27 in PDB entry 6zlw, assembly 1, top view.
Molecule details ›

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Small ribosomal subunit protein eS26
Chain: c
Length: 115 amino acids
Theoretical weight: 13.05 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62854 (Residues: 1-115; Coverage: 100%)
Gene name: RPS26
Pfam: Ribosomal protein S26e
InterPro:
Small ribosomal subunit protein eS26 in PDB entry 6zlw, assembly 1, front view.
Small ribosomal subunit protein eS26 in PDB entry 6zlw, assembly 1, side view.
Small ribosomal subunit protein eS26 in PDB entry 6zlw, assembly 1, top view.
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Small ribosomal subunit protein eS28
Chain: d
Length: 69 amino acids
Theoretical weight: 7.86 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62857 (Residues: 1-69; Coverage: 100%)
Gene name: RPS28
Pfam: Ribosomal protein S28e
InterPro:
Small ribosomal subunit protein eS28 in PDB entry 6zlw, assembly 1, front view.
Small ribosomal subunit protein eS28 in PDB entry 6zlw, assembly 1, side view.
Small ribosomal subunit protein eS28 in PDB entry 6zlw, assembly 1, top view.
Molecule details ›

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Small ribosomal subunit protein eS30
Chain: e
Length: 59 amino acids
Theoretical weight: 6.67 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62861 (Residues: 75-133; Coverage: 44%)
Gene name: FAU
Pfam: Ribosomal protein S30
InterPro: Small ribosomal subunit protein eS30
Small ribosomal subunit protein eS30 in PDB entry 6zlw, assembly 1, front view.
Small ribosomal subunit protein eS30 in PDB entry 6zlw, assembly 1, side view.
Small ribosomal subunit protein eS30 in PDB entry 6zlw, assembly 1, top view.
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Small ribosomal subunit protein uS14
Chain: f
Length: 56 amino acids
Theoretical weight: 6.69 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62273 (Residues: 1-56; Coverage: 100%)
Gene name: RPS29
Pfam: Ribosomal protein S14p/S29e
InterPro:
Small ribosomal subunit protein uS14 in PDB entry 6zlw, assembly 1, front view.
Small ribosomal subunit protein uS14 in PDB entry 6zlw, assembly 1, side view.
Small ribosomal subunit protein uS14 in PDB entry 6zlw, assembly 1, top view.
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Ubiquitin-ribosomal protein eS31 fusion protein
Chain: g
Length: 156 amino acids
Theoretical weight: 18 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62979 (Residues: 1-156; Coverage: 100%)
Gene names: RPS27A, UBA80, UBCEP1
Pfam:
InterPro:
Ubiquitin-ribosomal protein eS31 fusion protein in PDB entry 6zlw, assembly 1, front view.
Ubiquitin-ribosomal protein eS31 fusion protein in PDB entry 6zlw, assembly 1, side view.
Ubiquitin-ribosomal protein eS31 fusion protein in PDB entry 6zlw, assembly 1, top view.
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Small ribosomal subunit protein eS32
Chain: h
Length: 25 amino acids
Theoretical weight: 3.47 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62945 (Residues: 1-25; Coverage: 100%)
Gene name: RPL41
Pfam: Ribosomal protein L41
InterPro: Large ribosomal subunit protein eS32
Small ribosomal subunit protein eS32 in PDB entry 6zlw, assembly 1, front view.
Small ribosomal subunit protein eS32 in PDB entry 6zlw, assembly 1, side view.
Small ribosomal subunit protein eS32 in PDB entry 6zlw, assembly 1, top view.
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Small ribosomal subunit protein RACK1
Chain: j
Length: 317 amino acids
Theoretical weight: 35.12 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P63244 (Residues: 1-317; Coverage: 100%)
Gene names: GNB2L1, HLC7, PIG21, RACK1
Pfam: WD domain, G-beta repeat
InterPro:
Small ribosomal subunit protein RACK1 in PDB entry 6zlw, assembly 1, front view.
Small ribosomal subunit protein RACK1 in PDB entry 6zlw, assembly 1, side view.
Small ribosomal subunit protein RACK1 in PDB entry 6zlw, assembly 1, top view.
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Host translation inhibitor nsp1
Chain: i
Length: 180 amino acids
Theoretical weight: 19.8 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: P0DTD1 (Residues: 1-180; Coverage: 3%)
Gene names: 1a-1b, rep
Pfam: Betacoronavirus replicase NSP1
InterPro:
Host translation inhibitor nsp1 in PDB entry 6zlw, assembly 1, front view.
Host translation inhibitor nsp1 in PDB entry 6zlw, assembly 1, side view.
Host translation inhibitor nsp1 in PDB entry 6zlw, assembly 1, top view.
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RNA chain 2
Name: 18S Ribosomal RNA
Representative chains: 2
Length: 1868 nucleotides
Theoretical weight: 602.43 KDa
Rfam: Eukaryotic small subunit ribosomal RNA
18S Ribosomal RNA in PDB entry 6zlw, assembly 1, front view.
18S Ribosomal RNA in PDB entry 6zlw, assembly 1, side view.
18S Ribosomal RNA in PDB entry 6zlw, assembly 1, top view.
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