PDB 8ppk structure summary ‹ Protein Data Bank in Europe (PDBe)

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'-(N(7)-methyl 5'-triphosphoguanosine)-(ribonucleotide)-[mRNA] = S-adenosyl-L-homocysteine + a 5'-(N(7)-methyl 5'-triphosphoguanosine)-(2'-O-methyl-ribonucleotide)-[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).

ATP + H(2)O = ADP + phosphate

Biochemical function:

RNA binding

Biological process:

translation

Cellular component:

cytoplasm

Sequence domain:

Eukaryotic small subunit ribosomal RNA

Structure analysis Details

Assembly composition:

hetero 37-mer (preferred)

PDBe Complex ID:

PDB-CPX-268555 (preferred)

Entry contents:

36 distinct polypeptide molecules
1 distinct RNA molecule

Macromolecules (37 distinct):

Eukaryotic translation initiation factor 1 Chain: p

Molecule details ›

Chain: p
Length: 113 amino acids
Theoretical weight: 12.75 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:

Canonical: P41567 (Residues: 1-113; Coverage: 100%)

Gene names: EIF1, SUI1
Sequence domains: Translation initiation factor SUI1

Small ribosomal subunit protein uS2 Chain: A

Molecule details ›

Chain: A
Length: 295 amino acids
Theoretical weight: 32.93 KDa
Source organism: Homo sapiens
UniProt:

Canonical: P08865 (Residues: 1-295; Coverage: 100%)

Gene names: LAMBR, LAMR1, RPSA
Sequence domains:

Small ribosomal subunit protein eS1 Chain: B

Molecule details ›

Chain: B
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
Sequence domains: Ribosomal S3Ae family

Small ribosomal subunit protein uS5 Chain: C

Molecule details ›

Chain: C
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
Sequence domains:

Small ribosomal subunit protein uS3 Chain: D

Molecule details ›

Chain: D
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
Sequence domains:

Small ribosomal subunit protein eS4, X isoform Chain: E

Molecule details ›

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
Sequence domains:

Small ribosomal subunit protein uS7 Chain: F

Molecule details ›

Chain: F
Length: 204 amino acids
Theoretical weight: 22.91 KDa
Source organism: Homo sapiens
UniProt:

Canonical: P46782 (Residues: 1-204; Coverage: 100%)

Gene name: RPS5
Sequence domains: Ribosomal protein S7p/S5e

Small ribosomal subunit protein eS6 Chain: G

Molecule details ›

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
Sequence domains: Ribosomal protein S6e

Small ribosomal subunit protein eS7 Chain: H

Molecule details ›

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
Sequence domains: Ribosomal protein S7e

Small ribosomal subunit protein eS8 Chain: I

Molecule details ›

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
Sequence domains: Ribosomal protein S8e

Small ribosomal subunit protein uS4 Chain: J

Molecule details ›

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
Sequence domains:

Small ribosomal subunit protein eS10 Chain: K

Molecule details ›

Chain: K
Length: 165 amino acids
Theoretical weight: 18.93 KDa
Source organism: Homo sapiens
UniProt:

Canonical: P46783 (Residues: 1-165; Coverage: 100%)

Gene name: RPS10
Sequence domains: Plectin/S10 domain

Small ribosomal subunit protein uS17 Chain: L

Molecule details ›

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
Sequence domains:

Small ribosomal subunit protein eS12 Chain: M

Molecule details ›

Chain: M
Length: 132 amino acids
Theoretical weight: 14.54 KDa
Source organism: Homo sapiens
UniProt:

Canonical: P25398 (Residues: 1-132; Coverage: 100%)

Gene name: RPS12
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family

Small ribosomal subunit protein uS15 Chain: N

Molecule details ›

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
Sequence domains:

Small ribosomal subunit protein uS11 Chain: O

Molecule details ›

Chain: O
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
Sequence domains: Ribosomal protein S11

Small ribosomal subunit protein uS19 Chain: P

Molecule details ›

Chain: P
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
Sequence domains: Ribosomal protein S19

Small ribosomal subunit protein uS9 Chain: Q

Molecule details ›

Chain: Q
Length: 146 amino acids
Theoretical weight: 16.48 KDa
Source organism: Homo sapiens
UniProt:

Canonical: P62249 (Residues: 1-146; Coverage: 100%)

Gene name: RPS16
Sequence domains: Ribosomal protein S9/S16

Small ribosomal subunit protein eS17 Chain: R

Molecule details ›

Chain: R
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
Sequence domains: Ribosomal S17

Small ribosomal subunit protein uS13 Chain: S

Molecule details ›

Chain: S
Length: 152 amino acids
Theoretical weight: 17.8 KDa
Source organism: Homo sapiens
UniProt:

Canonical: P62269 (Residues: 1-152; Coverage: 100%)

Gene names: D6S218E, RPS18
Sequence domains: Ribosomal protein S13/S18

Small ribosomal subunit protein eS19 Chain: T

Molecule details ›

Chain: T
Length: 145 amino acids
Theoretical weight: 16.1 KDa
Source organism: Homo sapiens
UniProt:

Canonical: P39019 (Residues: 1-145; Coverage: 100%)

Gene name: RPS19
Sequence domains: Ribosomal protein S19e

Small ribosomal subunit protein uS10 Chain: U

Molecule details ›

Chain: U
Length: 119 amino acids
Theoretical weight: 13.4 KDa
Source organism: Homo sapiens
UniProt:

Canonical: P60866 (Residues: 1-119; Coverage: 100%)

Gene name: RPS20
Sequence domains: Ribosomal protein S10p/S20e

Small ribosomal subunit protein eS21 Chain: V

Molecule details ›

Chain: V
Length: 83 amino acids
Theoretical weight: 9.17 KDa
Source organism: Homo sapiens
UniProt:

Canonical: P63220 (Residues: 1-83; Coverage: 100%)

Gene name: RPS21
Sequence domains: Ribosomal protein S21e

Small ribosomal subunit protein uS8 Chain: W

Molecule details ›

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
Sequence domains: Ribosomal protein S8

Small ribosomal subunit protein uS12 Chain: X

Molecule details ›

Chain: X
Length: 143 amino acids
Theoretical weight: 15.86 KDa
Source organism: Homo sapiens
UniProt:

Canonical: P62266 (Residues: 1-143; Coverage: 100%)

Gene name: RPS23
Sequence domains: Ribosomal protein S12/S23

Small ribosomal subunit protein eS24 Chain: Y

Molecule details ›

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
Sequence domains: Ribosomal protein S24e

Small ribosomal subunit protein eS25 Chain: Z

Molecule details ›

Chain: Z
Length: 125 amino acids
Theoretical weight: 13.78 KDa
Source organism: Homo sapiens
UniProt:

Canonical: P62851 (Residues: 1-125; Coverage: 100%)

Gene name: RPS25
Sequence domains: S25 ribosomal protein

Small ribosomal subunit protein eS26 Chain: a

Molecule details ›

Chain: a
Length: 115 amino acids
Theoretical weight: 13.05 KDa
Source organism: Homo sapiens
UniProt:

Canonical: P62854 (Residues: 1-115; Coverage: 100%)

Gene name: RPS26
Sequence domains: Ribosomal protein S26e

Small ribosomal subunit protein eS27 Chain: b

Molecule details ›

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
Sequence domains: Ribosomal protein S27

Small ribosomal subunit protein eS28 Chain: c

Molecule details ›

Chain: c
Length: 69 amino acids
Theoretical weight: 7.86 KDa
Source organism: Homo sapiens
UniProt:

Canonical: P62857 (Residues: 1-69; Coverage: 100%)

Gene name: RPS28
Sequence domains: Ribosomal protein S28e

Small ribosomal subunit protein uS14 Chain: d

Molecule details ›

Chain: d
Length: 56 amino acids
Theoretical weight: 6.69 KDa
Source organism: Homo sapiens
UniProt:

Canonical: P62273 (Residues: 1-56; Coverage: 100%)

Gene name: RPS29
Sequence domains: Ribosomal protein S14p/S29e

Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein Chain: e

Molecule details ›

Chain: e
Length: 133 amino acids
Theoretical weight: 14.42 KDa
Source organism: Homo sapiens
UniProt:

Canonical: P62861 (Residues: 1-133; Coverage: 100%)

Gene name: FAU
Sequence domains:

Ubiquitin-ribosomal protein eS31 fusion protein Chain: f

Molecule details ›

Chain: f
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
Sequence domains:

Small ribosomal subunit protein RACK1 Chain: g

Molecule details ›

Chain: g
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
Sequence domains: WD domain, G-beta repeat

Small ribosomal subunit protein eS32 Chain: h

Molecule details ›

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
Sequence domains: Ribosomal protein L41

Nsp1 Chain: j

Molecule details ›

Chain: j
Length: 188 amino acids
Theoretical weight: 21.17 KDa
Source organism: Bat Hp-betacoronavirus/Zhejiang2013
Expression system: Escherichia coli
UniProt: