Function and Biology

48S late-stage initiation complex with m6A mRNA

Source organism: Oryctolagus cuniculus
Biochemical function: structural constituent of ribosome
Biological process: translation
Cellular component: ribosome

EC 4.2.99.18: DNA-(apurinic or apyrimidinic site) lyase

Reaction 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
Systematic name:
DNA-(apurinic or apyrimidinic site) 5'-phosphomonoester-lyase
Alternative Name(s):
  • AP endonuclease class I
  • AP lyase
  • AP site-DNA 5'-phosphomonoester-lyase
  • Deoxyribonuclease (apurinic or apyrimidinic)
  • E. coli endonuclease III
  • E.coli endonuclease III
  • Endodeoxyribonuclease (apurinic or apyrimidinic)
  • Micrococcus luteus UV endonuclease
  • Phage-T(4) UV endonuclease
  • Phage-T4 UV endonuclease
  • X-ray endonuclease III

GO terms

Biochemical function:
Biological process:
Cellular component:

Sequence families

Pfam Protein families (Pfam)
PF00400
Domain description: WD domain, G-beta repeat
Occurring in:
  1. Small ribosomal subunit protein RACK1
The deposited structure of PDB entry 8p03 contains 5 copies of Pfam domain PF00400 (WD domain, G-beta repeat) in Small ribosomal subunit protein RACK1. Showing 5 copies in chain IA [auth g].

PF00005
Domain description: ABC transporter
Occurring in:
  1. ATP binding cassette subfamily E member 1
The deposited structure of PDB entry 8p03 contains 2 copies of Pfam domain PF00005 (ABC transporter) in ATP binding cassette subfamily E member 1. Showing 2 copies in chain LA [auth k].

PF00240
The deposited structure of PDB entry 8p03 contains 1 copy of Pfam domain PF00240 (Ubiquitin family) in Small ribosomal subunit protein eS31. Showing 1 copy in chain HA [auth f].
The deposited structure of PDB entry 8p03 contains 1 copy of Pfam domain PF00240 (Ubiquitin family) in Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein. Showing 1 copy in chain JA [auth i] (this domain is out of the observed residue ranges!).

PF00318
Domain description: Ribosomal protein S2
Occurring in:
  1. Small ribosomal subunit protein uS2
The deposited structure of PDB entry 8p03 contains 2 copies of Pfam domain PF00318 (Ribosomal protein S2) in Small ribosomal subunit protein uS2. Showing 2 copies in chain E [auth C].

PF03297
Domain description: S25 ribosomal protein
Occurring in:
  1. Small ribosomal subunit protein eS25
The deposited structure of PDB entry 8p03 contains 1 copy of Pfam domain PF03297 (S25 ribosomal protein) in Small ribosomal subunit protein eS25. Showing 1 copy in chain NA [auth n].

PF05162
Domain description: Ribosomal protein L41
Occurring in:
  1. Small ribosomal subunit protein eS32
The deposited structure of PDB entry 8p03 contains 1 copy of Pfam domain PF05162 (Ribosomal protein L41) in Small ribosomal subunit protein eS32. Showing 1 copy in chain MA [auth l].

PF00037
Domain description: 4Fe-4S binding domain
Occurring in:
  1. ATP binding cassette subfamily E member 1
The deposited structure of PDB entry 8p03 contains 1 copy of Pfam domain PF00037 (4Fe-4S binding domain) in ATP binding cassette subfamily E member 1. Showing 1 copy in chain LA [auth k].

PF04068
Domain description: Possible Fer4-like domain in RNase L inhibitor, RLI
Occurring in:
  1. ATP binding cassette subfamily E member 1
The deposited structure of PDB entry 8p03 contains 1 copy of Pfam domain PF04068 (Possible Fer4-like domain in RNase L inhibitor, RLI) in ATP binding cassette subfamily E member 1. Showing 1 copy in chain LA [auth k].

PF01176
Domain description: Translation initiation factor 1A / IF-1
Occurring in:
  1. Eukaryotic translation initiation factor 4C
The deposited structure of PDB entry 8p03 contains 1 copy of Pfam domain PF01176 (Translation initiation factor 1A / IF-1) in Eukaryotic translation initiation factor 4C. Showing 1 copy in chain KA [auth j].

PF04758
Domain description: Ribosomal protein S30
Occurring in:
  1. Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein
The deposited structure of PDB entry 8p03 contains 1 copy of Pfam domain PF04758 (Ribosomal protein S30) in Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein. Showing 1 copy in chain JA [auth i].

PF01599
Domain description: Ribosomal protein S27a
Occurring in:
  1. Small ribosomal subunit protein eS31
The deposited structure of PDB entry 8p03 contains 1 copy of Pfam domain PF01599 (Ribosomal protein S27a) in Small ribosomal subunit protein eS31. Showing 1 copy in chain HA [auth f].

PF00253
Domain description: Ribosomal protein S14p/S29e
Occurring in:
  1. Small ribosomal subunit protein uS14
The deposited structure of PDB entry 8p03 contains 1 copy of Pfam domain PF00253 (Ribosomal protein S14p/S29e) in Small ribosomal subunit protein uS14. Showing 1 copy in chain GA [auth e].

PF01200
Domain description: Ribosomal protein S28e
Occurring in:
  1. Small ribosomal subunit protein eS28
The deposited structure of PDB entry 8p03 contains 1 copy of Pfam domain PF01200 (Ribosomal protein S28e) in Small ribosomal subunit protein eS28. Showing 1 copy in chain FA [auth d].

PF01667
Domain description: Ribosomal protein S27
Occurring in:
  1. Small ribosomal subunit protein eS27
The deposited structure of PDB entry 8p03 contains 1 copy of Pfam domain PF01667 (Ribosomal protein S27) in Small ribosomal subunit protein eS27. Showing 1 copy in chain EA [auth c].

PF01283
Domain description: Ribosomal protein S26e
Occurring in:
  1. Small ribosomal subunit protein eS26
The deposited structure of PDB entry 8p03 contains 1 copy of Pfam domain PF01283 (Ribosomal protein S26e) in Small ribosomal subunit protein eS26. Showing 1 copy in chain DA [auth b].

PF01282
Domain description: Ribosomal protein S24e
Occurring in:
  1. Small ribosomal subunit protein eS24
The deposited structure of PDB entry 8p03 contains 1 copy of Pfam domain PF01282 (Ribosomal protein S24e) in Small ribosomal subunit protein eS24. Showing 1 copy in chain CA [auth a].

PF00164
Domain description: Ribosomal protein S12/S23
Occurring in:
  1. Small ribosomal subunit protein uS12
The deposited structure of PDB entry 8p03 contains 1 copy of Pfam domain PF00164 (Ribosomal protein S12/S23) in Small ribosomal subunit protein uS12. Showing 1 copy in chain BA [auth Z].

PF00410
Domain description: Ribosomal protein S8
Occurring in:
  1. Small ribosomal subunit protein uS8
The deposited structure of PDB entry 8p03 contains 1 copy of Pfam domain PF00410 (Ribosomal protein S8) in Small ribosomal subunit protein uS8. Showing 1 copy in chain AA [auth Y].

PF01249
Domain description: Ribosomal protein S21e
Occurring in:
  1. Small ribosomal subunit protein eS21
The deposited structure of PDB entry 8p03 contains 1 copy of Pfam domain PF01249 (Ribosomal protein S21e ) in Small ribosomal subunit protein eS21. Showing 1 copy in chain Z [auth X].

PF00338
Domain description: Ribosomal protein S10p/S20e
Occurring in:
  1. Small ribosomal subunit protein uS10
The deposited structure of PDB entry 8p03 contains 1 copy of Pfam domain PF00338 (Ribosomal protein S10p/S20e) in Small ribosomal subunit protein uS10. Showing 1 copy in chain Y [auth W].

PF01090
Domain description: Ribosomal protein S19e
Occurring in:
  1. Small ribosomal subunit protein eS19
The deposited structure of PDB entry 8p03 contains 1 copy of Pfam domain PF01090 (Ribosomal protein S19e) in Small ribosomal subunit protein eS19. Showing 1 copy in chain X [auth V].

PF00416
Domain description: Ribosomal protein S13/S18
Occurring in:
  1. Small ribosomal subunit protein uS13
The deposited structure of PDB entry 8p03 contains 1 copy of Pfam domain PF00416 (Ribosomal protein S13/S18) in Small ribosomal subunit protein uS13. Showing 1 copy in chain W [auth U].

PF00833
Domain description: Ribosomal S17
Occurring in:
  1. Small ribosomal subunit protein eS17
The deposited structure of PDB entry 8p03 contains 1 copy of Pfam domain PF00833 (Ribosomal S17) in Small ribosomal subunit protein eS17. Showing 1 copy in chain V [auth T].

PF00380
Domain description: Ribosomal protein S9/S16
Occurring in:
  1. Small ribosomal subunit protein uS9
The deposited structure of PDB entry 8p03 contains 1 copy of Pfam domain PF00380 (Ribosomal protein S9/S16) in Small ribosomal subunit protein uS9. Showing 1 copy in chain U [auth S].

PF00203
Domain description: Ribosomal protein S19
Occurring in:
  1. Small ribosomal subunit protein uS19
The deposited structure of PDB entry 8p03 contains 1 copy of Pfam domain PF00203 (Ribosomal protein S19) in Small ribosomal subunit protein uS19. Showing 1 copy in chain T [auth R].

PF00411
Domain description: Ribosomal protein S11
Occurring in:
  1. Small ribosomal subunit protein uS11
The deposited structure of PDB entry 8p03 contains 1 copy of Pfam domain PF00411 (Ribosomal protein S11) in Small ribosomal subunit protein uS11. Showing 1 copy in chain S [auth Q].

PF00312
Domain description: Ribosomal protein S15
Occurring in:
  1. Small ribosomal subunit protein uS15
The deposited structure of PDB entry 8p03 contains 1 copy of Pfam domain PF00312 (Ribosomal protein S15) in Small ribosomal subunit protein uS15. Showing 1 copy in chain R [auth P].

PF08069
Domain description: Ribosomal S13/S15 N-terminal domain
Occurring in:
  1. Small ribosomal subunit protein uS15
The deposited structure of PDB entry 8p03 contains 1 copy of Pfam domain PF08069 (Ribosomal S13/S15 N-terminal domain) in Small ribosomal subunit protein uS15. Showing 1 copy in chain R [auth P].

PF01248
Domain description: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Occurring in:
  1. Small ribosomal subunit protein eS12
The deposited structure of PDB entry 8p03 contains 1 copy of Pfam domain PF01248 (Ribosomal protein L7Ae/L30e/S12e/Gadd45 family) in Small ribosomal subunit protein eS12. Showing 1 copy in chain Q [auth O].

PF00366
Domain description: Ribosomal protein S17
Occurring in:
  1. Small ribosomal subunit protein uS17
The deposited structure of PDB entry 8p03 contains 1 copy of Pfam domain PF00366 (Ribosomal protein S17) in Small ribosomal subunit protein uS17. Showing 1 copy in chain P [auth N].

PF16205
Domain description: Ribosomal_S17 N-terminal
Occurring in:
  1. Small ribosomal subunit protein uS17
The deposited structure of PDB entry 8p03 contains 1 copy of Pfam domain PF16205 (Ribosomal_S17 N-terminal) in Small ribosomal subunit protein uS17. Showing 1 copy in chain P [auth N].

PF03501
Domain description: Plectin/S10 domain
Occurring in:
  1. Small ribosomal subunit protein eS10
The deposited structure of PDB entry 8p03 contains 1 copy of Pfam domain PF03501 (Plectin/S10 domain) in Small ribosomal subunit protein eS10. Showing 1 copy in chain O [auth M].

PF01479
Domain description: S4 domain
Occurring in:
  1. Small ribosomal subunit protein uS4
The deposited structure of PDB entry 8p03 contains 1 copy of Pfam domain PF01479 (S4 domain) in Small ribosomal subunit protein uS4. Showing 1 copy in chain N [auth L].

PF00163
Domain description: Ribosomal protein S4/S9 N-terminal domain
Occurring in:
  1. Small ribosomal subunit protein uS4
The deposited structure of PDB entry 8p03 contains 1 copy of Pfam domain PF00163 (Ribosomal protein S4/S9 N-terminal domain) in Small ribosomal subunit protein uS4. Showing 1 copy in chain N [auth L].

PF01201
Domain description: Ribosomal protein S8e
Occurring in:
  1. Small ribosomal subunit protein eS8
The deposited structure of PDB entry 8p03 contains 1 copy of Pfam domain PF01201 (Ribosomal protein S8e) in Small ribosomal subunit protein eS8. Showing 1 copy in chain M [auth K].

PF01092
Domain description: Ribosomal protein S6e
Occurring in:
  1. 40S ribosomal protein S6
The deposited structure of PDB entry 8p03 contains 1 copy of Pfam domain PF01092 (Ribosomal protein S6e) in 40S ribosomal protein S6. Showing 1 copy in chain K [auth I].

PF00177
Domain description: Ribosomal protein S7p/S5e
Occurring in:
  1. Small ribosomal subunit protein uS7
The deposited structure of PDB entry 8p03 contains 1 copy of Pfam domain PF00177 (Ribosomal protein S7p/S5e) in Small ribosomal subunit protein uS7. Showing 1 copy in chain J [auth H].

PF16121
Domain description: 40S ribosomal protein S4 C-terminus
Occurring in:
  1. Small ribosomal subunit protein eS4
The deposited structure of PDB entry 8p03 contains 1 copy of Pfam domain PF16121 (40S ribosomal protein S4 C-terminus) in Small ribosomal subunit protein eS4. Showing 1 copy in chain I [auth G].

PF00467
Domain description: KOW motif
Occurring in:
  1. Small ribosomal subunit protein eS4
The deposited structure of PDB entry 8p03 contains 1 copy of Pfam domain PF00467 (KOW motif) in Small ribosomal subunit protein eS4. Showing 1 copy in chain I [auth G].

PF00900
Domain description: Ribosomal family S4e
Occurring in:
  1. Small ribosomal subunit protein eS4
The deposited structure of PDB entry 8p03 contains 1 copy of Pfam domain PF00900 (Ribosomal family S4e) in Small ribosomal subunit protein eS4. Showing 1 copy in chain I [auth G].

PF08071
Domain description: RS4NT (NUC023) domain
Occurring in:
  1. Small ribosomal subunit protein eS4
The deposited structure of PDB entry 8p03 contains 1 copy of Pfam domain PF08071 (RS4NT (NUC023) domain) in Small ribosomal subunit protein eS4. Showing 1 copy in chain I [auth G].

PF00189
Domain description: Ribosomal protein S3, C-terminal domain
Occurring in:
  1. Small ribosomal subunit protein uS3
The deposited structure of PDB entry 8p03 contains 1 copy of Pfam domain PF00189 (Ribosomal protein S3, C-terminal domain) in Small ribosomal subunit protein uS3. Showing 1 copy in chain H [auth F].

PF07650
Domain description: KH domain
Occurring in:
  1. Small ribosomal subunit protein uS3
The deposited structure of PDB entry 8p03 contains 1 copy of Pfam domain PF07650 (KH domain) in Small ribosomal subunit protein uS3. Showing 1 copy in chain H [auth F].

PF01015
Domain description: Ribosomal S3Ae family
Occurring in:
  1. Small ribosomal subunit protein eS1
The deposited structure of PDB entry 8p03 contains 1 copy of Pfam domain PF01015 (Ribosomal S3Ae family) in Small ribosomal subunit protein eS1. Showing 1 copy in chain F [auth D].

PF07541
Domain description: Eukaryotic translation initiation factor 2 alpha subunit
Occurring in:
  1. Eukaryotic translation initiation factor 2 subunit 1
The deposited structure of PDB entry 8p03 contains 1 copy of Pfam domain PF07541 (Eukaryotic translation initiation factor 2 alpha subunit) in Eukaryotic translation initiation factor 2 subunit 1. Showing 1 copy in chain D [auth A].

PF00575
Domain description: S1 RNA binding domain
Occurring in:
  1. Eukaryotic translation initiation factor 2 subunit 1
The deposited structure of PDB entry 8p03 contains 1 copy of Pfam domain PF00575 (S1 RNA binding domain) in Eukaryotic translation initiation factor 2 subunit 1. Showing 1 copy in chain D [auth A].

Rfam RNA families (Rfam)
RF00005
Domain description: tRNA
Occurring in:
  1. initiator methionylated tRNA
The deposited structure of PDB entry 8p03 contains 1 copy of Rfam domain RF00005 (tRNA) in initiator methionylated tRNA. Showing 1 copy in chain A [auth 1].

RF01960
Domain description: Eukaryotic small subunit ribosomal RNA
Occurring in:
  1. 18S Ribosomal RNA
The deposited structure of PDB entry 8p03 contains 1 copy of Rfam domain RF01960 (Eukaryotic small subunit ribosomal RNA) in 18S Ribosomal RNA. Showing 1 copy in chain B [auth 2].