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Rnase R bound to a 30S degradation intermediate (state II)

Source organism: Bacillus subtilis subsp. subtilis str. 168
Biochemical function: structural constituent of ribosome
Biological process: translation
Cellular component: ribonucleoprotein complex

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EC 3.1.13.1: Exoribonuclease II

Reaction catalysed:
Exonucleolytic cleavage in the 3'- to 5'-direction to yield nucleoside 5'-phosphates
Systematic name:
-
Alternative Name(s):
  • 5'-exoribonuclease
  • BN ribonuclease
  • Escherichia coli exo-RNase II
  • Exoribonuclease
  • RNase II
  • Ribonuclease II
  • Ribonuclease Q

GO terms

Biochemical function:
Biological process:
Cellular component:

Sequence families

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

PF01084
Domain description: Ribosomal protein S18
Occurring in:
  1. Small ribosomal subunit protein bS18
The deposited structure of PDB entry 8cdv contains 1 copy of Pfam domain PF01084 (Ribosomal protein S18) in Small ribosomal subunit protein bS18. Showing 1 copy in chain R [auth U].

PF01250
Domain description: Ribosomal protein S6
Occurring in:
  1. Small ribosomal subunit protein bS6
The deposited structure of PDB entry 8cdv contains 1 copy of Pfam domain PF01250 (Ribosomal protein S6) in Small ribosomal subunit protein bS6. Showing 1 copy in chain Q [auth T].

PF01649
Domain description: Ribosomal protein S20
Occurring in:
  1. Small ribosomal subunit protein bS20
The deposited structure of PDB entry 8cdv contains 1 copy of Pfam domain PF01649 (Ribosomal protein S20) in Small ribosomal subunit protein bS20. Showing 1 copy in chain P [auth S].

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

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

PF00886
Domain description: Ribosomal protein S16
Occurring in:
  1. Small ribosomal subunit protein bS16
The deposited structure of PDB entry 8cdv contains 1 copy of Pfam domain PF00886 (Ribosomal protein S16) in Small ribosomal subunit protein bS16. Showing 1 copy in chain M [auth P].

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

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

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

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

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

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

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

PF03719
Domain description: Ribosomal protein S5, C-terminal domain
Occurring in:
  1. Small ribosomal subunit protein uS5
The deposited structure of PDB entry 8cdv contains 1 copy of Pfam domain PF03719 (Ribosomal protein S5, C-terminal domain) in Small ribosomal subunit protein uS5. Showing 1 copy in chain E [auth G].

PF00333
Domain description: Ribosomal protein S5, N-terminal domain
Occurring in:
  1. Small ribosomal subunit protein uS5
The deposited structure of PDB entry 8cdv contains 1 copy of Pfam domain PF00333 (Ribosomal protein S5, N-terminal domain) in Small ribosomal subunit protein uS5. Showing 1 copy in chain E [auth G].

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

PF00163
Domain description: Ribosomal protein S4/S9 N-terminal domain
Occurring in:
  1. Small ribosomal subunit protein uS4
The deposited structure of PDB entry 8cdv 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 D [auth F].

PF00575
Domain description: S1 RNA binding domain
Occurring in:
  1. Ribonuclease R
The deposited structure of PDB entry 8cdv contains 1 copy of Pfam domain PF00575 (S1 RNA binding domain) in Ribonuclease R. Showing 1 copy in chain C (this domain is out of the observed residue ranges!).

PF00773
Domain description: RNB domain
Occurring in:
  1. Ribonuclease R
The deposited structure of PDB entry 8cdv contains 1 copy of Pfam domain PF00773 (RNB domain) in Ribonuclease R. Showing 1 copy in chain C.

PF17876
Domain description: Cold shock domain
Occurring in:
  1. Ribonuclease R
The deposited structure of PDB entry 8cdv contains 1 copy of Pfam domain PF17876 (Cold shock domain) in Ribonuclease R. Showing 1 copy in chain C (this domain is out of the observed residue ranges!).

PF08206
Domain description: Ribonuclease B OB domain
Occurring in:
  1. Ribonuclease R
The deposited structure of PDB entry 8cdv contains 1 copy of Pfam domain PF08206 (Ribonuclease B OB domain) in Ribonuclease R. Showing 1 copy in chain C (this domain is out of the observed residue ranges!).

Rfam RNA family (Rfam)
RF00177
Domain description: Bacterial small subunit ribosomal RNA
Occurring in:
  1. 16S ribosomal RNA
The deposited structure of PDB entry 8cdv contains 1 copy of Rfam domain RF00177 (Bacterial small subunit ribosomal RNA) in 16S ribosomal RNA. Showing 1 copy in chain A.

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