Cryo-EM structure of the 90S pre-ribosome from Saccharomyces cerevisiae, state Post-A1
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
| Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
|---|---|---|---|---|---|
| KB [auth Dc] | SCOP2B Superfamily | Nucleic acid-binding proteins | 8063430 | 3000135 | SCOP2B (2022-06-29) |
| HB [auth DW] | SCOP2B Superfamily | Ribosomal protein S8 | 8096922 | 3000709 | SCOP2B (2022-06-29) |
| EB [auth DQ] | SCOP2B Superfamily | Ribosomal protein S5 domain 2-like | 8103366 | 3000100 | SCOP2B (2022-06-29) |
| DB [auth DO] | SCOP2B Superfamily | Translational machinery components | 8095805 | 3000571 | SCOP2B (2022-06-29) |
| CB [auth DN] | SCOP2B Superfamily | S15/NS1 RNA-binding domain | 8052974 | 3001284 | SCOP2B (2022-06-29) |
| CB [auth DN] | SCOP2B Superfamily | Homeodomain-like | 8052973 | 3000001 | SCOP2B (2022-06-29) |
| BB [auth DL] | SCOP2B Superfamily | Nucleic acid-binding proteins | 8052738 | 3000135 | SCOP2B (2022-06-29) |
| BB [auth DL] | SCOP2B Superfamily | Ribosomal S17 N-terminal domain-like | 8052736 | 3002138 | SCOP2B (2022-06-29) |
| ZA [auth DI] | SCOP2B Superfamily | 50S Ribosomal protein L14-like | 8053083 | 3000433 | SCOP2B (2022-06-29) |
| XA [auth DG] | SCOP2B Superfamily | GS N-terminal domain-like | 8053173 | 3000408 | SCOP2B (2022-06-29) |
| WA [auth DF] | SCOP2B Superfamily | Ribosomal protein S7 | 8065999 | 3000799 | SCOP2B (2022-06-29) |
| VA [auth DE] | SCOP2B Superfamily | Translation proteins SH3-like KOW motif containing domain | 8052760 | 3000334 | SCOP2B (2022-06-29) |
| VA [auth DE] | SCOP2B Superfamily | Nucleic acid-binding proteins | 8052759 | 3000135 | SCOP2B (2022-06-29) |
| VA [auth DE] | SCOP2B Superfamily | Alpha-L RNA-binding motif | 8052758 | 3001473 | SCOP2B (2022-06-29) |
| UA [auth DA] | SCOP2B Superfamily | Ribosomal S3Ae-like | 8053211 | 3002166 | SCOP2B (2022-06-29) |
| MA [auth JG] | SCOP2B Superfamily | alpha/beta knot | 8037153 | 3001122 | SCOP2B (2022-06-29) |
| LA [auth JF] | SCOP2B Superfamily | alpha/beta knot | 8037153 | 3001122 | SCOP2B (2022-06-29) |
| JA [auth CN] | SCOP2B Superfamily | RRP7 C-terminal domain-like | 8053722 | 3002219 | SCOP2B (2022-06-29) |
| JA [auth CN] | SCOP2B Superfamily | RNA-binding domain, RBD | 8053724 | 3000110 | SCOP2B (2022-06-29) |
| CA [auth CG] | SCOP2B Superfamily | L30e-like | 8033484 | 3001739 | SCOP2B (2022-06-29) |
| BA [auth CF] | SCOP2B Superfamily | L30e-like | 8033484 | 3001739 | SCOP2B (2022-06-29) |
| Y [auth CB] | SCOP2B Superfamily | S-adenosyl-L-methionine-dependent methyltransferases | 8063662 | 3000118 | SCOP2B (2022-06-29) |
| X [auth CA] | SCOP2B Superfamily | S-adenosyl-L-methionine-dependent methyltransferases | 8063662 | 3000118 | SCOP2B (2022-06-29) |
| V [auth UV] | SCOP2B Superfamily | PAP/OAS1 substrate-binding domain-like | 8053727 | 3000941 | SCOP2B (2022-06-29) |
| V [auth UV] | SCOP2B Superfamily | Nucleotidyltransferase-like | 8053726 | 3000129 | SCOP2B (2022-06-29) |
| V [auth UV] | SCOP2B Superfamily | Nucleotidyltransferase-like | 8053725 | 3000129 | SCOP2B (2022-06-29) |
| V [auth UV] | SCOP2B Superfamily | PAP/Archaeal CCA-adding enzyme C-terminal domain-like | 8053730 | 3001147 | SCOP2B (2022-06-29) |
| V [auth UV] | SCOP2B Superfamily | PAP/OAS1 substrate-binding domain-like | 8053728 | 3000941 | SCOP2B (2022-06-29) |
| V [auth UV] | SCOP2B Superfamily | PAP/Archaeal CCA-adding enzyme C-terminal domain-like | 8053729 | 3001147 | SCOP2B (2022-06-29) |
| M [auth UM] | SCOP2B Superfamily | UTPB complex component-like | 8061270 | 3002330 | SCOP2B (2022-06-29) |
Domain Annotation: ECOD Classification ECOD Database Homepage
| Chains | Family Name | Domain Identifier | Architecture | Possible Homology | Homology | Topology | Family | Provenance Source (Version) |
|---|---|---|---|---|---|---|---|---|
| I [auth UI] | Ribosomal_L4 | e6zqdUI1 | A: alpha arrays | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: Ribosomal_L4 | ECOD (v295) |
| G [auth UG] | MIF | e6zqdUG1 | A: alpha arrays | X: HTH | H: HTH | T: Three-helical HTH | F: MIF | ECOD (v295) |
| KB [auth Dc] | Ribosomal_L4 | e6zqdDc1 | A: alpha arrays | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: Ribosomal_L4 | ECOD (v295) |
| F [auth UF] | MIF | e6zqdUF1 | A: alpha arrays | X: HTH | H: HTH | T: Three-helical HTH | F: MIF | ECOD (v295) |
| JB [auth DY] | Ribosomal_L4 | e6zqdDY1 | A: alpha arrays | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: Ribosomal_L4 | ECOD (v295) |
| IB [auth DX] | Ribosomal_L4 | e6zqdDX1 | A: alpha arrays | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: Ribosomal_L4 | ECOD (v295) |
| HB [auth DW] | Ribosomal_L4 | e6zqdDW1 | A: alpha arrays | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: Ribosomal_L4 | ECOD (v295) |
| GB [auth DT] | Ribosomal_L4 | e6zqdDT1 | A: alpha arrays | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: Ribosomal_L4 | ECOD (v295) |
| FB [auth DS] | Ribosomal_L4 | e6zqdDS1 | A: alpha arrays | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: Ribosomal_L4 | ECOD (v295) |
| EB [auth DQ] | Ribosomal_L4 | e6zqdDQ1 | A: alpha arrays | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: Ribosomal_L4 | ECOD (v295) |
| DB [auth DO] | Ribosomal_L4 | e6zqdDO1 | A: alpha arrays | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: Ribosomal_L4 | ECOD (v295) |
| CB [auth DN] | Ribosomal_L4 | e6zqdDN1 | A: alpha arrays | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: Ribosomal_L4 | ECOD (v295) |
| BB [auth DL] | Ribosomal_L4 | e6zqdDL1 | A: alpha arrays | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: Ribosomal_L4 | ECOD (v295) |
| AB [auth DJ] | Ribosomal_L4 | e6zqdDJ1 | A: alpha arrays | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: Ribosomal_L4 | ECOD (v295) |
| E [auth UE] | Ribosomal_L4 | e6zqdUE1 | A: alpha arrays | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: Ribosomal_L4 | ECOD (v295) |
| ZA [auth DI] | Ribosomal_L4 | e6zqdDI1 | A: alpha arrays | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: Ribosomal_L4 | ECOD (v295) |
| YA [auth DH] | Ribosomal_L4 | e6zqdDH1 | A: alpha arrays | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: Ribosomal_L4 | ECOD (v295) |
| XA [auth DG] | Ribosomal_L4 | e6zqdDG1 | A: alpha arrays | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: Ribosomal_L4 | ECOD (v295) |
| WA [auth DF] | Ribosomal_L4 | e6zqdDF1 | A: alpha arrays | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: Ribosomal_L4 | ECOD (v295) |
| VA [auth DE] | Ribosomal_L4 | e6zqdDE1 | A: alpha arrays | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: Ribosomal_L4 | ECOD (v295) |
| UA [auth DA] | Ribosomal_L4 | e6zqdDA1 | A: alpha arrays | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: Ribosomal_L4 | ECOD (v295) |
| TA [auth JJ] | Ribosomal_L4 | e6zqdJJ1 | A: alpha arrays | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: Ribosomal_L4 | ECOD (v295) |
| SA [auth Db] | Ribosomal_L4 | e6zqdDb1 | A: alpha arrays | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: Ribosomal_L4 | ECOD (v295) |
| RA [auth JP] | MIF | e6zqdJP1 | A: alpha arrays | X: HTH | H: HTH | T: Three-helical HTH | F: MIF | ECOD (v295) |
| D [auth UD] | Ribosomal_L4 | e6zqdUD1 | A: alpha arrays | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: Ribosomal_L4 | ECOD (v295) |
| PA [auth JL] | Ribosomal_L4 | e6zqdJL1 | A: alpha arrays | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: Ribosomal_L4 | ECOD (v295) |
| OA [auth JI] | Ribosomal_L4 | e6zqdJI1 | A: alpha arrays | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: Ribosomal_L4 | ECOD (v295) |
| NA [auth JH] | Ribosomal_L4 | e6zqdJH1 | A: alpha arrays | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: Ribosomal_L4 | ECOD (v295) |
| MA [auth JG] | Ribosomal_L4 | e6zqdJG1 | A: alpha arrays | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: Ribosomal_L4 | ECOD (v295) |
| LA [auth JF] | Ribosomal_L4 | e6zqdJF1 | A: alpha arrays | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: Ribosomal_L4 | ECOD (v295) |
| KA [auth JD] | MIF | e6zqdJD1 | A: alpha arrays | X: HTH | H: HTH | T: Three-helical HTH | F: MIF | ECOD (v295) |
| JA [auth CN] | BNR, BNR_2 | e6zqdCN1 | A: alpha arrays | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: BNR, BNR_2 | ECOD (v295) |
| IA [auth CM] | Ribosomal_L4 | e6zqdCM1 | A: alpha arrays | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: Ribosomal_L4 | ECOD (v295) |
| HA [auth CL] | MIF | e6zqdCL1 | A: alpha arrays | X: HTH | H: HTH | T: Three-helical HTH | F: MIF | ECOD (v295) |
| FA [auth CJ] | MIF | e6zqdCJ1 | A: alpha arrays | X: HTH | H: HTH | T: Three-helical HTH | F: MIF | ECOD (v295) |
| EA [auth CI] | Pyr_redox_3 | e6zqdCI1 | A: alpha arrays | X: CNF1/YfiH-like putative cysteine hydrolases | H: RIFT-related | T: FMN-binding split barrel 2 | F: Pyr_redox_3 | ECOD (v295) |
| DA [auth CH] | PA14 | e6zqdCH1 | A: alpha arrays | X: DNA methylase specificity domain | H: Bromodomain | T: Bromodomain | F: PA14 | ECOD (v295) |
| CA [auth CG] | Ribosomal_L4 | e6zqdCG1 | A: alpha arrays | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: Ribosomal_L4 | ECOD (v295) |
| BA [auth CF] | Ribosomal_L4 | e6zqdCF1 | A: alpha arrays | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: Ribosomal_L4 | ECOD (v295) |
| AA [auth CE] | MIF | e6zqdCE1 | A: alpha arrays | X: HTH | H: HTH | T: Three-helical HTH | F: MIF | ECOD (v295) |
| Z [auth CD] | Ribosomal_L4 | e6zqdCD1 | A: alpha arrays | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: Ribosomal_L4 | ECOD (v295) |
| Y [auth CB] | Ribosomal_L4 | e6zqdCB1 | A: alpha arrays | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: Ribosomal_L4 | ECOD (v295) |
| X [auth CA] | Ribosomal_L4 | e6zqdCA1 | A: alpha arrays | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: Ribosomal_L4 | ECOD (v295) |
| W [auth UX] | Ribosomal_L4 | e6zqdUX1 | A: alpha arrays | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: Ribosomal_L4 | ECOD (v295) |
| V [auth UV] | Ribosomal_L4 | e6zqdUV1 | A: alpha arrays | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: Ribosomal_L4 | ECOD (v295) |
| U [auth UU] | MIF | e6zqdUU1 | A: alpha arrays | X: HTH | H: HTH | T: Three-helical HTH | F: MIF | ECOD (v295) |
| R [auth UR] | MIF | e6zqdUR1 | A: alpha arrays | X: HTH | H: HTH | T: Three-helical HTH | F: MIF | ECOD (v295) |
| O [auth UO] | e6zqdUO1 | A: alpha arrays | X: Nuclear receptor ligand-binding domain | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: | ECOD (v295) | |
| M [auth UM] | Ribosomal_L4 | e6zqdUM1 | A: alpha arrays | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: Ribosomal_L4 | ECOD (v295) |
| L [auth UL] | Ribosomal_L4 | e6zqdUL1 | A: alpha arrays | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: Ribosomal_L4 | ECOD (v295) |
| J [auth UJ] | MIF | e6zqdUJ1 | A: alpha arrays | X: HTH | H: HTH | T: Three-helical HTH | F: MIF | ECOD (v295) |
| A [auth UA] | Ribosomal_L4 | e6zqdUA1 | A: alpha arrays | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: Ribosomal_L4 | ECOD (v295) |
Protein Family Annotation Pfam Database Homepage
| Chains | Accession | Name | Description | Comments | Source |
|---|---|---|---|---|---|
| G [auth UG] | PF08149 | BING4CT (NUC141) domain (BING4CT) | BING4CT (NUC141) domain | - | Repeat |
| G [auth UG] | PF00400 | WD domain, G-beta repeat (WD40) | WD domain, G-beta repeat | - | Repeat |
| F [auth UF] | PF08640 | U3 small nucleolar RNA-associated protein 6 (U3_assoc_6) | U3 small nucleolar RNA-associated protein 6 | - | Repeat |
| F [auth UF] | PF23240 | PRP39 N-terminal HAT repeat (HAT_PRP39_N) | PRP39 N-terminal HAT repeat | - | Repeat |
| JB [auth DY] | PF01282 | Ribosomal protein S24e (Ribosomal_S24e) | Ribosomal protein S24e | - | Family |
| IB [auth DX] | PF00164 | Ribosomal protein S12/S23 (Ribosom_S12_S23) | Ribosomal protein S12/S23 | This protein is known as S12 in bacteria and archaea and S23 in eukaryotes. | Domain |
| HB [auth DW] | PF00410 | Ribosomal protein S8 (Ribosomal_S8) | Ribosomal protein S8 | Domain | |
| GB [auth DT] | PF01090 | Ribosomal protein S19e (Ribosomal_S19e) | Ribosomal protein S19e | - | Family |
| FB [auth DS] | PF00416 | Ribosomal protein S13/S18 (Ribosomal_S13) | Ribosomal protein S13/S18 | - | Family |
| EB [auth DQ] | PF00380 | Ribosomal protein S9/S16 (Ribosomal_S9) | Ribosomal protein S9/S16 | - | Family |
| DB [auth DO] | PF00411 | Ribosomal protein S11 (Ribosomal_S11) | Ribosomal protein S11 | - | Family |
| CB [auth DN] | PF00312 | Ribosomal protein S15 (Ribosomal_S15) | Ribosomal protein S15 | Domain | |
| BB [auth DL] | PF16205 | Ribosomal_S17 N-terminal (Ribosomal_S17_N) | Ribosomal_S17 N-terminal | - | Family |
| BB [auth DL] | PF00366 | Ribosomal protein S17 (Ribosomal_S17) | Ribosomal protein S17 | Domain | |
| AB [auth DJ] | PF00163 | Ribosomal protein S4/S9 N-terminal domain (Ribosomal_S4) | Ribosomal protein S4/S9 N-terminal domain | - | Family |
| AB [auth DJ] | PF01479 | S4 domain (S4) | S4 domain | The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast pro ... | Domain |
| E [auth UE] | PF04003 | Dip2/Utp12 Family (Utp12) | Dip2/Utp12 Family | - | Family |
| ZA [auth DI] | PF01201 | Ribosomal protein S8e (Ribosomal_S8e) | Ribosomal protein S8e | - | Family |
| YA [auth DH] | PF01251 | Ribosomal protein S7e (Ribosomal_S7e) | Ribosomal protein S7e | - | Family |
| XA [auth DG] | PF01092 | Ribosomal protein S6e (Ribosomal_S6e) | Ribosomal protein S6e | - | Family |
| VA [auth DE] | PF00900 | Ribosomal family S4e (Ribosomal_S4e) | Ribosomal family S4e | - | Family |
| VA [auth DE] | PF16121 | 40S ribosomal protein S4 C-terminus (40S_S4_C) | 40S ribosomal protein S4 C-terminus | - | Family |
| VA [auth DE] | PF08071 | RS4NT (NUC023) domain (RS4NT) | RS4NT (NUC023) domain | This is the N-terminal domain of Ribosomal S4 / S4e proteins. This domain is associated with S4 and KOW domains [1]. | Domain |
| VA [auth DE] | PF01479 | S4 domain (S4) | S4 domain | The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast pro ... | Domain |
| VA [auth DE] | PF00467 | KOW motif (KOW) | KOW motif | - | Family |
| UA [auth DA] | PF01015 | Ribosomal S3Ae family (Ribosomal_S3Ae) | Ribosomal S3Ae family | - | Family |
| TA [auth JJ] | PF17903 | Krr1 KH1 domain (KH_KRR1_1st) | Krr1 KH1 domain | This entry represents the first KH domain in the KRR1 protein [1]. Krr1 is a ribosomal assembly factor. The KH1 domain is a divergent KH domain that lacks the RNA-binding GXXG motif and is involved in binding another assembly factor, Kri1 [1]. | Domain |
| TA [auth JJ] | PF22891 | Eukaryotic type KH-domain (KH-domain type I) (KH_PNO1_2nd) | Eukaryotic type KH-domain (KH-domain type I) | This entry represents the second KH domain found in the PNO1 protein. PNO1 is part of the small subunit (SSU) processome, first precursor of the small eukaryotic ribosomal subunit. | Domain |
| RA [auth JP] | PF04158 | Sof1-like domain (Sof1) | Sof1-like domain | - | Family |
| RA [auth JP] | PF00400 | WD domain, G-beta repeat (WD40) | WD domain, G-beta repeat | - | Repeat |
| D [auth UD] | PF00400 | WD domain, G-beta repeat (WD40) | WD domain, G-beta repeat | - | Repeat |
| OA [auth JI] | PF23240 | PRP39 N-terminal HAT repeat (HAT_PRP39_N) | PRP39 N-terminal HAT repeat | - | Repeat |
| LA [auth JF], MA [auth JG] | PF03587 | EMG1/NEP1 methyltransferase (EMG1) | EMG1/NEP1 methyltransferase | - | Family |
| KA [auth JD] | PF04408 | Helicase associated domain (HA2), winged-helix (WHD_HA2) | Helicase associated domain (HA2), winged-helix | The helicase associated domain (HA2) has an all alpha-helical fold and consists of a N-terminal winged-helix (WH) domain and a C-terminal degenerate helical-bundle domain, referred to as the ratchet-like domain [1,2,3]. These domains collaborate wit ... | Domain |
| KA [auth JD] | PF07717 | Oligonucleotide/oligosaccharide-binding (OB)-fold (OB_NTP_bind) | Oligonucleotide/oligosaccharide-binding (OB)-fold | This family is found towards the C-terminus of the DEAD-box helicases (Pfam:PF00270). In these helicases it is apparently always found in association with Pfam:PF04408. There do seem to be a couple of instances where it occurs by itself - e.g. Swiss: ... | Domain |
| KA [auth JD] | PF00270 | DEAD/DEAH box helicase (DEAD) | DEAD/DEAH box helicase | Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome ... | Domain |
| KA [auth JD] | PF21010 | Helicase associated domain (HA2), ratchet-like (HA2_C) | Helicase associated domain (HA2), ratchet-like | The helicase associated domain (HA2) has an all alpha-helical fold and consists of a N-terminal winged-helix (WH) domain (Pfam:PF04408) and a C-terminal degenerate helical-bundle domain, referred to as the ratchet-like domain [1,2,3]. These domains c ... | Domain |
| JA [auth CN] | PF17799 | Rrp7 RRM-like N-terminal domain (RRM_Rrp7) | Rrp7 RRM-like N-terminal domain | This domain corresponds to the N-terminal RNA-binding domain found in the Rrp7 protein. It has an RRM-like fold with a circular permutation [1]. | Domain |
| JA [auth CN] | PF12923 | Ribosomal RNA-processing protein 7 (RRP7) C-terminal domain (RRP7) | Ribosomal RNA-processing protein 7 (RRP7) C-terminal domain | RRP7 is an essential protein in yeast that is involved in pre-rRNA processing and ribosome assembly [1]. It is speculated to be required for correct assembly of rpS27 into the pre-ribosomal particle [1-2]. | Domain |
| IA [auth CM] | PF05189 | RNA 3'-terminal phosphate cyclase (RTC), insert domain (RTC_insert) | RNA 3'-terminal phosphate cyclase (RTC), insert domain | RNA cyclases are a family of RNA-modifying enzymes that are conserved in all cellular organisms. They catalyse the ATP-dependent conversion of the 3'-phosphate to the 2',3'-cyclic phosphodiester at the end of RNA, in a reaction involving formation o ... | Domain |
| IA [auth CM] | PF01137 | RNA 3'-terminal phosphate cyclase (RTC) | RNA 3'-terminal phosphate cyclase | RNA cyclases are a family of RNA-modifying enzymes that are conserved in all cellular organisms. They catalyse the ATP-dependent conversion of the 3'-phosphate to the 2',3'-cyclic phosphodiester at the end of RNA, in a reaction involving formation o ... | Domain |
| HA [auth CL] | PF08142 | AARP2CN (NUC121) domain (AARP2CN) | AARP2CN (NUC121) domain | This domain is the central domain of AARP2. It is weakly similar to the GTP-binding domain of elongation factor TU [1]. | Domain |
| HA [auth CL] | PF00004 | ATPase family associated with various cellular activities (AAA) (AAA) | ATPase family associated with various cellular activities (AAA) | AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes [2]. | Domain |
| FA [auth CJ] | PF04427 | Brix domain (Brix) | Brix domain | Domain | |
| EA [auth CI] | PF00163 | Ribosomal protein S4/S9 N-terminal domain (Ribosomal_S4) | Ribosomal protein S4/S9 N-terminal domain | - | Family |
| EA [auth CI] | PF01479 | S4 domain (S4) | S4 domain | The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast pro ... | Domain |
| DA [auth CH] | PF00400 | WD domain, G-beta repeat (WD40) | WD domain, G-beta repeat | - | Repeat |
| BA [auth CF], CA [auth CG] | PF01248 | Ribosomal protein L7Ae/L30e/S12e/Gadd45 family (Ribosomal_L7Ae) | Ribosomal protein L7Ae/L30e/S12e/Gadd45 family | This family includes: Ribosomal L7A from metazoa, Ribosomal L8-A and L8-B from fungi, 30S ribosomal protein HS6 from archaebacteria, 40S ribosomal protein S12 from eukaryotes, Ribosomal protein L30 from eukaryotes and archaebacteria. Gadd45 and MyD11 ... | Domain |
| AA [auth CE] | PF08156 | NOP5NT (NUC127) domain (NOP5NT) | NOP5NT (NUC127) domain | This N terminal domain is found in RNA-binding proteins of the NOP5 family [1]. | Domain |
| AA [auth CE] | PF01798 | snoRNA binding domain, fibrillarin (Nop) | snoRNA binding domain, fibrillarin | - | Family |
| Z [auth CD] | PF08156 | NOP5NT (NUC127) domain (NOP5NT) | NOP5NT (NUC127) domain | This N terminal domain is found in RNA-binding proteins of the NOP5 family [1]. | Domain |
| Z [auth CD] | PF01798 | snoRNA binding domain, fibrillarin (Nop) | snoRNA binding domain, fibrillarin | - | Family |
| X [auth CA], Y [auth CB] | PF01269 | Fibrillarin (Fibrillarin) | Fibrillarin | Domain | |
| W [auth UX] | PF04900 | Fcf1 (Fcf1) | Fcf1 | Fcf1 is a nucleolar protein involved in pre-rRNA processing [1]. Depletion of yeast Fcf1 and Fcf2 leads to a decrease in synthesis of the 18S rRNA and results in a deficit in 40S ribosomal subunits [1]. | Domain |
| V [auth UV] | PF03813 | Nrap protein domain 1 (Nrap) | Nrap protein domain 1 | Members of this family are nucleolar RNA-associated proteins (Nrap) which are highly conserved from yeast (Saccharomyces cerevisiae) to human. In the mouse, Nrap is ubiquitously expressed and is specifically localised in the nucleolus [1]. Nrap is a ... | Domain |
| V [auth UV] | PF17403 | Nrap protein PAP/OAS-like domain (Nrap_D2) | Nrap protein PAP/OAS-like domain | Members of this family are nucleolar RNA-associated proteins (Nrap) which are highly conserved from yeast (Saccharomyces cerevisiae) to human. In the mouse, Nrap is ubiquitously expressed and is specifically localised in the nucleolus [1]. Nrap is a ... | Domain |
| V [auth UV] | PF17406 | Nrap protein PAP/OAS1-like domain 5 (Nrap_D5) | Nrap protein PAP/OAS1-like domain 5 | Members of this family are nucleolar RNA-associated proteins (Nrap) which are highly conserved from yeast (Saccharomyces cerevisiae) to human. In the mouse, Nrap is ubiquitously expressed and is specifically localised in the nucleolus [1]. Nrap is a ... | Domain |
| V [auth UV] | PF17407 | Nrap protein domain 6 (Nrap_D6) | Nrap protein domain 6 | Members of this family are nucleolar RNA-associated proteins (Nrap) which are highly conserved from yeast (Saccharomyces cerevisiae) to human. In the mouse, Nrap is ubiquitously expressed and is specifically localised in the nucleolus [1]. Nrap is a ... | Domain |
| V [auth UV] | PF17404 | Nrap protein domain 3 (Nrap_D3) | Nrap protein domain 3 | Members of this family are nucleolar RNA-associated proteins (Nrap) which are highly conserved from yeast (Saccharomyces cerevisiae) to human. In the mouse, Nrap is ubiquitously expressed and is specifically localised in the nucleolus [1]. Nrap is a ... | Domain |
| V [auth UV] | PF17405 | Nrap protein nucleotidyltransferase domain 4 (Nrap_D4) | Nrap protein nucleotidyltransferase domain 4 | Members of this family are nucleolar RNA-associated proteins (Nrap) which are highly conserved from yeast (Saccharomyces cerevisiae) to human. In the mouse, Nrap is ubiquitously expressed and is specifically localised in the nucleolus [1]. Nrap is a ... | Domain |
| U [auth UU] | PF04192 | Utp21 specific WD40 associated putative domain (Utp21) | Utp21 specific WD40 associated putative domain | Utp21 is a subunit of U3 snoRNP, which is essential for synthesis of 18S rRNA. | Domain |
| U [auth UU] | PF00400 | WD domain, G-beta repeat (WD40) | WD domain, G-beta repeat | - | Repeat |
| T [auth UT] | PF20416 | U3 small nucleolar RNA-associated protein 20 domain (UTP20) | U3 small nucleolar RNA-associated protein 20 domain | - | Repeat |
| T [auth UT] | PF07539 | U3 small nucleolar RNA-associated protein 20, N-terminal (UTP20_N) | U3 small nucleolar RNA-associated protein 20, N-terminal | - | Repeat |
| B [auth UB] | PF04147 | Nop14-like family (Nop14) | Nop14-like family | - | Family |
| S [auth US] | PF03914 | CBF/Mak21 family (CBF) | CBF/Mak21 family | - | Repeat |
| R [auth UR] | PF00400 | WD domain, G-beta repeat (WD40) | WD domain, G-beta repeat | - | Repeat |
| Q [auth UQ] | PF00400 | WD domain, G-beta repeat (WD40) | WD domain, G-beta repeat | - | Repeat |
| O [auth UO] | PF09384 | UTP15 C terminal (UTP15_C) | UTP15 C terminal | - | Family |
| O [auth UO] | PF00400 | WD domain, G-beta repeat (WD40) | WD domain, G-beta repeat | - | Repeat |
| M [auth UM] | PF00400 | WD domain, G-beta repeat (WD40) | WD domain, G-beta repeat | - | Repeat |
| M [auth UM] | PF08625 | Utp13 specific WD40 associated domain (Utp13) | Utp13 specific WD40 associated domain | Utp13 is a component of the five protein Pwp2 complex that forms part of a stable particle subunit independent of the U3 small nucleolar ribonucleoprotein that is essential for the initial assembly steps of the 90S pre-ribosome [1]. Pwp2 is capable o ... | Domain |
| L [auth UL] | PF04003 | Dip2/Utp12 Family (Utp12) | Dip2/Utp12 Family | - | Family |
| L [auth UL] | PF00400 | WD domain, G-beta repeat (WD40) | WD domain, G-beta repeat | - | Repeat |
| K [auth UK] | PF03998 | Utp11 protein (Utp11) | Utp11 protein | - | Family |
| J [auth UJ] | PF08146 | BP28CT (NUC211) domain (BP28CT) | BP28CT (NUC211) domain | This C terminal domain is found in BAP28-like nucleolar proteins [1]. | Domain |
| J [auth UJ] | PF12397 | U3 small nucleolar RNA-associated protein 10 (U3snoRNP10) | U3 small nucleolar RNA-associated protein 10 | - | Family |
| A [auth UA] | PF04003 | Dip2/Utp12 Family (Utp12) | Dip2/Utp12 Family | - | Family |
| A [auth UA] | PF00400 | WD domain, G-beta repeat (WD40) | WD domain, G-beta repeat | - | Repeat |














