Cryo-EM structures of the 50S ribosome subunit bound with HflX
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
| Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
|---|---|---|---|---|---|
| D [auth 3] | SCOP2B Superfamily | L35p-like | 8035388 | 3000790 | SCOP2B (2022-06-29) |
| L [auth D] | SCOP2B Superfamily | Translational proteins | 8032955 | 3000811 | SCOP2B (2022-06-29) |
| M [auth E] | SCOP2B Superfamily | Ribosomal protein L4 | 8096356 | 3001146 | SCOP2B (2022-06-29) |
| O [auth G] | SCOP2B Superfamily | Ribosomal protein L6 | 8035398 | 3000724 | SCOP2B (2022-06-29) |
| O [auth G] | SCOP2B Superfamily | Ribosomal protein L6 | 8035397 | 3000724 | SCOP2B (2022-06-29) |
| P [auth H] | SCOP2B Superfamily | Ribosomal protein L9 C-domain | 8032958 | 3000329 | SCOP2B (2022-06-29) |
| P [auth H] | SCOP2B Superfamily | L9 N-domain-like | 8032960 | 3000338 | SCOP2B (2022-06-29) |
| U [auth M] | SCOP2B Superfamily | Ribosomal protein L16p/L10e | 8096366 | 3000884 | SCOP2B (2022-06-29) |
| V [auth N] | SCOP2B Superfamily | Prokaryotic ribosomal protein L17 | 8035409 | 3000995 | SCOP2B (2022-06-29) |
| W [auth O] | SCOP2B Superfamily | Translational machinery components | 8032969 | 3000571 | SCOP2B (2022-06-29) |
| X [auth P] | SCOP2B Superfamily | Translation proteins SH3-like KOW motif containing domain | 8096364 | 3000334 | SCOP2B (2022-06-29) |
| Z [auth R] | SCOP2B Superfamily | l21p-like | 8096354 | 3002005 | SCOP2B (2022-06-29) |
| AA [auth S] | SCOP2B Superfamily | Ribosomal protein L22 | 8096336 | 3001078 | SCOP2B (2022-06-29) |
| GA [auth Y] | SCOP2B Superfamily | Ribosomal protein L29 (L29p) | 8096370 | 3000713 | SCOP2B (2022-06-29) |
| H [auth 7] | SCOP2B Superfamily | Ribosomal protein L10-like | 8079773 | 3000665 | SCOP2B (2022-06-29) |
| G [auth 6] | SCOP2 Family | 50S ribosome-binding GTPase-like | 8045448 | 4004038 | SCOP2 (2022-06-29) |
| G [auth 6] | SCOP2 Family | HflX N-terminal region-like | 8048335 | 4007677 | SCOP2 (2022-06-29) |
| G [auth 6] | SCOP2 Family | GTPase HFLX C-terminal domain-like | 8057021 | 4007680 | SCOP2 (2022-06-29) |
| G [auth 6] | SCOP2 Superfamily | Ras-like P-loop GTPases | 8057027 | 3002022 | SCOP2 (2022-06-29) |
| G [auth 6] | SCOP2 Superfamily | HflX N-terminal domain-like | 8057028 | 3002367 | SCOP2 (2022-06-29) |
| G [auth 6] | SCOP2 Superfamily | EF-G C-terminal domain-like | 8057026 | 3001287 | SCOP2 (2022-06-29) |
| G [auth 6] | SCOP2 Superfamily | HflX middle domain-like | 8057029 | 3002366 | SCOP2 (2022-06-29) |
| F [auth 5] | SCOP2B Superfamily | Ribosomal protein L1p/L10e-like | 8065348 | 3001911 | SCOP2B (2022-06-29) |
| E [auth 4] | SCOP2B Superfamily | Ribosomal protein L36 | 8035391 | 3001346 | SCOP2B (2022-06-29) |
| HA [auth Z] | SCOP2B Superfamily | Ribosomal protein L30p/L7e | 8096372 | 3001378 | SCOP2B (2022-06-29) |
| FA [auth X] | SCOP2B Superfamily | L28p-like | 8035424 | 3001966 | SCOP2B (2022-06-29) |
| EA [auth W] | SCOP2B Superfamily | Ribosomal L27 protein-like | 8096338 | 3000539 | SCOP2B (2022-06-29) |
| DA [auth V] | SCOP2B Superfamily | Ribosomal protein L25-like | 8042538 | 3001161 | SCOP2B (2022-06-29) |
| CA [auth U] | SCOP2B Superfamily | Translation proteins SH3-like KOW motif containing domain | 8096358 | 3000334 | SCOP2B (2022-06-29) |
| BA [auth T] | SCOP2B Superfamily | Ribosomal proteins S24e, L23 and L15e | 8035415 | 3000210 | SCOP2B (2022-06-29) |
| Y [auth Q] | SCOP2B Superfamily | Ribosomal protein L20 | 8096382 | 3000563 | SCOP2B (2022-06-29) |
| T [auth L] | SCOP2B Superfamily | Ribosomal proteins L15p and L18e | 8070553 | 3001045 | SCOP2B (2022-06-29) |
| B [auth 1] | SCOP2B Superfamily | Zn-binding ribosomal proteins | 8096362 | 3001320 | SCOP2B (2022-06-29) |
| S [auth K] | SCOP2B Superfamily | 50S Ribosomal protein L14-like | 8103358 | 3000433 | SCOP2B (2022-06-29) |
| R [auth J] | SCOP2B Superfamily | Ribosomal protein L13 | 8096350 | 3001134 | SCOP2B (2022-06-29) |
| Q [auth I] | SCOP2B Superfamily | Ribosomal protein L11, C-terminal domain | 8032961 | 3001186 | SCOP2B (2022-06-29) |
| Q [auth I] | SCOP2B Superfamily | Ribosomal L11/L12e N-terminal domain-like | 8032963 | 3000950 | SCOP2B (2022-06-29) |
| N [auth F] | SCOP2B Superfamily | RL5-like | 8096352 | 3001709 | SCOP2B (2022-06-29) |
| K [auth C] | SCOP2B Superfamily | Nucleic acid-binding proteins | 8035394 | 3000135 | SCOP2B (2022-06-29) |
| K [auth C] | SCOP2B Superfamily | Translation proteins SH3-like KOW motif containing domain | 8035393 | 3000334 | SCOP2B (2022-06-29) |
| A [auth 0] | SCOP2B Superfamily | Zn-binding ribosomal proteins | 8096380 | 3001320 | 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) |
|---|---|---|---|---|---|---|---|---|
| C [auth 2] | GET4 | e5ady21 | A: a/b three-layered sandwiches | X: PH domain-like | H: PH domain-like | T: PH domain-like | F: GET4 | ECOD (v294.1) |
| D [auth 3] | GET4 | e5ady31 | A: a/b three-layered sandwiches | X: PH domain-like | H: PH domain-like | T: PH domain-like | F: GET4 | ECOD (v294.1) |
| L [auth D] | PemK_toxin | e5adyD1 | A: a/b three-layered sandwiches | X: SH3 | H: SH3 | T: SH3 | F: PemK_toxin | ECOD (v294.1) |
| M [auth E] | HrpJ | e5adyE1 | A: a/b three-layered sandwiches | X: C-terminal additional helical subdomain in reovirus polymerase lambda3 | H: C-terminal additional helical subdomain in reovirus polymerase lambda3 | T: C-terminal additional helical subdomain in reovirus polymerase lambda3 | F: HrpJ | ECOD (v294.1) |
| O [auth G] | GET4 | e5adyG1 | A: a/b three-layered sandwiches | X: PH domain-like | H: PH domain-like | T: PH domain-like | F: GET4 | ECOD (v294.1) |
| P [auth H] | HrpJ | e5adyH1 | A: a/b three-layered sandwiches | X: C-terminal additional helical subdomain in reovirus polymerase lambda3 | H: C-terminal additional helical subdomain in reovirus polymerase lambda3 | T: C-terminal additional helical subdomain in reovirus polymerase lambda3 | F: HrpJ | ECOD (v294.1) |
| P [auth H] | PemK_toxin | e5adyH2 | A: a/b three-layered sandwiches | X: SH3 | H: SH3 | T: SH3 | F: PemK_toxin | ECOD (v294.1) |
| U [auth M] | Peptidase_C78 | e5adyM1 | A: a/b three-layered sandwiches | X: MocoBD/DmpA-related | H: ferredoxin-like domain in periplasmic region of MacB | T: ferredoxin-like domain in periplasmic region of MacB | F: Peptidase_C78 | ECOD (v294.1) |
| V [auth N] | GET4 | e5adyN1 | A: a/b three-layered sandwiches | X: PH domain-like | H: PH domain-like | T: PH domain-like | F: GET4 | ECOD (v294.1) |
| W [auth O] | HrpJ | e5adyO1 | A: a/b three-layered sandwiches | X: C-terminal additional helical subdomain in reovirus polymerase lambda3 | H: C-terminal additional helical subdomain in reovirus polymerase lambda3 | T: C-terminal additional helical subdomain in reovirus polymerase lambda3 | F: HrpJ | ECOD (v294.1) |
| X [auth P] | Peptidase_C78 | e5adyP1 | A: a/b three-layered sandwiches | X: MocoBD/DmpA-related | H: ferredoxin-like domain in periplasmic region of MacB | T: ferredoxin-like domain in periplasmic region of MacB | F: Peptidase_C78 | ECOD (v294.1) |
| Z [auth R] | HrpJ | e5adyR1 | A: a/b three-layered sandwiches | X: C-terminal additional helical subdomain in reovirus polymerase lambda3 | H: C-terminal additional helical subdomain in reovirus polymerase lambda3 | T: C-terminal additional helical subdomain in reovirus polymerase lambda3 | F: HrpJ | ECOD (v294.1) |
| AA [auth S] | GET4 | e5adyS1 | A: a/b three-layered sandwiches | X: PH domain-like | H: PH domain-like | T: PH domain-like | F: GET4 | ECOD (v294.1) |
| GA [auth Y] | GET4 | e5adyY1 | A: a/b three-layered sandwiches | X: PH domain-like | H: PH domain-like | T: PH domain-like | F: GET4 | ECOD (v294.1) |
| H [auth 7] | HrpJ | e5ady71 | A: a/b three-layered sandwiches | X: C-terminal additional helical subdomain in reovirus polymerase lambda3 | H: C-terminal additional helical subdomain in reovirus polymerase lambda3 | T: C-terminal additional helical subdomain in reovirus polymerase lambda3 | F: HrpJ | ECOD (v294.1) |
| G [auth 6] | PK_Tyr_Ser-Thr | e5ady61 | A: a/b three-layered sandwiches | X: Lipocalins/Streptavidin | H: Fibronectin type I module-like | T: Fibronectin type I module | F: PK_Tyr_Ser-Thr | ECOD (v294.1) |
| F [auth 5] | GET4 | e5ady51 | A: a/b three-layered sandwiches | X: PH domain-like | H: PH domain-like | T: PH domain-like | F: GET4 | ECOD (v294.1) |
| E [auth 4] | GET4 | e5ady41 | A: a/b three-layered sandwiches | X: PH domain-like | H: PH domain-like | T: PH domain-like | F: GET4 | ECOD (v294.1) |
| HA [auth Z] | HrpJ | e5adyZ1 | A: a/b three-layered sandwiches | X: C-terminal additional helical subdomain in reovirus polymerase lambda3 | H: C-terminal additional helical subdomain in reovirus polymerase lambda3 | T: C-terminal additional helical subdomain in reovirus polymerase lambda3 | F: HrpJ | ECOD (v294.1) |
| FA [auth X] | GET4 | e5adyX1 | A: a/b three-layered sandwiches | X: PH domain-like | H: PH domain-like | T: PH domain-like | F: GET4 | ECOD (v294.1) |
| EA [auth W] | GET4 | e5adyW1 | A: a/b three-layered sandwiches | X: PH domain-like | H: PH domain-like | T: PH domain-like | F: GET4 | ECOD (v294.1) |
| DA [auth V] | GET4 | e5adyV1 | A: a/b three-layered sandwiches | X: PH domain-like | H: PH domain-like | T: PH domain-like | F: GET4 | ECOD (v294.1) |
| CA [auth U] | GET4 | e5adyU1 | A: a/b three-layered sandwiches | X: PH domain-like | H: PH domain-like | T: PH domain-like | F: GET4 | ECOD (v294.1) |
| BA [auth T] | GET4 | e5adyT1 | A: a/b three-layered sandwiches | X: PH domain-like | H: PH domain-like | T: PH domain-like | F: GET4 | ECOD (v294.1) |
| Y [auth Q] | PemK_toxin | e5adyQ1 | A: a/b three-layered sandwiches | X: SH3 | H: SH3 | T: SH3 | F: PemK_toxin | ECOD (v294.1) |
| T [auth L] | PemK_toxin | e5adyL1 | A: a/b three-layered sandwiches | X: SH3 | H: SH3 | T: SH3 | F: PemK_toxin | ECOD (v294.1) |
| B [auth 1] | PemK_toxin | e5ady11 | A: a/b three-layered sandwiches | X: SH3 | H: SH3 | T: SH3 | F: PemK_toxin | ECOD (v294.1) |
| S [auth K] | GET4 | e5adyK1 | A: a/b three-layered sandwiches | X: PH domain-like | H: PH domain-like | T: PH domain-like | F: GET4 | ECOD (v294.1) |
| R [auth J] | GET4 | e5adyJ1 | A: a/b three-layered sandwiches | X: PH domain-like | H: PH domain-like | T: PH domain-like | F: GET4 | ECOD (v294.1) |
| Q [auth I] | GET4 | e5adyI1 | A: a/b three-layered sandwiches | X: PH domain-like | H: PH domain-like | T: PH domain-like | F: GET4 | ECOD (v294.1) |
| N [auth F] | HrpJ | e5adyF1 | A: a/b three-layered sandwiches | X: C-terminal additional helical subdomain in reovirus polymerase lambda3 | H: C-terminal additional helical subdomain in reovirus polymerase lambda3 | T: C-terminal additional helical subdomain in reovirus polymerase lambda3 | F: HrpJ | ECOD (v294.1) |
| K [auth C] | GET4 | e5adyC1 | A: a/b three-layered sandwiches | X: PH domain-like | H: PH domain-like | T: PH domain-like | F: GET4 | ECOD (v294.1) |
| A [auth 0] | HrpJ | e5ady01 | A: a/b three-layered sandwiches | X: C-terminal additional helical subdomain in reovirus polymerase lambda3 | H: C-terminal additional helical subdomain in reovirus polymerase lambda3 | T: C-terminal additional helical subdomain in reovirus polymerase lambda3 | F: HrpJ | ECOD (v294.1) |
Protein Family Annotation Pfam Database Homepage
| Chains | Accession | Name | Description | Comments | Source |
|---|---|---|---|---|---|
| C [auth 2] | PF00468 | Ribosomal protein L34 (Ribosomal_L34) | Ribosomal protein L34 | - | Family |
| D [auth 3] | PF01632 | Ribosomal protein L35 (Ribosomal_L35p) | Ribosomal protein L35 | - | Family |
| L [auth D] | PF00297 | Ribosomal protein L3 (Ribosomal_L3) | Ribosomal protein L3 | - | Family |
| M [auth E] | PF00573 | Ribosomal protein L4/L1 family (Ribosomal_L4) | Ribosomal protein L4/L1 family | - | Family |
| O [auth G] | PF00347 | Ribosomal protein L6 (Ribosomal_L6) | Ribosomal protein L6 | Domain | |
| P [auth H] | PF01281 | Ribosomal protein L9, N-terminal domain (Ribosomal_L9_N) | Ribosomal protein L9, N-terminal domain | Domain | |
| P [auth H] | PF03948 | Ribosomal protein L9, C-terminal domain (Ribosomal_L9_C) | Ribosomal protein L9, C-terminal domain | Domain | |
| U [auth M] | PF00252 | Ribosomal protein L16p/L10e (Ribosomal_L16) | Ribosomal protein L16p/L10e | Domain | |
| V [auth N] | PF01196 | Ribosomal protein L17 (Ribosomal_L17) | Ribosomal protein L17 | - | Family |
| X [auth P] | PF01245 | Ribosomal protein L19 (Ribosomal_L19) | Ribosomal protein L19 | - | Family |
| Z [auth R] | PF00829 | Ribosomal prokaryotic L21 protein (Ribosomal_L21p) | Ribosomal prokaryotic L21 protein | - | Family |
| AA [auth S] | PF00237 | Ribosomal protein L22p/L17e (Ribosomal_L22) | Ribosomal protein L22p/L17e | This family includes L22 from prokaryotes and chloroplasts and L17 from eukaryotes. | Domain |
| GA [auth Y] | PF00831 | Ribosomal L29 protein (Ribosomal_L29) | Ribosomal L29 protein | - | Family |
| H [auth 7] | PF00466 | Ribosomal protein L10 (Ribosomal_L10) | Ribosomal protein L10 | - | Family |
| G [auth 6] | PF19275 | HflX C-terminal domain (HflX_C) | HflX C-terminal domain | This entry represents the C-terminal domain of the HflX protein [1]. HflX binds to the intersubunit face of the 50S subunit. Its C-terminal domain (CTD) predominantly interacts with the NTD of uL11 at the bL12 stalk base. Truncation of the CTD rende ... | Domain |
| G [auth 6] | PF16360 | GTP-binding GTPase Middle Region (GTP-bdg_M) | GTP-binding GTPase Middle Region | - | Family |
| G [auth 6] | PF01926 | 50S ribosome-binding GTPase (MMR_HSR1) | 50S ribosome-binding GTPase | - | Family |
| G [auth 6] | PF13167 | GTP-binding GTPase N-terminal (GTP-bdg_N) | GTP-binding GTPase N-terminal | - | Family |
| F [auth 5] | PF00687 | Ribosomal protein L1p/L10e family (Ribosomal_L1) | Ribosomal protein L1p/L10e family | This family includes prokaryotic L1 and eukaryotic L10. | Domain |
| E [auth 4] | PF00444 | Ribosomal protein L36 (Ribosomal_L36) | Ribosomal protein L36 | Domain | |
| HA [auth Z] | PF00327 | Ribosomal protein L30p/L7e (Ribosomal_L30) | Ribosomal protein L30p/L7e | This family includes prokaryotic L30 and eukaryotic L7. | Domain |
| FA [auth X] | PF00830 | Ribosomal L28 family (Ribosomal_L28) | Ribosomal L28 family | - | Family |
| DA [auth V] | PF01386 | Ribosomal L25p family (Ribosomal_L25p) | Ribosomal L25p family | Ribosomal protein L25 is an RNA binding protein, that binds 5S rRNA. This family includes Ctc from B. subtilis Swiss:P14194, which is induced by stress. | Domain |
| CA [auth U] | PF17136 | Large ribosomal subunit protein uL24, C-terminal domain (ribosomal_L24) | Large ribosomal subunit protein uL24, C-terminal domain | This entry describes the C-terminal domain in large ribosomal subunit protein uL24 (also known as RPL26). RPL26 is one of the proteins from the large ribosomal subunit. In their mature form, these proteins have 103 to 150 amino-acid residues. RPL26 m ... | Domain |
| CA [auth U] | PF00467 | KOW motif (KOW) | KOW motif | - | Family |
| BA [auth T] | PF00276 | Ribosomal protein L23 (Ribosomal_L23) | Ribosomal protein L23 | - | Family |
| Y [auth Q] | PF00453 | Ribosomal protein L20 (Ribosomal_L20) | Ribosomal protein L20 | - | Family |
| T [auth L] | PF00828 | Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A (Ribosomal_L27A) | Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A | This family includes higher eukaryotic ribosomal 60S L27A, archaeal 50S L18e, prokaryotic 50S L15, fungal mitochondrial L10, plant L27A, mitochondrial L15 and chloroplast L18-3 proteins. | Domain |
| B [auth 1] | PF00471 | Ribosomal protein L33 (Ribosomal_L33) | Ribosomal protein L33 | - | Family |
| R [auth J] | PF00572 | Ribosomal protein L13 (Ribosomal_L13) | Ribosomal protein L13 | - | Family |
| Q [auth I] | PF03946 | Ribosomal protein L11, N-terminal domain (Ribosomal_L11_N) | Ribosomal protein L11, N-terminal domain | The N-terminal domain of Ribosomal protein L11 adopts an alpha/beta fold and is followed by the RNA binding C-terminal domain. | Domain |
| Q [auth I] | PF00298 | Ribosomal protein L11, RNA binding domain (Ribosomal_L11) | Ribosomal protein L11, RNA binding domain | Domain | |
| N [auth F] | PF00281 | Ribosomal protein L5 (Ribosomal_L5) | Ribosomal protein L5 | Domain | |
| N [auth F] | PF00673 | ribosomal L5P family C-terminus (Ribosomal_L5_C) | ribosomal L5P family C-terminus | This region is found associated with Pfam:PF00281. | Domain |
| K [auth C] | PF03947 | Ribosomal Proteins L2, C-terminal domain (Ribosomal_L2_C) | Ribosomal Proteins L2, C-terminal domain | Domain | |
| K [auth C] | PF00181 | Ribosomal Proteins L2, RNA binding N-terminal domain (Ribosomal_L2_N) | Ribosomal Proteins L2, RNA binding N-terminal domain | Domain | |
| A [auth 0] | PF01783 | Ribosomal L32p protein family (Ribosomal_L32p) | Ribosomal L32p protein family | - | Family |














