Cryo-EM structure of the human 39S mitoribosome with 10uM Tigecycline
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
| Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
|---|---|---|---|---|---|
| I [auth LM] | SCOP2B Superfamily | Ribosomal protein L13 | 8100460 | 3001134 | SCOP2B (2022-06-29) |
| E [auth LD] | SCOP2B Superfamily | Ribosomal protein L4 | 8080706 | 3001146 | SCOP2B (2022-06-29) |
| HA [auth Lo] | SCOP2B Superfamily | Mitochondrial ribosomal protein L27-like | 8053893 | 3002240 | SCOP2B (2022-06-29) |
| CA [auth Lj] | SCOP2B Superfamily | Ribosomal protein L36 | 8083324 | 3001346 | SCOP2B (2022-06-29) |
| Z [auth Lg] | SCOP2B Superfamily | Zn-binding ribosomal proteins | 8075050 | 3001320 | SCOP2B (2022-06-29) |
| M [auth LQ] | SCOP2B Superfamily | Prokaryotic ribosomal protein L17 | 8033689 | 3000995 | SCOP2B (2022-06-29) |
| J [auth LN] | SCOP2B Superfamily | 50S Ribosomal protein L14-like | 8072072 | 3000433 | 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 LM] | UCR_hinge | e8xt3LM1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: UCR_hinge | ECOD (v295.2) |
| H [auth LK] | UCR_hinge | e8xt3LK1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: UCR_hinge | ECOD (v295.2) |
| G [auth LJ] | UCR_hinge | e8xt3LJ1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: UCR_hinge | ECOD (v295.2) |
| F [auth LI] | UCR_hinge | e8xt3LI1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: UCR_hinge | ECOD (v295.2) |
| ZA [auth Sf] | UCR_hinge | e8xt3Sf1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: UCR_hinge | ECOD (v295.2) |
| YA [auth SR] | UCR_hinge | e8xt3SR1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: UCR_hinge | ECOD (v295.2) |
| XA [auth L8] | UCR_hinge | e8xt3L81 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: UCR_hinge | ECOD (v295.2) |
| E [auth LD] | UCR_hinge | e8xt3LD1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: UCR_hinge | ECOD (v295.2) |
| WA [auth L7] | UCR_hinge | e8xt3L71 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: UCR_hinge | ECOD (v295.2) |
| VA [auth L6] | UCR_hinge | e8xt3L61 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: UCR_hinge | ECOD (v295.2) |
| UA [auth L5] | UCR_hinge | e8xt3L51 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: UCR_hinge | ECOD (v295.2) |
| SA [auth L3] | UCR_hinge | e8xt3L31 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: UCR_hinge | ECOD (v295.2) |
| RA [auth Lz] | UCR_hinge | e8xt3Lz1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: UCR_hinge | ECOD (v295.2) |
| QA [auth Ly] | UCR_hinge | e8xt3Ly1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: UCR_hinge | ECOD (v295.2) |
| PA [auth Lx] | UCR_hinge | e8xt3Lx1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: UCR_hinge | ECOD (v295.2) |
| OA [auth Lw] | UCR_hinge | e8xt3Lw1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: UCR_hinge | ECOD (v295.2) |
| NA [auth Lv] | UCR_hinge | e8xt3Lv1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: UCR_hinge | ECOD (v295.2) |
| D [auth LC] | UCR_hinge | e8xt3LC1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: UCR_hinge | ECOD (v295.2) |
| MA [auth Lt] | UCR_hinge | e8xt3Lt1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: UCR_hinge | ECOD (v295.2) |
| LA [auth Ls] | UCR_hinge | e8xt3Ls1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: UCR_hinge | ECOD (v295.2) |
| KA [auth Lr] | UCR_hinge | e8xt3Lr1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: UCR_hinge | ECOD (v295.2) |
| JA [auth Lq] | UCR_hinge | e8xt3Lq1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: UCR_hinge | ECOD (v295.2) |
| IA [auth Lp] | UCR_hinge | e8xt3Lp1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: UCR_hinge | ECOD (v295.2) |
| HA [auth Lo] | UCR_hinge | e8xt3Lo1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: UCR_hinge | ECOD (v295.2) |
| GA [auth Ln] | UCR_hinge | e8xt3Ln1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: UCR_hinge | ECOD (v295.2) |
| FA [auth Lm] | UCR_hinge | e8xt3Lm1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: UCR_hinge | ECOD (v295.2) |
| EA [auth Ll] | UCR_hinge | e8xt3Ll1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: UCR_hinge | ECOD (v295.2) |
| DA [auth Lk] | UCR_hinge | e8xt3Lk1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: UCR_hinge | ECOD (v295.2) |
| C [auth LB] | UCR_hinge | e8xt3LB1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: UCR_hinge | ECOD (v295.2) |
| CA [auth Lj] | UCR_hinge | e8xt3Lj1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: UCR_hinge | ECOD (v295.2) |
| BA [auth Li] | UCR_hinge | e8xt3Li1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: UCR_hinge | ECOD (v295.2) |
| AA [auth Lh] | UCR_hinge | e8xt3Lh1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: UCR_hinge | ECOD (v295.2) |
| Z [auth Lg] | UCR_hinge | e8xt3Lg1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: UCR_hinge | ECOD (v295.2) |
| Y [auth Lf] | UCR_hinge | e8xt3Lf1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: UCR_hinge | ECOD (v295.2) |
| X [auth Ld] | UCR_hinge | e8xt3Ld1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: UCR_hinge | ECOD (v295.2) |
| W [auth Lu] | UCR_hinge | e8xt3Lu1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: UCR_hinge | ECOD (v295.2) |
| V [auth Lb] | UCR_hinge | e8xt3Lb1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: UCR_hinge | ECOD (v295.2) |
| U [auth La] | UCR_hinge | e8xt3La1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: UCR_hinge | ECOD (v295.2) |
| T [auth LX] | UCR_hinge | e8xt3LX1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: UCR_hinge | ECOD (v295.2) |
| S [auth LW] | UCR_hinge | e8xt3LW1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: UCR_hinge | ECOD (v295.2) |
| R [auth LV] | UCR_hinge | e8xt3LV1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: UCR_hinge | ECOD (v295.2) |
| Q [auth LU] | UCR_hinge | e8xt3LU1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: UCR_hinge | ECOD (v295.2) |
| P [auth LT] | UCR_hinge | e8xt3LT1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: UCR_hinge | ECOD (v295.2) |
| O [auth LS] | UCR_hinge | e8xt3LS1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: UCR_hinge | ECOD (v295.2) |
| N [auth LR] | UCR_hinge | e8xt3LR1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: UCR_hinge | ECOD (v295.2) |
| M [auth LQ] | UCR_hinge | e8xt3LQ1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: UCR_hinge | ECOD (v295.2) |
| L [auth LP] | UCR_hinge | e8xt3LP1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: UCR_hinge | ECOD (v295.2) |
| K [auth LO] | UCR_hinge | e8xt3LO1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: UCR_hinge | ECOD (v295.2) |
| J [auth LN] | UCR_hinge | e8xt3LN1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: UCR_hinge | ECOD (v295.2) |
Protein Family Annotation Pfam Database Homepage
| Chains | Accession | Name | Description | Comments | Source |
|---|---|---|---|---|---|
| I [auth LM] | PF00572 | Ribosomal protein L13 (Ribosomal_L13) | Ribosomal protein L13 | - | Family |
| H [auth LK] | 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 |
| H [auth LK] | PF00298 | Ribosomal protein L11, RNA binding domain (Ribosomal_L11) | Ribosomal protein L11, RNA binding domain | Domain | |
| G [auth LJ] | PF00466 | Ribosomal protein L10 (Ribosomal_L10) | Ribosomal protein L10 | - | Family |
| G [auth LJ] | PF00444 | Ribosomal protein L36 (Ribosomal_L36) | Ribosomal protein L36 | Domain | |
| F [auth LI] | PF01281 | Ribosomal protein L9, N-terminal domain (Ribosomal_L9_N) | Ribosomal protein L9, N-terminal domain | Domain | |
| F [auth LI] | PF25131 | Large ribosomal subunit protein bL9m N-terminal domain (bL9m_N) | Large ribosomal subunit protein bL9m N-terminal domain | This is a presumed domain found at the very N-terminal of Large ribosomal subunit protein bL9m from animals, a structural component of the large subunit of the ribosome. According to structure predictions, it may consist in a hairpin with two beta-sh ... | Domain |
| F [auth LI] | PF01632 | Ribosomal protein L35 (Ribosomal_L35p) | Ribosomal protein L35 | - | Family |
| YA [auth SR] | PF01084 | Ribosomal protein S18 (Ribosomal_S18) | Ribosomal protein S18 | - | Family |
| E [auth LD] | PF00327 | Ribosomal protein L30p/L7e (Ribosomal_L30) | Ribosomal protein L30p/L7e | This family includes prokaryotic L30 and eukaryotic L7. | Domain |
| E [auth LD] | PF00573 | Ribosomal protein L4/L1 family (Ribosomal_L4) | Ribosomal protein L4/L1 family | - | Family |
| VA [auth L6] | PF14978 | Mitochondrial ribosome protein 63 (MRP-63) | Mitochondrial ribosome protein 63 | - | Family |
| TA [auth L4] | PF08561 | Mitochondrial ribosomal protein L37 (Ribosomal_L37) | Mitochondrial ribosomal protein L37 | - | Family |
| SA [auth L3] | PF10780 | 39S ribosomal protein L53/MRP-L53 (MRP_L53) | 39S ribosomal protein L53/MRP-L53 | - | Family |
| D [auth LC] | PF00297 | Ribosomal protein L3 (Ribosomal_L3) | Ribosomal protein L3 | - | Family |
| C [auth LB] | PF03947 | Ribosomal Proteins L2, C-terminal domain (Ribosomal_L2_C) | Ribosomal Proteins L2, C-terminal domain | Domain | |
| C [auth LB] | PF00181 | Ribosomal Proteins L2, RNA binding N-terminal domain (Ribosomal_L2_N) | Ribosomal Proteins L2, RNA binding N-terminal domain | Domain | |
| C [auth LB] | PF00830 | Ribosomal L28 family (Ribosomal_L28) | Ribosomal L28 family | - | Family |
| T [auth LX] | 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 |
| T [auth LX] | PF10501 | Ribosomal subunit 39S (Ribosomal_L50) | Ribosomal subunit 39S | The 39S ribosomal protein appears to be a subunit of one of the larger mitochondrial 66S or 70S units [1]. Under conditions of ethanol-stress in rats the larger subunit is largely dissociated into its smaller components [2]. In E. coli, in the absenc ... | Domain |
| T [auth LX] | PF00467 | KOW motif (KOW) | KOW motif | - | Family |
| S [auth LW] | PF05046 | Mitochondrial large subunit ribosomal protein (Img2) (Img2) | Mitochondrial large subunit ribosomal protein (Img2) | This family of proteins have been identified as part of the mitochondrial large ribosomal subunit in yeast [1]. | Domain |
| S [auth LW] | PF00276 | Ribosomal protein L23 (Ribosomal_L23) | Ribosomal protein L23 | - | Family |
| R [auth LV] | PF00237 | Ribosomal protein L22p/L17e (Ribosomal_L22) | Ribosomal protein L22p/L17e | This family includes L22 from prokaryotes and chloroplasts and L17 from eukaryotes. | Domain |
| R [auth LV] | PF00338 | Ribosomal protein S10p/S20e (Ribosomal_S10) | Ribosomal protein S10p/S20e | This family includes small ribosomal subunit S10 from prokaryotes and S20 from eukaryotes. | Domain |
| Q [auth LU] | PF00829 | Ribosomal prokaryotic L21 protein (Ribosomal_L21p) | Ribosomal prokaryotic L21 protein | - | Family |
| Q [auth LU] | PF06984 | Mitochondrial 39-S ribosomal protein L47 (MRP-L47) (MRP-L47) | Mitochondrial 39-S ribosomal protein L47 (MRP-L47) | - | Family |
| P [auth LT] | PF00453 | Ribosomal protein L20 (Ribosomal_L20) | Ribosomal protein L20 | - | Family |
| P [auth LT] | PF11788 | 39S mitochondrial ribosomal protein L46 (MRP-L46) | 39S mitochondrial ribosomal protein L46 | - | Family |
| O [auth LS] | PF04280 | Tim44-like domain (Tim44) | Tim44-like domain | Tim44 is an essential component of the machinery that mediates the translocation of nuclear-encoded proteins across the mitochondrial inner membrane [1]. Tim44 is thought to bind phospholipids of the mitochondrial inner membrane both by electrostati ... | Domain |
| O [auth LS] | PF01245 | Ribosomal protein L19 (Ribosomal_L19) | Ribosomal protein L19 | - | Family |
| N [auth LR] | PF22935 | Large ribosomal subunit protein mL44, endonuclease domain (RM44_endonuclase) | Large ribosomal subunit protein mL44, endonuclease domain | Large ribosomal subunit protein mL44 (RM44) is a component of the 39S subunit of mitochondrial ribosome. It may play a role in the assembly/stability of nascent mitochondrial polypeptides exiting the ribosome. This entry represents the endonuclease ( ... | Domain |
| N [auth LR] | PF00861 | Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast (Ribosomal_L18p) | Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast | - | Family |
| M [auth LQ] | PF01196 | Ribosomal protein L17 (Ribosomal_L17) | Ribosomal protein L17 | - | Family |
| M [auth LQ] | PF05047 | Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain (L51_S25_CI-B8) | Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain | The proteins in this family are located in the mitochondrion. The family includes ribosomal protein L51, and S25. This family also includes mitochondrial NADH-ubiquinone oxidoreductase B8 subunit (CI-B8) EC:1.6.5.3. It is not known whether all member ... | Domain |
| L [auth LP] | PF10210 | Mitochondrial 28S ribosomal protein S32 (MRP-S32) | Mitochondrial 28S ribosomal protein S32 | - | Family |
| L [auth LP] | PF00252 | Ribosomal protein L16p/L10e (Ribosomal_L16) | Ribosomal protein L16p/L10e | Domain | |
| K [auth LO] | 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 |
| J [auth LN] | PF00238 | Ribosomal protein L14p/L23e (Ribosomal_L14) | Ribosomal protein L14p/L23e | Domain | |














