Cryo-EM structure of late human 39S mitoribosome assembly intermediates, state 1
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
| Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
|---|---|---|---|---|---|
| I [auth O] | SCOP2B Superfamily | Prokaryotic ribosomal protein L17 | 8033689 | 3000995 | SCOP2B (2022-06-29) |
| F [auth L] | SCOP2B Superfamily | 50S Ribosomal protein L14-like | 8072072 | 3000433 | SCOP2B (2022-06-29) |
| E [auth K] | SCOP2B Superfamily | Ribosomal protein L13 | 8100460 | 3001134 | SCOP2B (2022-06-29) |
| KA [auth u] | SCOP2B Superfamily | Nucleotidyltransferase-like | 8100396 | 3000129 | SCOP2B (2022-06-29) |
| C [auth F] | SCOP2B Superfamily | Ribosomal protein L4 | 8080706 | 3001146 | SCOP2B (2022-06-29) |
| W [auth 9] | SCOP2B Superfamily | Mitochondrial ribosomal protein L27-like | 8053893 | 3002240 | 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 O] | V-set | e7oi6O1 | A: a/b three-layered sandwiches | X: RNase A-like | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: V-set | ECOD (v294.1) |
| H [auth N] | V-set | e7oi6N1 | A: a/b three-layered sandwiches | X: RNase A-like | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: V-set | ECOD (v294.1) |
| G [auth M] | V-set | e7oi6M1 | A: a/b three-layered sandwiches | X: RNase A-like | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: V-set | ECOD (v294.1) |
| F [auth L] | V-set | e7oi6L1 | A: a/b three-layered sandwiches | X: RNase A-like | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: V-set | ECOD (v294.1) |
| XA [auth k] | V-set | e7oi6k1 | A: a/b three-layered sandwiches | X: RNase A-like | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: V-set | ECOD (v294.1) |
| E [auth K] | V-set | e7oi6K1 | A: a/b three-layered sandwiches | X: RNase A-like | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: V-set | ECOD (v294.1) |
| WA [auth J] | Cation_ATPase | e7oi6J1 | A: a/b three-layered sandwiches | X: RNase A-like | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: Cation_ATPase | ECOD (v294.1) |
| VA [auth I] | V-set | e7oi6I1 | A: a/b three-layered sandwiches | X: RNase A-like | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: V-set | ECOD (v294.1) |
| UA [auth 6] | V-set | e7oi661 | A: a/b three-layered sandwiches | X: RNase A-like | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: V-set | ECOD (v294.1) |
| TA [auth W] | V-set | e7oi6W1 | A: a/b three-layered sandwiches | X: RNase A-like | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: V-set | ECOD (v294.1) |
| SA [auth P] | V-set | e7oi6P1 | A: a/b three-layered sandwiches | X: RNase A-like | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: V-set | ECOD (v294.1) |
| ZA [auth 1] | V-set | e7oi611 | A: a/b three-layered sandwiches | X: RNase A-like | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: V-set | ECOD (v294.1) |
| QA [auth z] | V-set | e7oi6z1 | A: a/b three-layered sandwiches | X: RNase A-like | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: V-set | ECOD (v294.1) |
| PA [auth y] | V-set | e7oi6y1 | A: a/b three-layered sandwiches | X: RNase A-like | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: V-set | ECOD (v294.1) |
| OA [auth x] | V-set | e7oi6x1 | A: a/b three-layered sandwiches | X: RNase A-like | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: V-set | ECOD (v294.1) |
| D [auth H] | V-set | e7oi6H1 | A: a/b three-layered sandwiches | X: RNase A-like | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: V-set | ECOD (v294.1) |
| MA [auth w] | V-set | e7oi6w1 | A: a/b three-layered sandwiches | X: RNase A-like | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: V-set | ECOD (v294.1) |
| LA [auth v] | V-set | e7oi6v1 | A: a/b three-layered sandwiches | X: RNase A-like | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: V-set | ECOD (v294.1) |
| KA [auth u] | V-set | e7oi6u1 | A: a/b three-layered sandwiches | X: RNase A-like | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: V-set | ECOD (v294.1) |
| JA [auth s] | V-set | e7oi6s1 | A: a/b three-layered sandwiches | X: RNase A-like | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: V-set | ECOD (v294.1) |
| IA [auth r] | V-set | e7oi6r1 | A: a/b three-layered sandwiches | X: RNase A-like | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: V-set | ECOD (v294.1) |
| HA [auth q] | Cation_ATPase | e7oi6q1 | A: a/b three-layered sandwiches | X: RNase A-like | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: Cation_ATPase | ECOD (v294.1) |
| GA [auth p] | V-set | e7oi6p1 | A: a/b three-layered sandwiches | X: RNase A-like | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: V-set | ECOD (v294.1) |
| FA [auth o] | V-set | e7oi6o1 | A: a/b three-layered sandwiches | X: RNase A-like | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: V-set | ECOD (v294.1) |
| EA [auth j] | V-set | e7oi6j1 | A: a/b three-layered sandwiches | X: RNase A-like | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: V-set | ECOD (v294.1) |
| DA [auth i] | V-set | e7oi6i1 | A: a/b three-layered sandwiches | X: RNase A-like | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: V-set | ECOD (v294.1) |
| C [auth F] | V-set | e7oi6F1 | A: a/b three-layered sandwiches | X: RNase A-like | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: V-set | ECOD (v294.1) |
| CA [auth h] | V-set | e7oi6h1 | A: a/b three-layered sandwiches | X: RNase A-like | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: V-set | ECOD (v294.1) |
| BA [auth g] | V-set | e7oi6g1 | A: a/b three-layered sandwiches | X: RNase A-like | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: V-set | ECOD (v294.1) |
| AA [auth d] | V-set | e7oi6d1 | A: a/b three-layered sandwiches | X: RNase A-like | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: V-set | ECOD (v294.1) |
| Z [auth c] | V-set | e7oi6c1 | A: a/b three-layered sandwiches | X: RNase A-like | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: V-set | ECOD (v294.1) |
| Y [auth b] | V-set | e7oi6b1 | A: a/b three-layered sandwiches | X: RNase A-like | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: V-set | ECOD (v294.1) |
| X [auth a] | V-set | e7oi6a1 | A: a/b three-layered sandwiches | X: RNase A-like | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: V-set | ECOD (v294.1) |
| W [auth 9] | V-set | e7oi691 | A: a/b three-layered sandwiches | X: RNase A-like | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: V-set | ECOD (v294.1) |
| V [auth 7] | Cation_ATPase | e7oi671 | A: a/b three-layered sandwiches | X: RNase A-like | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: Cation_ATPase | ECOD (v294.1) |
| U [auth 5] | V-set | e7oi651 | A: a/b three-layered sandwiches | X: RNase A-like | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: V-set | ECOD (v294.1) |
| T [auth 2] | V-set | e7oi621 | A: a/b three-layered sandwiches | X: RNase A-like | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: V-set | ECOD (v294.1) |
| B [auth E] | Cation_ATPase | e7oi6E1 | A: a/b three-layered sandwiches | X: RNase A-like | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: Cation_ATPase | ECOD (v294.1) |
| S [auth 0] | V-set | e7oi601 | A: a/b three-layered sandwiches | X: RNase A-like | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: V-set | ECOD (v294.1) |
| R [auth Z] | V-set | e7oi6Z1 | A: a/b three-layered sandwiches | X: RNase A-like | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: V-set | ECOD (v294.1) |
| Q [auth Y] | V-set | e7oi6Y1 | A: a/b three-layered sandwiches | X: RNase A-like | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: V-set | ECOD (v294.1) |
| P [auth X] | V-set | e7oi6X1 | A: a/b three-layered sandwiches | X: RNase A-like | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: V-set | ECOD (v294.1) |
| O [auth V] | V-set | e7oi6V1 | A: a/b three-layered sandwiches | X: RNase A-like | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: V-set | ECOD (v294.1) |
| N [auth U] | V-set | e7oi6U1 | A: a/b three-layered sandwiches | X: RNase A-like | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: V-set | ECOD (v294.1) |
| M [auth T] | V-set | e7oi6T1 | A: a/b three-layered sandwiches | X: RNase A-like | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: V-set | ECOD (v294.1) |
| L [auth S] | V-set | e7oi6S1 | A: a/b three-layered sandwiches | X: RNase A-like | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: V-set | ECOD (v294.1) |
| K [auth R] | V-set | e7oi6R1 | A: a/b three-layered sandwiches | X: RNase A-like | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: V-set | ECOD (v294.1) |
| J [auth Q] | Cation_ATPase | e7oi6Q1 | A: a/b three-layered sandwiches | X: RNase A-like | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: Cation_ATPase | ECOD (v294.1) |
| A [auth D] | V-set | e7oi6D1 | A: a/b three-layered sandwiches | X: RNase A-like | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: V-set | ECOD (v294.1) |
Protein Family Annotation Pfam Database Homepage
| Chains | Accession | Name | Description | Comments | Source |
|---|---|---|---|---|---|
| I [auth O] | PF01196 | Ribosomal protein L17 (Ribosomal_L17) | Ribosomal protein L17 | - | Family |
| H [auth N] | PF00252 | Ribosomal protein L16p/L10e (Ribosomal_L16) | Ribosomal protein L16p/L10e | Domain | |
| G [auth M] | 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 |
| F [auth L] | PF00238 | Ribosomal protein L14p/L23e (Ribosomal_L14) | Ribosomal protein L14p/L23e | Domain | |
| E [auth K] | PF10780 | 39S ribosomal protein L53/MRP-L53 (MRP_L53) | 39S ribosomal protein L53/MRP-L53 | - | Family |
| E [auth K] | PF00572 | Ribosomal protein L13 (Ribosomal_L13) | Ribosomal protein L13 | - | Family |
| WA [auth J] | 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 |
| WA [auth J] | PF00298 | Ribosomal protein L11, RNA binding domain (Ribosomal_L11) | Ribosomal protein L11, RNA binding domain | Domain | |
| WA [auth J] | PF18699 | Mitoribosomal protein mL52 (MRPL52) | Mitoribosomal protein mL52 | - | Family |
| VA [auth I] | PF10244 | Mitochondrial ribosomal subunit (MRP-L51) | Mitochondrial ribosomal subunit | - | Family |
| VA [auth I] | PF00466 | Ribosomal protein L10 (Ribosomal_L10) | Ribosomal protein L10 | - | Family |
| UA [auth 6] | PF01161 | Phosphatidylethanolamine-binding protein (PBP) | Phosphatidylethanolamine-binding protein | Domain | |
| TA [auth W] | PF00550 | Phosphopantetheine attachment site (PP-binding) | Phosphopantetheine attachment site | A 4'-phosphopantetheine prosthetic group is attached through a serine. This prosthetic group acts as a a 'swinging arm' for the attachment of activated fatty acid and amino-acid groups. This domain forms a four helix bundle. This family includes memb ... | Domain |
| SA [auth P] | PF00861 | Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast (Ribosomal_L18p) | Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast | - | Family |
| QA [auth z], ZA [auth 1] | PF22435 | MRM3-like substrate binding domain (MRM3-like_sub_bind) | MRM3-like substrate binding domain | MRM3 catalyses the formation of 2'-O-methylguanosine at position 1370 Gm1370) in the 16S mitochondrial large subunit ribosomal RNA (mtLSU rRNA), a conserved modification in the peptidyl transferase domain of the mtLSU rRNA [1-3]. This entry represent ... | Domain |
| QA [auth z], ZA [auth 1] | PF00588 | SpoU rRNA Methylase family (SpoU_methylase) | SpoU rRNA Methylase family | - | Family |
| NA [auth A] | PF10210 | Mitochondrial 28S ribosomal protein S32 (MRP-S32) | Mitochondrial 28S ribosomal protein S32 | - | Family |
| D [auth H] | PF01281 | Ribosomal protein L9, N-terminal domain (Ribosomal_L9_N) | Ribosomal protein L9, N-terminal domain | Domain | |
| D [auth H] | 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 |
| D [auth H] | 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 |
| C [auth F] | PF00573 | Ribosomal protein L4/L1 family (Ribosomal_L4) | Ribosomal protein L4/L1 family | - | Family |
| U [auth 5] | PF07147 | Mitochondrial 28S ribosomal protein S30 (PDCD9) (PDCD9) | Mitochondrial 28S ribosomal protein S30 (PDCD9) | - | Family |
| B [auth E] | PF00297 | Ribosomal protein L3 (Ribosomal_L3) | Ribosomal protein L3 | - | Family |
| S [auth 0] | PF01783 | Ribosomal L32p protein family (Ribosomal_L32p) | Ribosomal L32p protein family | - | Family |
| R [auth Z] | PF00327 | Ribosomal protein L30p/L7e (Ribosomal_L30) | Ribosomal protein L30p/L7e | This family includes prokaryotic L30 and eukaryotic L7. | Domain |
| R [auth Z] | PF22435 | MRM3-like substrate binding domain (MRM3-like_sub_bind) | MRM3-like substrate binding domain | MRM3 catalyses the formation of 2'-O-methylguanosine at position 1370 Gm1370) in the 16S mitochondrial large subunit ribosomal RNA (mtLSU rRNA), a conserved modification in the peptidyl transferase domain of the mtLSU rRNA [1-3]. This entry represent ... | Domain |
| Q [auth Y] | PF01018 | GTP1/OBG (GTP1_OBG) | GTP1/OBG | The N-terminal domain of Swiss:P20964 has the OBG fold, which is formed by three glycine-rich regions inserted into a small 8-stranded beta-sandwich these regions form six left-handed collagen-like helices packed and H-bonded together. | Domain |
| Q [auth Y] | PF01926 | 50S ribosome-binding GTPase (MMR_HSR1) | 50S ribosome-binding GTPase | - | Family |
| Q [auth Y] | PF06984 | Mitochondrial 39-S ribosomal protein L47 (MRP-L47) (MRP-L47) | Mitochondrial 39-S ribosomal protein L47 (MRP-L47) | - | Family |
| P [auth X] | 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 |
| P [auth X] | PF00830 | Ribosomal L28 family (Ribosomal_L28) | Ribosomal L28 family | - | Family |
| O [auth V] | PF05347 | Complex 1 protein (LYR family) (Complex1_LYR) | Complex 1 protein (LYR family) | - | Family |
| O [auth V] | 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 |
| O [auth V] | PF00467 | KOW motif (KOW) | KOW motif | - | Family |
| N [auth U] | PF02410 | Ribosomal silencing factor during starvation (RsfS) | Ribosomal silencing factor during starvation | - | Family |
| N [auth U] | PF00276 | Ribosomal protein L23 (Ribosomal_L23) | Ribosomal protein L23 | - | Family |
| M [auth T] | PF00237 | Ribosomal protein L22p/L17e (Ribosomal_L22) | Ribosomal protein L22p/L17e | This family includes L22 from prokaryotes and chloroplasts and L17 from eukaryotes. | Domain |
| L [auth S] | PF00829 | Ribosomal prokaryotic L21 protein (Ribosomal_L21p) | Ribosomal prokaryotic L21 protein | - | Family |
| K [auth R] | PF01084 | Ribosomal protein S18 (Ribosomal_S18) | Ribosomal protein S18 | - | Family |
| K [auth R] | PF00453 | Ribosomal protein L20 (Ribosomal_L20) | Ribosomal protein L20 | - | Family |
| J [auth Q] | PF01245 | Ribosomal protein L19 (Ribosomal_L19) | Ribosomal protein L19 | - | Family |
| A [auth D] | PF03947 | Ribosomal Proteins L2, C-terminal domain (Ribosomal_L2_C) | Ribosomal Proteins L2, C-terminal domain | Domain | |
| A [auth D] | 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 |
| A [auth D] | PF00181 | Ribosomal Proteins L2, RNA binding N-terminal domain (Ribosomal_L2_N) | Ribosomal Proteins L2, RNA binding N-terminal domain | Domain |














