6GAZ
Unique features of mammalian mitochondrial translation initiation revealed by cryo-EM. This file contains the 28S ribosomal subunit.
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
D [auth AB] | SCOP2B Superfamily | SIS domain/Ribosomal protein S2-like | 8063848 | 3001397 | SCOP2B (2022-06-29) |
K [auth AK] | SCOP2B Superfamily | Translational machinery components | 8096616 | 3000571 | SCOP2B (2022-06-29) |
M [auth AN] | SCOP2B Superfamily | Glucocorticoid receptor-like (DNA-binding domain) | 8052589 | 3000068 | SCOP2B (2022-06-29) |
R [auth AU] | SCOP2B Superfamily | Ribosomal protein S21 | 8083456 | 3002159 | SCOP2B (2022-06-29) |
V [auth Aa] | SCOP2B Superfamily | Mitochondrial 28S ribosomal protein S22-like | 8096620 | 3002074 | SCOP2B (2022-06-29) |
L [auth AL] | SCOP2B Superfamily | Nucleic acid-binding proteins | 8096284 | 3000135 | 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) |
---|---|---|---|---|---|---|---|---|
A [auth BC] | GTP_EFTU_D2_3 | e6gazBC1 | A: beta barrels | X: cradle loop barrel | H: RIFT-related | T: Alanine racemase-C | F: GTP_EFTU_D2_3 | ECOD (1.6) |
A [auth BC] | GTP_EFTU_D2 | e6gazBC4 | A: beta barrels | X: cradle loop barrel | H: RIFT-related | T: Alanine racemase-C | F: GTP_EFTU_D2 | ECOD (1.6) |
A [auth BC] | MnmE_helical_2nd | e6gazBC3 | A: a/b three-layered sandwiches | X: P-loop domains-like | H: P-loop domains-related | T: P-loop containing nucleoside triphosphate hydrolases | F: MnmE_helical_2nd | ECOD (1.6) |
A [auth BC] | IF-2 | e6gazBC2 | A: a/b three-layered sandwiches | X: Initiation factor IF2/eIF5b, domain 3 (From Topology) | H: Initiation factor IF2/eIF5b, domain 3 (From Topology) | T: Initiation factor IF2/eIF5b, domain 3 | F: IF-2 | ECOD (1.6) |
D [auth AB] | Ribosomal_S2_1 | e6gazAB1 | A: a/b three-layered sandwiches | X: Flavodoxin-like | H: Ribosomal protein S2/SIS domain (From Topology) | T: Ribosomal protein S2/SIS domain | F: Ribosomal_S2_1 | ECOD (1.6) |
E [auth AC] | MRP-S24 | e6gazAC1 | A: a+b two layers | X: Alpha-lytic protease prodomain-like | H: KH-domains | T: Prokaryotic type KH domain (KH-domain type II) | F: MRP-S24 | ECOD (1.6) |
F [auth AE] | Ribosomal_S5_C | e6gazAE3 | A: a+b two layers | X: Ribosomal protein S5 domain 2-like (From Topology) | H: Ribosomal protein S5 domain 2-like (From Topology) | T: Ribosomal protein S5 domain 2-like | F: Ribosomal_S5_C | ECOD (1.6) |
F [auth AE] | Ribosomal_S5_1 | e6gazAE1 | A: a+b two layers | X: dsRBD-like | H: dsRNA-binding domain-like (From Topology) | T: dsRNA-binding domain-like | F: Ribosomal_S5_1 | ECOD (1.6) |
F [auth AE] | KOG2646 | e6gazAE2 | A: extended segments | X: N-terminal region in 40S ribosomal protein rpS2 (S5p) (From Topology) | H: N-terminal region in 40S ribosomal protein rpS2 (S5p) (From Topology) | T: N-terminal region in 40S ribosomal protein rpS2 (S5p) | F: KOG2646 | ECOD (1.6) |
G [auth AF] | Ribosomal_S6_1 | e6gazAF1 | A: a+b two layers | X: Alpha-beta plaits | H: Ribosomal protein S6 (From Topology) | T: Ribosomal protein S6 | F: Ribosomal_S6_1 | ECOD (1.6) |
H [auth AG] | Ribosomal_S7 | e6gazAG1 | A: alpha arrays | X: Ribosomal protein S7 (From Topology) | H: Ribosomal protein S7 (From Topology) | T: Ribosomal protein S7 | F: Ribosomal_S7 | ECOD (1.6) |
I [auth AI] | Ribosomal_S9 | e6gazAI1 | A: a+b two layers | X: Ribosomal protein S5 domain 2-like (From Topology) | H: Ribosomal protein S5 domain 2-like (From Topology) | T: Ribosomal protein S5 domain 2-like | F: Ribosomal_S9 | ECOD (1.6) |
J [auth AJ] | Ribosomal_S10_2 | e6gazAJ1 | A: a+b two layers | X: Alpha-beta plaits | H: Ribosomal protein S10 (From Topology) | T: Ribosomal protein S10 | F: Ribosomal_S10_2 | ECOD (1.6) |
K [auth AK] | Ribosomal_S11 | e6gazAK1 | A: mixed a+b and a/b | X: Ribonuclease H-like | H: Ribonuclease H-like (From Topology) | T: Ribonuclease H-like | F: Ribosomal_S11 | ECOD (1.6) |
M [auth AN] | Ribosomal_S14_1 | e6gazAN1 | A: few secondary structure elements | X: Glucocorticoid receptor-like | H: LIM domain-like | T: LIM domain-like | F: Ribosomal_S14_1 | ECOD (1.6) |
N [auth AO] | Ribosomal_S15_1 | e6gazAO1 | A: alpha arrays | X: S15/NS1 RNA-binding domain (From Topology) | H: S15/NS1 RNA-binding domain (From Topology) | T: S15/NS1 RNA-binding domain | F: Ribosomal_S15_1 | ECOD (1.6) |
O [auth AP] | Ribosomal_S16 | e6gazAP1 | A: a+b two layers | X: Ribosomal protein S16 (From Topology) | H: Ribosomal protein S16 (From Topology) | T: Ribosomal protein S16 | F: Ribosomal_S16 | ECOD (1.6) |
P [auth AQ] | Ribosomal_S17_1 | e6gazAQ1 | A: beta barrels | X: OB-fold | H: Nucleic acid-binding proteins (From Topology) | T: Nucleic acid-binding proteins | F: Ribosomal_S17_1 | ECOD (1.6) |
Q [auth AR] | Ribosomal_S18 | e6gazAR1 | A: alpha arrays | X: HTH | H: HTH | T: tri-helical | F: Ribosomal_S18 | ECOD (1.6) |
R [auth AU] | Ribosomal_S21_2 | e6gazAU1 | A: extended segments | X: 30S ribosomal protein S21 (From Topology) | H: 30S ribosomal protein S21 (From Topology) | T: 30S ribosomal protein S21 | F: Ribosomal_S21_2 | ECOD (1.6) |
V [auth Aa] | MRP-S22 | e6gazAa1 | A: a+b complex topology | X: Mitoribosomal protein mS22 (From Topology) | H: Mitoribosomal protein mS22 (From Topology) | T: Mitoribosomal protein mS22 | F: MRP-S22 | ECOD (1.6) |
W [auth Ab] | MRP-S23 | e6gazAb1 | A: alpha arrays | X: RuvA-C | H: Mitoribosomal protein mS23 (From Topology) | T: Mitoribosomal protein mS23 | F: MRP-S23 | ECOD (1.6) |
X [auth Ac] | L51_S25_CI-B8 | e6gazAc1 | A: a+b three layers | X: Thioredoxin-like | H: Thioredoxin-like (From Topology) | T: Thioredoxin-like | F: L51_S25_CI-B8 | ECOD (1.6) |
AA [auth Af] | MRP-S35 | e6gazAf1 | A: beta barrels | X: OB-fold | H: Nucleic acid-binding proteins (From Topology) | T: Nucleic acid-binding proteins | F: MRP-S35 | ECOD (1.6) |
BA [auth Ag] | DAP3_C | e6gazAg1 | A: alpha arrays | X: Histone-like | H: Histone-related | T: AAA+ ATPase lid domain | F: DAP3_C | ECOD (1.6) |
BA [auth Ag] | DAP3_N | e6gazAg2 | A: a/b three-layered sandwiches | X: P-loop domains-like | H: P-loop domains-related | T: P-loop containing nucleoside triphosphate hydrolases | F: DAP3_N | ECOD (1.6) |
CA [auth Ah] | MRP-S31 | e6gazAh1 | A: extended segments | X: Mitoribosomal protein mS31 (From Topology) | H: Mitoribosomal protein mS31 (From Topology) | T: Mitoribosomal protein mS31 | F: MRP-S31 | ECOD (1.6) |
DA [auth Ai] | MRP-S33 | e6gazAi1 | A: extended segments | X: Mitoribosomal protein mS33 (From Topology) | H: Mitoribosomal protein mS33 (From Topology) | T: Mitoribosomal protein mS33 | F: MRP-S33 | ECOD (1.6) |
EA [auth Aj] | MRP-S34 | e6gazAj1 | A: beta barrels | X: SH3 | H: Mitoribosomal protein mS34 (From Topology) | T: Mitoribosomal protein mS34 | F: MRP-S34 | ECOD (1.6) |
FA [auth Ak] | UNK_F_TYPE | e6gazAk1 | A: a+b two layers | X: dsRBD-like | H: Peptidyl-tRNA hydrolase domain-like (From Topology) | T: Peptidyl-tRNA hydrolase domain-like | F: UNK_F_TYPE | ECOD (1.6) |
GA [auth Am] | KOG4695 | e6gazAm1 | A: few secondary structure elements | X: p8-MTCP1-related (From Topology) | H: p8-MTCP1-related (From Topology) | T: p8-MTCP1-related | F: KOG4695 | ECOD (1.6) |
HA [auth An] | DUF1713 | e6gazAn1 | A: extended segments | X: Mitoribosomal protein mS38 (From Topology) | H: Mitoribosomal protein mS38 (From Topology) | T: Mitoribosomal protein mS38 | F: DUF1713 | ECOD (1.6) |
JA [auth Ap] | Ribosomal_S18 | e6gazAp1 | A: alpha arrays | X: HTH | H: HTH | T: tri-helical | F: Ribosomal_S18 | ECOD (1.6) |
L [auth AL] | Ribosom_S12_S23 | e6gazAL1 | A: beta barrels | X: OB-fold | H: Nucleic acid-binding proteins (From Topology) | T: Nucleic acid-binding proteins | F: Ribosom_S12_S23 | ECOD (1.6) |
Y [auth Ad] | MRP-S26 | e6gazAd1 | A: extended segments | X: Mitoribosomal protein mS26 (From Topology) | H: Mitoribosomal protein mS26 (From Topology) | T: Mitoribosomal protein mS26 | F: MRP-S26 | ECOD (1.6) |
Z [auth Ae] | H2O2_YaaD,MRP-S27 | e6gazAe1 | A: alpha superhelices | X: Repetitive alpha hairpins | H: ARM repeat (From Topology) | T: ARM repeat | F: H2O2_YaaD,MRP-S27 | ECOD (1.6) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
A [auth BC] | PF00009 | Elongation factor Tu GTP binding domain (GTP_EFTU) | Elongation factor Tu GTP binding domain | This domain contains a P-loop motif, also found in several other families such as Pfam:PF00071, Pfam:PF00025 and Pfam:PF00063. Elongation factor Tu consists of three structural domains, this plus two C-terminal beta barrel domains. | Domain |
A [auth BC] | PF11987 | Translation-initiation factor 2 (IF-2) | Translation-initiation factor 2 | IF-2 is a translation initiator in each of the three main phylogenetic domains (Eukaryotes [1], Bacteria [2] and Archaea [3]). IF2 interacts with formylmethionine-tRNA, GTP, IF1, IF3 and both ribosomal subunits [2]. Through these interactions, IF2 pr ... | Domain |
D [auth AB] | PF00318 | Ribosomal protein S2 (Ribosomal_S2) | Ribosomal protein S2 | - | Family |
E [auth AC] | PF14955 | Mitochondrial ribosome subunit S24 (MRP-S24) | Mitochondrial ribosome subunit S24 | - | Family |
F [auth AE] | PF21251 | 40S ribosomal protein rpS2 (S5p), N-terminal (S5p_N) | 40S ribosomal protein rpS2 (S5p), N-terminal | This entry represents an extension found at the N-terminal of mammalian 28S ribosomal protein S5 [1,2]. This lines a part of the mRNA entry path and connects the 28S subunit body to the head forming a latch across the mRNA channel entrance [2]. | Domain |
F [auth AE] | PF03719 | Ribosomal protein S5, C-terminal domain (Ribosomal_S5_C) | Ribosomal protein S5, C-terminal domain | - | Domain |
F [auth AE] | PF00333 | Ribosomal protein S5, N-terminal domain (Ribosomal_S5) | Ribosomal protein S5, N-terminal domain | - | Domain |
G [auth AF] | PF01250 | Ribosomal protein S6 (Ribosomal_S6) | Ribosomal protein S6 | - | Domain |
H [auth AG] | PF00177 | Ribosomal protein S7p/S5e (Ribosomal_S7) | Ribosomal protein S7p/S5e | This family contains ribosomal protein S7 from prokaryotes and S5 from eukaryotes. | Domain |
I [auth AI] | PF00380 | Ribosomal protein S9/S16 (Ribosomal_S9) | Ribosomal protein S9/S16 | - | Family |
J [auth AJ] | 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 |
K [auth AK] | PF00411 | Ribosomal protein S11 (Ribosomal_S11) | Ribosomal protein S11 | - | Family |
M [auth AN] | PF00253 | Ribosomal protein S14p/S29e (Ribosomal_S14) | Ribosomal protein S14p/S29e | - | Family |
P [auth AQ] | PF00366 | Ribosomal protein S17 (Ribosomal_S17) | Ribosomal protein S17 | - | Domain |
Q [auth AR] | PF01084 | Ribosomal protein S18 (Ribosomal_S18) | Ribosomal protein S18 | - | Family |
R [auth AU] | PF01165 | Ribosomal protein S21 (Ribosomal_S21) | Ribosomal protein S21 | - | Family |
V [auth Aa] | PF10245 | Mitochondrial 28S ribosomal protein S22 (MRP-S22) | Mitochondrial 28S ribosomal protein S22 | - | Family |
W [auth Ab] | PF10484 | Mitochondrial ribosomal protein S23 (MRP-S23) | Mitochondrial ribosomal protein S23 | - | Family |
X [auth Ac] | 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 |
AA [auth Af] | PF10246 | Mitochondrial ribosomal protein MRP-S35 (MRP-S35) | Mitochondrial ribosomal protein MRP-S35 | - | Family |
BA [auth Ag] | PF10236 | Mitochondrial ribosomal death-associated protein 3 (DAP3) | Mitochondrial ribosomal death-associated protein 3 | - | Family |
DA [auth Ai] | PF08293 | Mitochondrial ribosomal subunit S27 (MRP-S33) | Mitochondrial ribosomal subunit S27 | - | Family |
FA [auth Ak] | PF10213 | Mitochondrial ribosomal subunit protein (MRP-S28) | Mitochondrial ribosomal subunit protein | - | Family |
GA [auth Am] | PF06747 | CHCH domain (CHCH) | CHCH domain | we have identified a conserved motif in the LOC118487 protein that we have called the CHCH motif. Alignment of this protein with related members showed the presence of three subgroups of proteins, which are called the S (Small), N (N-terminal extende ... | Domain |
HA [auth An] | PF08213 | Mitochondrial mRNA-processing protein COX24, C-terminal (COX24_C) | Mitochondrial mRNA-processing protein COX24, C-terminal | This domain of unknown function is found at the C terminal end of Mitochondrial small ribosomal subunit protein mS38, also known as Mitochondrial mRNA-processing protein COX24 in yeast which is involved in the splicing of the COX1 mRNA [1]. COX24 is ... | Domain |
IA [auth Ao] | PF13812 | Pentatricopeptide repeat domain (PPR_3) | Pentatricopeptide repeat domain | - | Repeat |
JA [auth Ap] | PF01084 | Ribosomal protein S18 (Ribosomal_S18) | Ribosomal protein S18 | - | Family |
L [auth AL] | PF00164 | Ribosomal protein S12/S23 (Ribosom_S12_S23) | Ribosomal protein S12/S23 | - | Family |
Z [auth Ae] | PF10037 | Mitochondrial 28S ribosomal protein S27 (MRP-S27) | Mitochondrial 28S ribosomal protein S27 | - | Repeat |
Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage
InterPro: Protein Family Classification InterPro Database Homepage
Pharos: Disease Associations Pharos Homepage Annotation
Chains | Drug Target   | Associated Disease |
---|---|---|
A [auth BC] | P46199 | :