6YWV
The structure of the Atp25 bound assembly intermediate of the mitoribosome from Neurospora crassa
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
J [auth I] | SCOP2 Family | Ribosomal protein L14 | 8101688 | 4001826 | SCOP2 (2021-05-27) |
J [auth I] | SCOP2 Superfamily | 50S Ribosomal protein L14-like | 8101689 | 3000433 | SCOP2 (2021-05-27) |
Y [auth X] | SCOP2B Superfamily | Zn-binding ribosomal proteins | 8101773 | 3001320 | SCOP2B (2021-05-27) |
AA [auth 0] | SCOP2 Family | Ribosomal protein L36 | 8101684 | 4003715 | SCOP2 (2021-05-27) |
AA [auth 0] | SCOP2 Superfamily | Ribosomal protein L36 | 8101685 | 3001346 | SCOP2 (2021-05-27) |
Domain Annotation: ECOD Classification ECOD Database Homepage
Chains | Family Name | Domain Identifier | Architecture | Possible Homology | Homology | Topology | Family | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
B | PF00181 | e6ywvB1 | A: beta barrels | X: OB-fold | H: Nucleic acid-binding proteins (From Topology) | T: Nucleic acid-binding proteins | F: PF00181 | ECOD (1.6) |
B | PF03947 | e6ywvB2 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: PF03947 | ECOD (1.6) |
D | PF00573 | e6ywvD1 | A: a/b three-layered sandwiches | X: Ribosomal protein L4 (From Topology) | H: Ribosomal protein L4 (From Topology) | T: Ribosomal protein L4 | F: PF00573 | ECOD (1.6) |
F | F_UNCLASSIFIED | e6ywvF2 | A: a+b two layers | X: Ribosomal protein L6 (From Topology) | H: Ribosomal protein L6 (From Topology) | T: Ribosomal protein L6 | F: F_UNCLASSIFIED | ECOD (1.6) |
F | PF00347 | e6ywvF1 | A: a+b two layers | X: Ribosomal protein L6 (From Topology) | H: Ribosomal protein L6 (From Topology) | T: Ribosomal protein L6 | F: PF00347 | ECOD (1.6) |
H [auth g] | PF00298 | e6ywvg1 | A: alpha arrays | X: HTH | H: HTH | T: Ribosomal protein L11, C-terminal domain | F: PF00298 | ECOD (1.6) |
H [auth g] | PF03946 | e6ywvg2 | A: a+b two layers | X: Ribosomal protein L11/L12e N-terminal domain-like | H: Ribosomal protein L11/L12e N-terminal domain (From Topology) | T: Ribosomal protein L11/L12e N-terminal domain | F: PF03946 | ECOD (1.6) |
I [auth H] | PF00572 | e6ywvH1 | A: a/b three-layered sandwiches | X: Ribosomal protein L13/L15p/L18e/L32e | H: Ribosomal protein L13 and L16-A (From Topology) | T: Ribosomal protein L13 and L16-A | F: PF00572 | ECOD (1.6) |
J [auth I] | PF00238 | e6ywvI1 | A: beta barrels | X: Ribosomal protein L14-like | H: Ribosomal protein L14-related (From Topology) | T: Ribosomal protein L14-related | F: PF00238 | ECOD (1.6) |
K [auth J] | PF00828 | e6ywvJ1 | A: a/b three-layered sandwiches | X: Ribosomal protein L13/L15p/L18e/L32e | H: Ribosomal proteins L15p and L18e (From Topology) | T: Ribosomal proteins L15p and L18e | F: PF00828 | ECOD (1.6) |
L [auth K] | PF00252 | e6ywvK1 | A: a+b complex topology | X: alpha/beta-Hammerhead/Barrel-sandwich hybrid | H: alpha/beta-Hammerhead/Barrel-sandwich hybrid | T: Ribosomal protein L10e | F: PF00252 | ECOD (1.6) |
O [auth N] | PF00829 | e6ywvN1 | A: beta barrels | X: Ribosomal protein L21p (From Topology) | H: Ribosomal protein L21p (From Topology) | T: Ribosomal protein L21p | F: PF00829 | ECOD (1.6) |
V [auth U] | PF00327 | e6ywvU1 | A: a+b two layers | X: Ribosomal protein L30p/L7e (From Topology) | H: Ribosomal protein L30p/L7e (From Topology) | T: Ribosomal protein L30p/L7e | F: PF00327 | ECOD (1.6) |
W [auth V] | PF21492 | e6ywvV1 | A: few secondary structure elements | X: Ribosomal protein L31p (From Topology) | H: Ribosomal protein L31p (From Topology) | T: Ribosomal protein L31p | F: PF21492 | ECOD (1.6) |
X [auth W] | PF01783 | e6ywvW1 | A: few secondary structure elements | X: Rubredoxin-like | H: Rubredoxin-related | T: Rubredoxin-related | F: PF01783 | ECOD (1.6) |
Y [auth X] | PF00471 | e6ywvX1 | A: few secondary structure elements | X: Rubredoxin-like | H: Rubredoxin-related | T: Rubredoxin-related | F: PF00471 | ECOD (1.6) |
Z [auth Y] | PF00468 | e6ywvY1 | A: extended segments | X: 50S ribosomal protein L34 (From Topology) | H: 50S ribosomal protein L34 (From Topology) | T: 50S ribosomal protein L34 | F: PF00468 | ECOD (1.6) |
AA [auth 0] | PF00444 | e6ywv01 | A: few secondary structure elements | X: Ribosomal protein L36 (From Topology) | H: Ribosomal protein L36 (From Topology) | T: Ribosomal protein L36 | F: PF00444 | ECOD (1.6) |
CA [auth 2] | F_UNCLASSIFIED | e6ywv21 | A: extended segments | X: Mitochondrial 54S ribosomal protein L28 (From Topology) | H: Mitochondrial 54S ribosomal protein L28 (From Topology) | T: Mitochondrial 54S ribosomal protein L28 | F: F_UNCLASSIFIED | ECOD (1.6) |
DA [auth 3] | PF09809 | e6ywv31 | A: extended segments | X: Mitochondrial 54S ribosomal protein L27 (From Topology) | H: Mitochondrial 54S ribosomal protein L27 (From Topology) | T: Mitochondrial 54S ribosomal protein L27 | F: PF09809 | ECOD (1.6) |
EA [auth 4] | PF05047 | e6ywv41 | A: a+b three layers | X: Thioredoxin-like | H: Thioredoxin-like (From Topology) | T: Thioredoxin-like | F: PF05047 | ECOD (1.6) |
FA [auth 5] | F_UNCLASSIFIED | e6ywv51 | A: alpha arrays | X: RNase III catalytic domain-like (From Topology) | H: RNase III catalytic domain-like (From Topology) | T: RNase III catalytic domain-like | F: F_UNCLASSIFIED | ECOD (1.6) |
FA [auth 5] | PF00035 | e6ywv52 | A: a+b two layers | X: dsRBD-like | H: dsRNA-binding domain-like (From Topology) | T: dsRNA-binding domain-like | F: PF00035 | ECOD (1.6) |
GA [auth 6] | PF00293,PF11788 | e6ywv61 | A: a+b two layers | X: beta-Grasp | H: Nudix (From Topology) | T: Nudix | F: PF00293,PF11788 | ECOD (1.6) |
HA [auth 7] | PF05046 | e6ywv71 | A: a+b two layers | X: Glucose permease domain IIB-like | H: eIF1-like (From Topology) | T: eIF1-like | F: PF05046 | ECOD (1.6) |
JA [auth h] | PF10780 | e6ywvh1 | A: a+b three layers | X: Thioredoxin-like | H: Thioredoxin-like (From Topology) | T: Thioredoxin-like | F: PF10780 | ECOD (1.6) |
LA [auth 9] | PF14622 | e6ywv91 | A: alpha arrays | X: RNase III catalytic domain-like (From Topology) | H: RNase III catalytic domain-like (From Topology) | T: RNase III catalytic domain-like | F: PF14622 | ECOD (1.6) |
MA [auth a] | PF12824 | e6ywva1 | A: alpha arrays | X: HTH | H: HTH | T: tri-helical | F: PF12824 | ECOD (1.6) |
NA [auth b] | PF18126 | e6ywvb1 | A: extended segments | X: Mitochondrial 54S ribosomal protein L25 (From Topology) | H: Mitochondrial 54S ribosomal protein L25 (From Topology) | T: Mitochondrial 54S ribosomal protein L25 | F: PF18126 | ECOD (1.6) |
OA [auth c] | PF09784 | e6ywvc1 | A: extended segments | X: Mitochondrial 54S ribosomal protein L31 (From Topology) | H: Mitochondrial 54S ribosomal protein L31 (From Topology) | T: Mitochondrial 54S ribosomal protein L31 | F: PF09784 | ECOD (1.6) |
PA [auth d] | PF12829 | e6ywvd1 | A: a+b three layers | X: Mitochondrial homologous recombination protein 1 (From Topology) | H: Mitochondrial homologous recombination protein 1 (From Topology) | T: Mitochondrial homologous recombination protein 1 | F: PF12829 | ECOD (1.6) |
QA [auth n] | PF02410 | e6ywvn1 | A: a+b three layers | X: Nucleotidyltransferase-like | H: Nucleotidyltransferase (From Topology) | T: Nucleotidyltransferase | F: PF02410 | ECOD (1.6) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
PF03947 | Ribosomal Proteins L2, C-terminal domain (Ribosomal_L2_C) | Ribosomal Proteins L2, C-terminal domain | - | Domain | |
PF00181 | Ribosomal Proteins L2, RNA binding domain (Ribosomal_L2) | Ribosomal Proteins L2, RNA binding domain | - | Domain | |
PF18126 | Mitochondrial ribosomal protein mL59 (Mitoc_mL59) | Mitochondrial ribosomal protein mL59 | This domain is a protein found in mitochondrial ribosome 54S large sub unit present in species such as Saccharomyces cerevisiae. The domain used to be referred to as MRP25 but is now called mL59 protein. mL59 is known to partially stabilize a change ... | Domain | |
PF00297 | Ribosomal protein L3 (Ribosomal_L3) | Ribosomal protein L3 | - | Family | |
PF12829 | Transcriptional regulation of mitochondrial recombination (Mhr1) | Transcriptional regulation of mitochondrial recombination | - | Family | |
PF00573 | Ribosomal protein L4/L1 family (Ribosomal_L4) | Ribosomal protein L4/L1 family | - | Family | |
PF00673 | ribosomal L5P family C-terminus (Ribosomal_L5_C) | ribosomal L5P family C-terminus | This region is found associated with Pfam:PF00281. | Domain | |
PF00347 | Ribosomal protein L6 (Ribosomal_L6) | Ribosomal protein L6 | - | Domain | |
I [auth H] | PF10780 | 39S ribosomal protein L53/MRP-L53 (MRP_L53) | 39S ribosomal protein L53/MRP-L53 | - | Family |
I [auth H] | PF00572 | Ribosomal protein L13 (Ribosomal_L13) | Ribosomal protein L13 | - | Family |
J [auth I] | PF00238 | Ribosomal protein L14p/L23e (Ribosomal_L14) | Ribosomal protein L14p/L23e | - | Domain |
K [auth J] | PF00828 | Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A (Ribosomal_L27A) | Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A | - | Family |
L [auth K] | PF00252 | Ribosomal protein L16p/L10e (Ribosomal_L16) | Ribosomal protein L16p/L10e | - | Domain |
M [auth L] | PF01196 | Ribosomal protein L17 (Ribosomal_L17) | Ribosomal protein L17 | - | Family |
N [auth M] | PF01245 | Ribosomal protein L19 (Ribosomal_L19) | Ribosomal protein L19 | - | Family |
O [auth N] | PF00829 | Ribosomal prokaryotic L21 protein (Ribosomal_L21p) | Ribosomal prokaryotic L21 protein | - | Family |
O [auth N] | PF02410 | Ribosomal silencing factor during starvation (RsfS) | Ribosomal silencing factor during starvation | - | Family |
P [auth O] | PF00237 | Ribosomal protein L22p/L17e (Ribosomal_L22) | Ribosomal protein L22p/L17e | This family includes L22 from prokaryotes and chloroplasts and L17 from eukaryotes. | Domain |
Q [auth P] | PF00276 | Ribosomal protein L23 (Ribosomal_L23) | Ribosomal protein L23 | - | Family |
R [auth Q] | PF22682 | Large ribosomal subunit protein uL24m (Ribosomal_uL24m-like) | Large ribosomal subunit protein uL24m | This entry represents a domain found in the homologues of large ribosomal subunit protein uL24m. This protein is a component of the mitochondrial ribosome (mitoribosome) [6]. | Domain |
R [auth Q] | PF00467 | KOW motif (KOW) | KOW motif | - | Family |
T [auth S] | PF00830 | Ribosomal L28 family (Ribosomal_L28) | Ribosomal L28 family | - | Family |
U [auth T] | PF06984 | Mitochondrial 39-S ribosomal protein L47 (MRP-L47) (MRP-L47) | Mitochondrial 39-S ribosomal protein L47 (MRP-L47) | - | Family |
V [auth U] | PF00327 | Ribosomal protein L30p/L7e (Ribosomal_L30) | Ribosomal protein L30p/L7e | This family includes prokaryotic L30 and eukaryotic L7. | Domain |
W [auth V] | PF21492 | Ribosomal protein L31p, N-terminal (bL31_N) | Ribosomal protein L31p, N-terminal | Ribosomal protein L31p (bL31, also known as 54S ribosomal protein L36), is a component of the mitochondrial ribosome. Overexpression of bL31m suppresses mutations in the COX2 leader peptide-encoding and initiation codon regions [1,2]. This entry repr ... | Domain |
X [auth W] | PF01783 | Ribosomal L32p protein family (Ribosomal_L32p) | Ribosomal L32p protein family | - | Family |
Y [auth X] | PF00471 | Ribosomal protein L33 (Ribosomal_L33) | Ribosomal protein L33 | - | Family |
Z [auth Y] | PF00468 | Ribosomal protein L34 (Ribosomal_L34) | Ribosomal protein L34 | - | Family |
AA [auth 0] | PF00444 | Ribosomal protein L36 (Ribosomal_L36) | Ribosomal protein L36 | - | Domain |
BA [auth 1] | PF01161 | Phosphatidylethanolamine-binding protein (PBP) | Phosphatidylethanolamine-binding protein | - | Domain |
DA [auth 3] | PF09809 | Mitochondrial ribosomal protein L27 (MRP-L27) | Mitochondrial ribosomal protein L27 | - | Family |
EA [auth 4] | 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 |
FA [auth 5] | PF00035 | Double-stranded RNA binding motif (dsrm) | Double-stranded RNA binding motif | Sequences gathered for seed by HMM_iterative_training Putative motif shared by proteins that bind to dsRNA. At least some DSRM proteins seem to bind to specific RNA targets. Exemplified by Staufen, which is involved in localisation of at least five d ... | Domain |
GA [auth 6] | PF00293 | NUDIX domain (NUDIX) | NUDIX domain | - | Domain |
GA [auth 6] | PF11788 | 39S mitochondrial ribosomal protein L46 (MRP-L46) | 39S mitochondrial ribosomal protein L46 | - | Family |
HA [auth 7] | 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 |
IA [auth 8] | 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 |
LA [auth 9] | PF14622 | Ribonuclease-III-like (Ribonucleas_3_3) | Ribonuclease-III-like | - | Family |