3J6B
Structure of the yeast mitochondrial large ribosomal subunit
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
Z | SCOP2 Family | Ribosomal protein L35p | 8098751 | 4003406 | SCOP2 (2022-06-29) |
Z | SCOP2 Superfamily | L35p-like | 8098752 | 3000790 | SCOP2 (2022-06-29) |
AA [auth 0] | SCOP2 Family | Ribosomal protein L36 | 8083317 | 4003715 | SCOP2 (2022-06-29) |
AA [auth 0] | SCOP2 Superfamily | Ribosomal protein L36 | 8083318 | 3001346 | SCOP2 (2022-06-29) |
C | SCOP2B Superfamily | Translational proteins | 8098614 | 3000811 | SCOP2B (2022-06-29) |
DA [auth 3] | SCOP2 Family | Mitochondrial ribosomal protein L27-like | 8045632 | 4004579 | SCOP2 (2022-06-29) |
DA [auth 3] | SCOP2 Superfamily | Mitochondrial ribosomal protein L27-like | 8053894 | 3002240 | SCOP2 (2022-06-29) |
H | SCOP2 Family | Ribosomal protein L13 | 8066070 | 4003623 | SCOP2 (2022-06-29) |
H | SCOP2 Superfamily | Ribosomal protein L13 | 8066071 | 3001134 | SCOP2 (2022-06-29) |
I | SCOP2 Family | Ribosomal protein L14 | 8072039 | 4001826 | SCOP2 (2022-06-29) |
I | SCOP2 Superfamily | 50S Ribosomal protein L14-like | 8072040 | 3000433 | SCOP2 (2022-06-29) |
Domain Annotation: ECOD Classification ECOD Database Homepage
Chains | Family Name | Domain Identifier | Architecture | Possible Homology | Homology | Topology | Family | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
V | PF21492 | e3j6bV1 | 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) |
J | PF00828 | e3j6bJ1 | 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) |
K | PF00252 | e3j6bK1 | 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) |
L | PF18502 | e3j6bL2 | A: alpha arrays | X: KaiA/RbsU domain-like | H: Mitochondrial 54S ribosomal protein L8 C-terminal domain (From Topology) | T: Mitochondrial 54S ribosomal protein L8 C-terminal domain | F: PF18502 | ECOD (1.6) |
L | PF01196 | e3j6bL1 | A: a+b two layers | X: Enolase-N/ribosomal protein | H: Prokaryotic ribosomal protein L17 (From Topology) | T: Prokaryotic ribosomal protein L17 | F: PF01196 | ECOD (1.6) |
M | PF01245 | e3j6bM1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: PF01245 | ECOD (1.6) |
N | PF00829 | e3j6bN1 | A: beta barrels | X: Ribosomal protein L21p (From Topology) | H: Ribosomal protein L21p (From Topology) | T: Ribosomal protein L21p | F: PF00829 | ECOD (1.6) |
O | PF00237 | e3j6bO1 | A: a+b two layers | X: Enolase-N/ribosomal protein | H: Ribosomal protein L22 (From Topology) | T: Ribosomal protein L22 | F: PF00237 | ECOD (1.6) |
P | PF00276 | e3j6bP1 | A: a+b two layers | X: Alpha-beta plaits | H: Ribosomal proteins S24e, L23 and L15e (From Topology) | T: Ribosomal proteins S24e, L23 and L15e | F: PF00276 | ECOD (1.6) |
Q | PF22682 | e3j6bQ1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: PF22682 | ECOD (1.6) |
R | PF18471 | e3j6bR2 | A: alpha arrays | X: Mitochondrial 54S ribosomal protein L2 (From Topology) | H: Mitochondrial 54S ribosomal protein L2 (From Topology) | T: Mitochondrial 54S ribosomal protein L2 | F: PF18471 | ECOD (1.6) |
R | PF01016 | e3j6bR1 | A: a+b complex topology | X: alpha/beta-Hammerhead/Barrel-sandwich hybrid | H: alpha/beta-Hammerhead/Barrel-sandwich hybrid | T: Ribosomal L27 protein | F: PF01016 | ECOD (1.6) |
S | PF00830 | e3j6bS1 | A: few secondary structure elements | X: Ribosomal protein bL28-related (From Homology) | H: Ribosomal protein bL28-related | T: Ribosomal protein L28 | F: PF00830 | ECOD (1.6) |
B | PF00181 | e3j6bB2 | 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 | e3j6bB1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: PF03947 | ECOD (1.6) |
T | PF06984 | e3j6bT1 | A: alpha bundles | X: Long alpha-hairpin | H: Ribosomal protein L29 (L29p) (From Topology) | T: Ribosomal protein L29 (L29p) | F: PF06984 | ECOD (1.6) |
U | PF00327 | e3j6bU1 | 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 | PF01783 | e3j6bW1 | A: few secondary structure elements | X: Rubredoxin-like | H: Rubredoxin-related | T: Rubredoxin-related | F: PF01783 | ECOD (1.6) |
X | F_UNCLASSIFIED | e3j6bX1 | A: few secondary structure elements | X: Rubredoxin-like | H: Rubredoxin-related | T: Rubredoxin-related | F: F_UNCLASSIFIED | ECOD (1.6) |
Y | PF00468 | e3j6bY1 | 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) |
Z | PF01632 | e3j6bZ1 | A: a+b two layers | X: Ribosomal protein L35p (From Topology) | H: Ribosomal protein L35p (From Topology) | T: Ribosomal protein L35p | F: PF01632 | ECOD (1.6) |
AA [auth 0] | PF00444 | e3j6b01 | 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) |
BA [auth 1] | PF01161 | e3j6b11 | A: beta sandwiches | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: PEBP-like | F: PF01161 | ECOD (1.6) |
CA [auth 2] | PF09812 | e3j6b21 | 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: PF09812 | ECOD (1.6) |
C | PF00297 | e3j6bC1 | A: beta barrels | X: cradle loop barrel | H: RIFT-related | T: Alanine racemase-C | F: PF00297 | ECOD (1.6) |
DA [auth 3] | PF09809 | e3j6b31 | 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 | e3j6b41 | A: a+b three layers | X: Thioredoxin-like | H: Thioredoxin-like (From Topology) | T: Thioredoxin-like | F: PF05047 | ECOD (1.6) |
FA [auth 5] | PF00636 | e3j6b51 | 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: PF00636 | ECOD (1.6) |
FA [auth 5] | PF00035 | e3j6b52 | 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] | PF11788 | e3j6b61 | A: a+b two layers | X: beta-Grasp | H: Nudix (From Topology) | T: Nudix | F: PF11788 | ECOD (1.6) |
HA [auth 7] | PF05046 | e3j6b71 | A: a+b two layers | X: Glucose permease domain IIB-like | H: eIF1-like (From Topology) | T: eIF1-like | F: PF05046 | ECOD (1.6) |
IA [auth 8] | PF10501 | e3j6b81 | A: alpha bundles | X: ACP-like | H: Acyl-carrier protein (ACP) (From Topology) | T: Acyl-carrier protein (ACP) | F: PF10501 | ECOD (1.6) |
JA [auth 9] | PF14622 | e3j6b91 | 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) |
KA [auth a] | PF12824 | e3j6ba1 | A: alpha arrays | X: HTH | H: HTH | T: tri-helical | F: PF12824 | ECOD (1.6) |
LA [auth b] | PF18126 | e3j6bb1 | 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) |
MA [auth c] | PF09784 | e3j6bc1 | 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) |
D | PF00573 | e3j6bD1 | 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) |
NA [auth d] | PF12829 | e3j6bd1 | 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) |
E | PF00281,PF00673 | e3j6bE1 | A: a+b two layers | X: Ribosomal protein L5 (From Topology) | H: Ribosomal protein L5 (From Topology) | T: Ribosomal protein L5 | F: PF00281,PF00673 | ECOD (1.6) |
F | PF00347 | e3j6bF1 | 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) |
G | PF01281 | e3j6bG1 | A: a+b two layers | X: L9 N-domain-like | H: L9 N-domain-like (From Topology) | T: L9 N-domain-like | F: PF01281 | ECOD (1.6) |
H | PF00572 | e3j6bH1 | 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) |
I | PF00238 | e3j6bI1 | 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) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
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 | |
PF12824 | Mitochondrial ribosomal protein subunit L20 (MRP-L20) | Mitochondrial ribosomal protein subunit L20 | This family is the essential mitochondrial ribosomal protein subunit L20 of fungi. | Domain | |
PF00828 | Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A (Ribosomal_L27A) | Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A | - | Family | |
PF00252 | Ribosomal protein L16p/L10e (Ribosomal_L16) | Ribosomal protein L16p/L10e | - | Domain | |
PF01196 | Ribosomal protein L17 (Ribosomal_L17) | Ribosomal protein L17 | - | Family | |
PF18502 | 54S ribosomal protein L8 C-terminal domain (Mrpl_C) | 54S ribosomal protein L8 C-terminal domain | This is the C-terminal domain of mitochondrial 54S ribosomal protein L8. | Domain | |
PF01245 | Ribosomal protein L19 (Ribosomal_L19) | Ribosomal protein L19 | - | Family | |
PF00829 | Ribosomal prokaryotic L21 protein (Ribosomal_L21p) | Ribosomal prokaryotic L21 protein | - | Family | |
PF00237 | Ribosomal protein L22p/L17e (Ribosomal_L22) | Ribosomal protein L22p/L17e | This family includes L22 from prokaryotes and chloroplasts and L17 from eukaryotes. | Domain | |
PF00276 | Ribosomal protein L23 (Ribosomal_L23) | Ribosomal protein L23 | - | Family | |
PF18471 | Ribosomal L27 protein C-terminal domain (Ribosomal_L27_C) | Ribosomal L27 protein C-terminal domain | This is the C-terminal domain of 54S ribosomal protein L2 (also known as Mitochondrial large ribosomal subunit protein bL27m). bL27 C-terminal region interacts with an expansion segment of 21S rRNA to form part of the central protuberance [1]. | Domain | |
PF00830 | Ribosomal L28 family (Ribosomal_L28) | Ribosomal L28 family | - | Family | |
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 | |
PF06984 | Mitochondrial 39-S ribosomal protein L47 (MRP-L47) (MRP-L47) | Mitochondrial 39-S ribosomal protein L47 (MRP-L47) | - | Family | |
PF00327 | Ribosomal protein L30p/L7e (Ribosomal_L30) | Ribosomal protein L30p/L7e | This family includes prokaryotic L30 and eukaryotic L7. | Domain | |
PF01783 | Ribosomal L32p protein family (Ribosomal_L32p) | Ribosomal L32p protein family | - | Family | |
PF00468 | Ribosomal protein L34 (Ribosomal_L34) | Ribosomal protein L34 | - | Family | |
PF01632 | Ribosomal protein L35 (Ribosomal_L35p) | Ribosomal protein L35 | - | 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 |
PF00297 | Ribosomal protein L3 (Ribosomal_L3) | Ribosomal protein L3 | - | Family | |
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] | PF00636 | Ribonuclease III domain (Ribonuclease_3) | Ribonuclease III domain | - | Family |
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] | 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 |
JA [auth 9] | PF00636 | Ribonuclease III domain (Ribonuclease_3) | Ribonuclease III domain | - | 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 | |
PF00281 | Ribosomal protein L5 (Ribosomal_L5) | Ribosomal protein L5 | - | Domain | |
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 | |
PF00572 | Ribosomal protein L13 (Ribosomal_L13) | Ribosomal protein L13 | - | Family | |
PF00238 | Ribosomal protein L14p/L23e (Ribosomal_L14) | Ribosomal protein L14p/L23e | - | Domain |