3JCS
2.8 Angstrom cryo-EM structure of the large ribosomal subunit from the eukaryotic parasite Leishmania
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
K [auth C] | SCOP2 Family | 60S ribosomal protein L4 C-terminal domain-like | 8049945 | 4006700 | SCOP2 (2022-06-29) |
K [auth C] | SCOP2 Family | Ribosomal protein L4 | 8052824 | 4003628 | SCOP2 (2022-06-29) |
K [auth C] | SCOP2 Superfamily | 60S ribosomal protein L4 C-terminal domain-like | 8052825 | 3002143 | SCOP2 (2022-06-29) |
K [auth C] | SCOP2 Superfamily | Ribosomal protein L4 | 8052826 | 3001146 | SCOP2 (2022-06-29) |
L [auth D] | SCOP2B Superfamily | RL5-like | 8077509 | 3001709 | SCOP2B (2022-06-29) |
R [auth J] | SCOP2 Family | Ribosomal protein L14 | 8072045 | 4001826 | SCOP2 (2022-06-29) |
R [auth J] | SCOP2 Superfamily | 50S Ribosomal protein L14-like | 8072046 | 3000433 | SCOP2 (2022-06-29) |
R [auth J] | SCOP2B Superfamily | 50S Ribosomal protein L14-like | 8107090 | 3000433 | SCOP2B (2022-06-29) |
T [auth L] | SCOP2 Family | Ribosomal proteins L15p and L18e | 8077128 | 4003555 | SCOP2 (2022-06-29) |
T [auth L] | SCOP2 Superfamily | Ribosomal proteins L15p and L18e | 8077129 | 3001045 | SCOP2 (2022-06-29) |
T [auth L] | SCOP2B Superfamily | Ribosomal proteins L15p and L18e | 8107086 | 3001045 | SCOP2B (2022-06-29) |
U [auth M] | SCOP2 Family | L15e | 8082482 | 4000945 | SCOP2 (2022-06-29) |
U [auth M] | SCOP2 Superfamily | Ribosomal proteins S24e, L23 and L15e | 8082483 | 3000210 | SCOP2 (2022-06-29) |
V [auth N] | SCOP2B Superfamily | Ribosomal protein L16p/L10e | 8107098 | 3000884 | SCOP2B (2022-06-29) |
W [auth O] | SCOP2 Family | Ribosomal protein L5e and archael L18-like | 8049691 | 4006591 | SCOP2 (2022-06-29) |
W [auth O] | SCOP2 Superfamily | Translational machinery components | 8052892 | 3000571 | SCOP2 (2022-06-29) |
W [auth O] | SCOP2B Superfamily | Translational machinery components | 8107094 | 3000571 | SCOP2B (2022-06-29) |
X [auth P] | SCOP2 Family | Ribosomal proteins L15p and L18e | 8046516 | 4003555 | SCOP2 (2022-06-29) |
X [auth P] | SCOP2 Superfamily | Ribosomal proteins L15p and L18e | 8095981 | 3001045 | SCOP2 (2022-06-29) |
Y [auth Q] | SCOP2 Family | Ribosomal protein L19 (L19e) | 8077478 | 4001138 | SCOP2 (2022-06-29) |
Y [auth Q] | SCOP2 Superfamily | Ribosomal protein L19 (L19e) | 8077479 | 3000890 | SCOP2 (2022-06-29) |
BA [auth T] | SCOP2B Superfamily | Ribosomal protein L22 | 8107100 | 3001078 | SCOP2B (2022-06-29) |
CA [auth U] | SCOP2 Family | 60S Ribosomal protein L22e | 8049499 | 4006528 | SCOP2 (2022-06-29) |
CA [auth U] | SCOP2 Superfamily | 60S Ribosomal protein L22e | 8053066 | 3002158 | SCOP2 (2022-06-29) |
DA [auth V] | SCOP2 Family | L23p | 8061167 | 4000943 | SCOP2 (2022-06-29) |
DA [auth V] | SCOP2 Superfamily | Ribosomal proteins S24e, L23 and L15e | 8077083 | 3000210 | SCOP2 (2022-06-29) |
GA [auth Y] | SCOP2 Family | Ribosomal protein L27e | 8049510 | 4006529 | SCOP2 (2022-06-29) |
GA [auth Y] | SCOP2 Superfamily | Translation proteins SH3-like KOW motif containing domain | 8053056 | 3000334 | SCOP2 (2022-06-29) |
JA [auth b] | SCOP2 Family | Ribosomal protein L29e | 8049525 | 4006531 | SCOP2 (2022-06-29) |
JA [auth b] | SCOP2 Superfamily | Ribosomal protein L29e | 8053039 | 3002157 | SCOP2 (2022-06-29) |
KA [auth c] | SCOP2 Family | Ribosomal L30p/L7e protein, N-terminal domain-lke | 8050360 | 4006854 | SCOP2 (2022-06-29) |
KA [auth c] | SCOP2 Family | Ribosomal protein L30p/L7e | 8052942 | 4001360 | SCOP2 (2022-06-29) |
KA [auth c] | SCOP2 Superfamily | Ribosomal L30p/L7e protein, N-terminal domain-lke | 8052943 | 3002152 | SCOP2 (2022-06-29) |
KA [auth c] | SCOP2 Superfamily | Ribosomal protein L30p/L7e | 8052944 | 3001378 | SCOP2 (2022-06-29) |
LA [auth d] | SCOP2B Superfamily | L30e-like | 8107084 | 3001739 | SCOP2B (2022-06-29) |
NA [auth f] | SCOP2 Family | Ribosomal protein L32e | 8107243 | 4003517 | SCOP2 (2022-06-29) |
NA [auth f] | SCOP2 Superfamily | Ribosomal protein L32e | 8107244 | 3000982 | SCOP2 (2022-06-29) |
OA [auth g] | SCOP2B Superfamily | Translational proteins | 8107088 | 3000811 | SCOP2B (2022-06-29) |
PA [auth h] | SCOP2 Family | Ribosomal protein L34e-like | 8048733 | 4006193 | SCOP2 (2022-06-29) |
PA [auth h] | SCOP2 Superfamily | Ribosomal protein L34e-like | 8053539 | 3002203 | SCOP2 (2022-06-29) |
QA [auth i] | SCOP2 Family | Ribosomal protein L36e | 8048626 | 4006168 | SCOP2 (2022-06-29) |
QA [auth i] | SCOP2 Superfamily | Ribosomal protein L36e | 8053118 | 3002161 | SCOP2 (2022-06-29) |
SA [auth k] | SCOP2 Family | Ribosomal L38e protein-like | 8049537 | 4006532 | SCOP2 (2022-06-29) |
SA [auth k] | SCOP2 Superfamily | Ribosomal L38e protein-like | 8053568 | 3002206 | SCOP2 (2022-06-29) |
TA [auth l] | SCOP2 Family | ribosomal protein l39e | 8097699 | 4001518 | SCOP2 (2022-06-29) |
TA [auth l] | SCOP2 Superfamily | Ribosomal protein L39e | 8097700 | 3001756 | SCOP2 (2022-06-29) |
UA [auth m] | SCOP2B Superfamily | Zn-binding ribosomal proteins | 8101419 | 3001320 | 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 A] | Ribosomal_L2_1 | e3jcsA1 | A: beta barrels | X: OB-fold | H: Nucleic acid-binding proteins (From Topology) | T: Nucleic acid-binding proteins | F: Ribosomal_L2_1 | ECOD (1.6) |
I [auth A] | Ribosomal_L2_C_2 | e3jcsA2 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: Ribosomal_L2_C_2 | ECOD (1.6) |
J [auth B] | Ribosomal_L3 | e3jcsB1 | A: beta barrels | X: cradle loop barrel | H: RIFT-related | T: Alanine racemase-C | F: Ribosomal_L3 | ECOD (1.6) |
K [auth C] | Ribosomal_L4 | e3jcsC1 | A: a/b three-layered sandwiches | X: Ribosomal protein L4 (From Topology) | H: Ribosomal protein L4 (From Topology) | T: Ribosomal protein L4 | F: Ribosomal_L4 | ECOD (1.6) |
L [auth D] | Ribosomal_L5_C | e3jcsD1 | A: a+b two layers | X: Ribosomal protein L5 (From Topology) | H: Ribosomal protein L5 (From Topology) | T: Ribosomal protein L5 | F: Ribosomal_L5_C | ECOD (1.6) |
M [auth E] | Ribosomal_L6_2 | e3jcsE2 | A: a+b two layers | X: Ribosomal protein L6 (From Topology) | H: Ribosomal protein L6 (From Topology) | T: Ribosomal protein L6 | F: Ribosomal_L6_2 | ECOD (1.6) |
M [auth E] | Ribosomal_L6 | e3jcsE1 | A: a+b two layers | X: Ribosomal protein L6 (From Topology) | H: Ribosomal protein L6 (From Topology) | T: Ribosomal protein L6 | F: Ribosomal_L6 | ECOD (1.6) |
N [auth F] | Ribosomal_L6e | e3jcsF1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: Ribosomal_L6e | ECOD (1.6) |
O [auth G] | Ribosomal_L7Ae_1 | e3jcsG1 | A: a+b three layers | X: Bacillus chorismate mutase-like | H: L30e-like (From Topology) | T: L30e-like | F: Ribosomal_L7Ae_1 | ECOD (1.6) |
P [auth H] | Ribosomal_L13 | e3jcsH1 | 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: Ribosomal_L13 | ECOD (1.6) |
R [auth J] | Ribosomal_L14 | e3jcsJ1 | A: beta barrels | X: Ribosomal protein L14-like | H: Ribosomal protein L14-related (From Topology) | T: Ribosomal protein L14-related | F: Ribosomal_L14 | ECOD (1.6) |
S [auth K] | Ribosomal_L14e | e3jcsK1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: Ribosomal_L14e | ECOD (1.6) |
T [auth L] | Ribosomal_L18 | e3jcsL1 | 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: Ribosomal_L18 | ECOD (1.6) |
U [auth M] | Ribosomal_L15e | e3jcsM1 | 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: Ribosomal_L15e | ECOD (1.6) |
V [auth N] | Ribosomal_L16 | e3jcsN1 | A: a+b complex topology | X: alpha/beta-Hammerhead/Barrel-sandwich hybrid | H: alpha/beta-Hammerhead/Barrel-sandwich hybrid | T: Ribosomal protein L10e | F: Ribosomal_L16 | ECOD (1.6) |
W [auth O] | Ribosomal_L5e | e3jcsO1 | A: mixed a+b and a/b | X: Ribonuclease H-like | H: Ribonuclease H-like (From Topology) | T: Ribonuclease H-like | F: Ribosomal_L5e | ECOD (1.6) |
X [auth P] | Ribosomal_L18 | e3jcsP1 | 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: Ribosomal_L18 | ECOD (1.6) |
Y [auth Q] | Ribosomal_L19e_N | e3jcsQ2 | A: alpha arrays | X: Ribosomal protein L19 (L19e) N-terminal domain (From Topology) | H: Ribosomal protein L19 (L19e) N-terminal domain (From Topology) | T: Ribosomal protein L19 (L19e) N-terminal domain | F: Ribosomal_L19e_N | ECOD (1.6) |
Y [auth Q] | Ribosomal_L19e_C | e3jcsQ1 | A: alpha bundles | X: Ribosomal protein L19 (L19e) C-terminal domain (From Topology) | H: Ribosomal protein L19 (L19e) C-terminal domain (From Topology) | T: Ribosomal protein L19 (L19e) C-terminal domain | F: Ribosomal_L19e_C | ECOD (1.6) |
Z [auth R] | Ribosomal_L18A | e3jcsR1 | A: a+b two layers | X: GP2-like | H: RplX-like (From Topology) | T: RplX-like | F: Ribosomal_L18A | ECOD (1.6) |
AA [auth S] | Ribosomal_L21e | e3jcsS1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: Ribosomal_L21e | ECOD (1.6) |
BA [auth T] | Ribosomal_L22 | e3jcsT1 | A: a+b two layers | X: Enolase-N/ribosomal protein | H: Ribosomal protein L22 (From Topology) | T: Ribosomal protein L22 | F: Ribosomal_L22 | ECOD (1.6) |
CA [auth U] | Ribosomal_L22e | e3jcsU1 | A: a+b two layers | X: Ribosomal protein L22e (From Topology) | H: Ribosomal protein L22e (From Topology) | T: Ribosomal protein L22e | F: Ribosomal_L22e | ECOD (1.6) |
DA [auth V] | Ribosomal_L23_3 | e3jcsV1 | 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: Ribosomal_L23_3 | ECOD (1.6) |
EA [auth W] | Ribosomal_L26 | e3jcsW1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: Ribosomal_L26 | ECOD (1.6) |
FA [auth X] | Ribosomal_L24e | e3jcsX1 | A: few secondary structure elements | X: Glucocorticoid receptor-like | H: LIM domain-like | T: LIM domain-like | F: Ribosomal_L24e | ECOD (1.6) |
GA [auth Y] | Ribosomal_L27e | e3jcsY1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: Ribosomal_L27e | ECOD (1.6) |
HA [auth Z] | Ribosomal_L28e | e3jcsZ1 | A: a+b two layers | X: RPL28 (From Topology) | H: RPL28 (From Topology) | T: RPL28 | F: Ribosomal_L28e | ECOD (1.6) |
IA [auth a] | Ribosomal_L29_2 | e3jcsa1 | A: alpha bundles | X: Long alpha-hairpin | H: Ribosomal protein L29 (L29p) (From Topology) | T: Ribosomal protein L29 (L29p) | F: Ribosomal_L29_2 | ECOD (1.6) |
JA [auth b] | Ribosomal_L29e | e3jcsb1 | A: extended segments | X: RPL29 (From Topology) | H: RPL29 (From Topology) | T: RPL29 | F: Ribosomal_L29e | ECOD (1.6) |
KA [auth c] | Ribosomal_L30_1 | e3jcsc1 | 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: Ribosomal_L30_1 | ECOD (1.6) |
LA [auth d] | Ribosomal_L7Ae | e3jcsd1 | A: a+b three layers | X: Bacillus chorismate mutase-like | H: L30e-like (From Topology) | T: L30e-like | F: Ribosomal_L7Ae | ECOD (1.6) |
MA [auth e] | Ribosomal_L31e | e3jcse1 | A: a+b two layers | X: Ribosomal protein L31e-like | H: Ribosomal protein L31e/gp120 outer domain (From Topology) | T: Ribosomal protein L31e/gp120 outer domain | F: Ribosomal_L31e | ECOD (1.6) |
NA [auth f] | Ribosomal_L32e | e3jcsf1 | A: a/b three-layered sandwiches | X: Ribosomal protein L13/L15p/L18e/L32e | H: Ribosomal protein L32e (From Topology) | T: Ribosomal protein L32e | F: Ribosomal_L32e | ECOD (1.6) |
OA [auth g] | Ribosomal_L35Ae | e3jcsg1 | A: beta barrels | X: cradle loop barrel | H: RIFT-related | T: Alanine racemase-C | F: Ribosomal_L35Ae | ECOD (1.6) |
PA [auth h] | Ribosomal_L34e | e3jcsh1 | A: few secondary structure elements | X: Glucocorticoid receptor-like | H: RPL34 (From Topology) | T: RPL34 | F: Ribosomal_L34e | ECOD (1.6) |
QA [auth i] | Ribosomal_L36e | e3jcsi1 | A: alpha arrays | X: 60S ribosomal protein rpL36 (L36e) (From Topology) | H: 60S ribosomal protein rpL36 (L36e) (From Topology) | T: 60S ribosomal protein rpL36 (L36e) | F: Ribosomal_L36e | ECOD (1.6) |
RA [auth j] | Ribosomal_L37e | e3jcsj1 | A: few secondary structure elements | X: Rubredoxin-like | H: Rubredoxin-related | T: Rubredoxin-related | F: Ribosomal_L37e | ECOD (1.6) |
SA [auth k] | Ribosomal_L38e | e3jcsk1 | A: a+b two layers | X: SRP9/14-like | H: Signal recognition particle alu RNA binding heterodimer SRP9/14-related (From Topology) | T: Signal recognition particle alu RNA binding heterodimer SRP9/14-related | F: Ribosomal_L38e | ECOD (1.6) |
TA [auth l] | Ribosomal_L39 | e3jcsl1 | A: extended segments | X: Ribosomal protein L39e (From Topology) | H: Ribosomal protein L39e (From Topology) | T: Ribosomal protein L39e | F: Ribosomal_L39 | ECOD (1.6) |
UA [auth m] | Ribosomal_L37ae | e3jcsm1 | A: few secondary structure elements | X: Rubredoxin-like | H: Rubredoxin-related | T: Rubredoxin-related | F: Ribosomal_L37ae | ECOD (1.6) |
VA [auth n] | Ribosomal_L44 | e3jcsn1 | A: few secondary structure elements | X: Rubredoxin-like | H: Rubredoxin-related | T: Rubredoxin-related | F: Ribosomal_L44 | ECOD (1.6) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
I [auth A] | PF00831 | Ribosomal L29 protein (Ribosomal_L29) | Ribosomal L29 protein | - | Family |
K [auth C] | PF00327 | Ribosomal protein L30p/L7e (Ribosomal_L30) | Ribosomal protein L30p/L7e | This family includes prokaryotic L30 and eukaryotic L7. | Domain |
K [auth C] | PF14374 | 60S ribosomal protein L4 C-terminal domain (Ribos_L4_asso_C) | 60S ribosomal protein L4 C-terminal domain | This family is found at the very C-terminal of 60 ribosomal L4 proteins. | Domain |
K [auth C] | PF00573 | Ribosomal protein L4/L1 family (Ribosomal_L4) | Ribosomal protein L4/L1 family | - | Family |
L [auth D] | PF00281 | Ribosomal protein L5 (Ribosomal_L5) | Ribosomal protein L5 | Domain | |
L [auth D] | PF00673 | ribosomal L5P family C-terminus (Ribosomal_L5_C) | ribosomal L5P family C-terminus | This region is found associated with Pfam:PF00281. | Domain |
M [auth E] | PF00347 | Ribosomal protein L6 (Ribosomal_L6) | Ribosomal protein L6 | Domain | |
M [auth E] | PF01198 | Ribosomal protein L31e (Ribosomal_L31e) | Ribosomal protein L31e | - | Family |
N [auth F] | PF01655 | Ribosomal protein L32 (Ribosomal_L32e) | Ribosomal protein L32 | - | Family |
O [auth G] | PF01248 | Ribosomal protein L7Ae/L30e/S12e/Gadd45 family (Ribosomal_L7Ae) | Ribosomal protein L7Ae/L30e/S12e/Gadd45 family | This family includes: Ribosomal L7A from metazoa, Ribosomal L8-A and L8-B from fungi, 30S ribosomal protein HS6 from archaebacteria, 40S ribosomal protein S12 from eukaryotes, Ribosomal protein L30 from eukaryotes and archaebacteria. Gadd45 and MyD11 ... | Domain |
O [auth G] | PF01247 | Ribosomal protein L35Ae (Ribosomal_L35Ae) | Ribosomal protein L35Ae | Domain | |
R [auth J] | PF00238 | Ribosomal protein L14p/L23e (Ribosomal_L14) | Ribosomal protein L14p/L23e | Domain | |
R [auth J] | PF01907 | Ribosomal protein L37e (Ribosomal_L37e) | Ribosomal protein L37e | - | Family |
S [auth K] | PF01781 | Ribosomal L38e protein family (Ribosomal_L38e) | Ribosomal L38e protein family | - | Family |
S [auth K] | PF01929 | Ribosomal protein L14 (Ribosomal_L14e) | Ribosomal protein L14 | - | Family |
S [auth K] | PF00467 | KOW motif (KOW) | KOW motif | - | Family |
T [auth L] | PF00832 | Ribosomal L39 protein (Ribosomal_L39) | Ribosomal L39 protein | - | Family |
T [auth L] | 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 |
U [auth M] | PF00827 | Ribosomal L15 (Ribosomal_L15e) | Ribosomal L15 | - | Family |
U [auth M] | PF01780 | Ribosomal L37ae protein family (Ribosomal_L37ae) | Ribosomal L37ae protein family | - | Family |
V [auth N] | PF00252 | Ribosomal protein L16p/L10e (Ribosomal_L16) | Ribosomal protein L16p/L10e | Domain | |
W [auth O] | PF17144 | Ribosomal large subunit proteins 60S L5, and 50S L18 (Ribosomal_L5e) | Ribosomal large subunit proteins 60S L5, and 50S L18 | - | Family |
W [auth O] | PF14204 | Ribosomal L18 C-terminal region (Ribosomal_L18_c) | Ribosomal L18 C-terminal region | This domain is the C-terminal end of ribosomal L18/L5 proteins. | Domain |
Y [auth Q] | PF01280 | Ribosomal protein L19e (Ribosomal_L19e) | Ribosomal protein L19e | - | Family |
Z [auth R] | PF01775 | Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A (Ribosomal_L18A) | Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A | This family includes: archaeal 50S ribosomal protein L18Ae, often referred to as L20e or LX; fungal 60S ribosomal protein L20; and higher eukaryote 60S ribosomal protein L18A. | Domain |
BA [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 |
DA [auth V] | PF00276 | Ribosomal protein L23 (Ribosomal_L23) | Ribosomal protein L23 | - | Family |
GA [auth Y] | PF01777 | Ribosomal L27e protein family (Ribosomal_L27e) | Ribosomal L27e protein family | - | Family |
GA [auth Y] | PF00467 | KOW motif (KOW) | KOW motif | - | Family |
HA [auth Z] | PF01778 | Ribosomal L28e protein family (Ribosomal_L28e) | Ribosomal L28e protein family | - | Family |