Cryo-EM structure of large subunit of Giardia lamblia ribosome at 2.7 A resolution
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
K [auth I] | SCOP2B Superfamily | Ribosomal protein L16p/L10e | 8107186 | 3000884 | SCOP2B (2022-06-29) |
L [auth J] | SCOP2B Superfamily | RL5-like | 8107182 | 3001709 | SCOP2B (2022-06-29) |
O [auth N] | SCOP2B Superfamily | Ribosomal proteins S24e, L23 and L15e | 8107174 | 3000210 | SCOP2B (2022-06-29) |
Q [auth P] | SCOP2 Family | Ribosomal protein L22 | 8107175 | 4001212 | SCOP2 (2022-06-29) |
Q [auth P] | SCOP2 Superfamily | Ribosomal protein L22 | 8107176 | 3001078 | SCOP2 (2022-06-29) |
S [auth R] | SCOP2B Superfamily | Ribosomal protein L19 (L19e) | 8107180 | 3000890 | SCOP2B (2022-06-29) |
W [auth V] | SCOP2 Family | Ribosomal protein L14 | 8107197 | 4001826 | SCOP2 (2022-06-29) |
W [auth V] | SCOP2 Superfamily | 50S Ribosomal protein L14-like | 8107198 | 3000433 | SCOP2 (2022-06-29) |
AA [auth a] | SCOP2B Superfamily | Ribosomal proteins L15p and L18e | 8107206 | 3001045 | SCOP2B (2022-06-29) |
CA [auth c] | SCOP2 Family | L30e/L7ae ribosomal proteins | 8107171 | 4001513 | SCOP2 (2022-06-29) |
CA [auth c] | SCOP2 Superfamily | L30e-like | 8107172 | 3001739 | SCOP2 (2022-06-29) |
EA [auth e] | SCOP2B Superfamily | Ribosomal protein L32e | 8107188 | 3000982 | SCOP2B (2022-06-29) |
GA [auth g] | SCOP2B Superfamily | Ribosomal protein L34e-like | 8107190 | 3002203 | SCOP2B (2022-06-29) |
LA [auth l] | SCOP2 Family | ribosomal protein l39e | 8107107 | 4001518 | SCOP2 (2022-06-29) |
LA [auth l] | SCOP2 Superfamily | Ribosomal protein L39e | 8107108 | 3001756 | SCOP2 (2022-06-29) |
MA [auth m] | SCOP2 Family | Ribosomal protein L40e | 8107201 | 4002847 | SCOP2 (2022-06-29) |
MA [auth m] | SCOP2 Superfamily | Zn-binding ribosomal proteins | 8107202 | 3001320 | SCOP2 (2022-06-29) |
OA [auth p] | SCOP2B Superfamily | Zn-binding ribosomal proteins | 8107192 | 3001320 | SCOP2B (2022-06-29) |
E [auth B] | SCOP2 Family | Ribosomal protein L3 | 8107195 | 4002103 | SCOP2 (2022-06-29) |
E [auth B] | SCOP2 Superfamily | Translational proteins | 8107196 | 3000811 | SCOP2 (2022-06-29) |
G [auth D] | SCOP2B Superfamily | Translational machinery components | 8107236 | 3000571 | 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) |
---|---|---|---|---|---|---|---|---|
U [auth T] | Ribosomal_L21e | e7pwgT1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: Ribosomal_L21e | ECOD (1.6) |
J [auth H] | Ribosomal_L6_2 | e7pwgH1 | 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) |
J [auth H] | Ribosomal_L6 | e7pwgH2 | 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) |
K [auth I] | Ribosomal_L16 | e7pwgI1 | 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) |
L [auth J] | Ribosomal_L5_C | e7pwgJ1 | 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 L] | Ribosomal_L13e | e7pwgL1 | A: extended segments | X: RPL13 (From Topology) | H: RPL13 (From Topology) | T: RPL13 | F: Ribosomal_L13e | ECOD (1.6) |
N [auth M] | Ribosomal_L14e | e7pwgM1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: Ribosomal_L14e | ECOD (1.6) |
O [auth N] | Ribosomal_L15e | e7pwgN1 | 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) |
P [auth O] | Ribosomal_L13 | e7pwgO1 | 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) |
Q [auth P] | Ribosomal_L22 | e7pwgP1 | 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) |
R [auth Q] | Ribosomal_L18 | e7pwgQ1 | 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) |
S [auth R] | Ribosomal_L19e_N | e7pwgR2 | 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) |
S [auth R] | Ribosomal_L19e_C | e7pwgR1 | 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) |
T [auth S] | Ribosomal_L18A | e7pwgS2 | A: a+b two layers | X: GP2-like | H: RplX-like (From Topology) | T: RplX-like | F: Ribosomal_L18A | ECOD (1.6) |
V [auth U] | Ribosomal_L22e | e7pwgU1 | 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) |
W [auth V] | Ribosomal_L14 | e7pwgV1 | 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) |
X | Ribosomal_L23_3 | e7pwgX1 | 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) |
Y | Ribosomal_L26 | e7pwgY1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: Ribosomal_L26 | ECOD (1.6) |
Z | Ribosomal_L27e | e7pwgZ1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: Ribosomal_L27e | ECOD (1.6) |
AA [auth a] | Ribosomal_L18 | e7pwga1 | 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) |
BA [auth b] | Ribosomal_L29e | e7pwgb1 | A: extended segments | X: RPL29 (From Topology) | H: RPL29 (From Topology) | T: RPL29 | F: Ribosomal_L29e | ECOD (1.6) |
CA [auth c] | Ribosomal_L7Ae | e7pwgc1 | A: a+b three layers | X: Bacillus chorismate mutase-like | H: L30e-like (From Topology) | T: L30e-like | F: Ribosomal_L7Ae | ECOD (1.6) |
DA [auth d] | Ribosomal_L31e | e7pwgd1 | 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) |
EA [auth e] | Ribosomal_L32e | e7pwge1 | 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) |
FA [auth f] | Ribosomal_L35Ae | e7pwgf1 | A: beta barrels | X: cradle loop barrel | H: RIFT-related | T: Alanine racemase-C | F: Ribosomal_L35Ae | ECOD (1.6) |
GA [auth g] | Ribosomal_L34e | e7pwgg1 | A: few secondary structure elements | X: Glucocorticoid receptor-like | H: RPL34 (From Topology) | T: RPL34 | F: Ribosomal_L34e | ECOD (1.6) |
HA [auth h] | Ribosomal_L29_2 | e7pwgh1 | 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 j] | Ribosomal_L37e | e7pwgj1 | A: few secondary structure elements | X: Rubredoxin-like | H: Rubredoxin-related | T: Rubredoxin-related | F: Ribosomal_L37e | ECOD (1.6) |
KA [auth k] | Ribosomal_L38e | e7pwgk1 | 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) |
LA [auth l] | Ribosomal_L39 | e7pwgl1 | 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) |
MA [auth m] | Ribosomal_L40e | e7pwgm1 | A: few secondary structure elements | X: Rubredoxin-like | H: Rubredoxin-related | T: Rubredoxin-related | F: Ribosomal_L40e | ECOD (1.6) |
D [auth A] | Ribosomal_L2_1 | e7pwgA2 | 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) |
D [auth A] | Ribosomal_L2_C_2 | e7pwgA1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: Ribosomal_L2_C_2 | ECOD (1.6) |
NA [auth o] | Ribosomal_L44 | e7pwgo1 | A: few secondary structure elements | X: Rubredoxin-like | H: Rubredoxin-related | T: Rubredoxin-related | F: Ribosomal_L44 | ECOD (1.6) |
OA [auth p] | Ribosomal_L37ae | e7pwgp1 | A: few secondary structure elements | X: Rubredoxin-like | H: Rubredoxin-related | T: Rubredoxin-related | F: Ribosomal_L37ae | ECOD (1.6) |
QA [auth W] | Ribosomal_L24e | e7pwgW1 | A: few secondary structure elements | X: Glucocorticoid receptor-like | H: LIM domain-like | T: LIM domain-like | F: Ribosomal_L24e | ECOD (1.6) |
E [auth B] | Ribosomal_L3 | e7pwgB1 | A: beta barrels | X: cradle loop barrel | H: RIFT-related | T: Alanine racemase-C | F: Ribosomal_L3 | ECOD (1.6) |
G [auth D] | Ribosomal_L5e | e7pwgD1 | 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) |
H [auth F] | Ribosomal_L30_1 | e7pwgF1 | 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) |
I [auth G] | Ribosomal_L7Ae_1 | e7pwgG1 | 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) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
J [auth H] | PF00347 | Ribosomal protein L6 (Ribosomal_L6) | Ribosomal protein L6 | Domain | |
J [auth H] | PF00831 | Ribosomal L29 protein (Ribosomal_L29) | Ribosomal L29 protein | - | Family |
K [auth I] | PF00252 | Ribosomal protein L16p/L10e (Ribosomal_L16) | Ribosomal protein L16p/L10e | Domain | |
K [auth I] | PF01158 | Ribosomal protein L36e (Ribosomal_L36e) | Ribosomal protein L36e | - | Family |
L [auth J] | PF00281 | Ribosomal protein L5 (Ribosomal_L5) | Ribosomal protein L5 | Domain | |
L [auth J] | PF01907 | Ribosomal protein L37e (Ribosomal_L37e) | Ribosomal protein L37e | - | Family |
L [auth J] | 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 L] | PF00832 | Ribosomal L39 protein (Ribosomal_L39) | Ribosomal L39 protein | - | Family |
N [auth M] | PF01020 | Ribosomal L40e family (Ribosomal_L40e) | Ribosomal L40e family | Bovine L40 has been identified as a secondary RNA binding protein [1]. L40 is fused to a ubiquitin protein [2]. | Domain |
N [auth M] | PF01929 | Ribosomal protein L14 (Ribosomal_L14e) | Ribosomal protein L14 | - | Family |
O [auth N] | PF00827 | Ribosomal L15 (Ribosomal_L15e) | Ribosomal L15 | - | Family |
P [auth O] | PF00935 | Ribosomal protein L44 (Ribosomal_L44) | Ribosomal protein L44 | - | Family |
P [auth O] | PF00572 | Ribosomal protein L13 (Ribosomal_L13) | Ribosomal protein L13 | - | Family |
Q [auth P] | 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] | PF01780 | Ribosomal L37ae protein family (Ribosomal_L37ae) | Ribosomal L37ae protein family | - | Family |
R [auth Q] | PF17135 | Ribosomal protein 60S L18 and 50S L18e (Ribosomal_L18) | Ribosomal protein 60S L18 and 50S L18e | - | Family |
S [auth R] | PF01280 | Ribosomal protein L19e, N-terminal domain (Ribosomal_L19e) | Ribosomal protein L19e, N-terminal domain | This domain is found at the N-terminal end of the large ribosomal subunit protein eL19 found in eukaryotes and archaea. This is an helical domain that assumes an orthogonal bundle topology. | Domain |
W [auth V] | PF00238 | Ribosomal protein L14p/L23e (Ribosomal_L14) | Ribosomal protein L14p/L23e | Domain | |
PF00276 | Ribosomal protein L23 (Ribosomal_L23) | Ribosomal protein L23 | - | Family | |
PF16906 | Ribosomal proteins L26 eukaryotic, L24P archaeal (Ribosomal_L26) | Ribosomal proteins L26 eukaryotic, L24P archaeal | - | Family | |
PF01777 | Ribosomal L27e protein family (Ribosomal_L27e) | Ribosomal L27e protein family | - | Family | |
PF00467 | KOW motif (KOW) | KOW motif | - | Family | |
D [auth A] | PF03947 | Ribosomal Proteins L2, C-terminal domain (Ribosomal_L2_C) | Ribosomal Proteins L2, C-terminal domain | Domain | |
D [auth A] | PF00181 | Ribosomal Proteins L2, RNA binding domain (Ribosomal_L2) | Ribosomal Proteins L2, RNA binding domain | Domain | |
D [auth A] | 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 |
QA [auth W] | PF01246 | Ribosomal protein L24e (Ribosomal_L24e) | Ribosomal protein L24e | Domain | |
E [auth B] | PF01779 | Ribosomal L29e protein family (Ribosomal_L29e) | Ribosomal L29e protein family | - | Family |
F [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 |
F [auth C] | PF00573 | Ribosomal protein L4/L1 family (Ribosomal_L4) | Ribosomal protein L4/L1 family | - | Family |
F [auth C] | 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 |
G [auth D] | PF17144 | Ribosomal large subunit proteins 60S L5, and 50S L18 (Ribosomal_L5e) | Ribosomal large subunit proteins 60S L5, and 50S L18 | - | Family |
G [auth D] | PF01198 | Ribosomal protein L31e (Ribosomal_L31e) | Ribosomal protein L31e | - | Family |
G [auth D] | 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 |
H [auth F] | PF00327 | Ribosomal protein L30p/L7e (Ribosomal_L30) | Ribosomal protein L30p/L7e | This family includes prokaryotic L30 and eukaryotic L7. | Domain |
H [auth F] | PF01247 | Ribosomal protein L35Ae (Ribosomal_L35Ae) | Ribosomal protein L35Ae | Domain | |