Cryo-EM structure of the spinach chloroplast ribosome reveals the location of plastid-specific ribosomal proteins and extensions
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
G | SCOP2 Family | Ribosomal protein L5 | 8073875 | 4001498 | SCOP2 (2022-06-29) |
G | SCOP2 Superfamily | RL5-like | 8073876 | 3001709 | SCOP2 (2022-06-29) |
Q [auth S] | SCOP2B Superfamily | Ribosomal protein L20 | 8075018 | 3000563 | SCOP2B (2022-06-29) |
T [auth V] | SCOP2B Superfamily | Ribosomal proteins S24e, L23 and L15e | 8077091 | 3000210 | SCOP2B (2022-06-29) |
CA [auth 6] | SCOP2 Family | Ribosomal protein L36 | 8083319 | 4003715 | SCOP2 (2022-06-29) |
CA [auth 6] | SCOP2 Superfamily | Ribosomal protein L36 | 8083320 | 3001346 | SCOP2 (2022-06-29) |
J [auth L] | SCOP2B Superfamily | Ribosomal protein L13 | 8066065 | 3001134 | SCOP2B (2022-06-29) |
K [auth M] | SCOP2B Superfamily | 50S Ribosomal protein L14-like | 8072036 | 3000433 | SCOP2B (2022-06-29) |
L [auth N] | SCOP2B Superfamily | Ribosomal proteins L15p and L18e | 8070567 | 3001045 | SCOP2B (2022-06-29) |
M [auth O] | SCOP2B Superfamily | Ribosomal protein L16p/L10e | 8076047 | 3000884 | SCOP2B (2022-06-29) |
N [auth P] | SCOP2B Superfamily | Prokaryotic ribosomal protein L17 | 8089018 | 3000995 | SCOP2B (2022-06-29) |
O [auth Q] | SCOP2B Superfamily | Translational machinery components | 8074012 | 3000571 | SCOP2B (2022-06-29) |
P [auth R] | SCOP2 Family | Ribosomal protein L19 | 8089129 | 4001761 | SCOP2 (2022-06-29) |
P [auth R] | SCOP2 Superfamily | Translation proteins SH3-like KOW motif containing domain | 8089130 | 3000334 | SCOP2 (2022-06-29) |
R [auth T] | SCOP2B Superfamily | l21p-like | 8082449 | 3002005 | SCOP2B (2022-06-29) |
U [auth W] | SCOP2B Superfamily | Translation proteins SH3-like KOW motif containing domain | 8082517 | 3000334 | SCOP2B (2022-06-29) |
W [auth Y] | SCOP2B Superfamily | L28p-like | 8089408 | 3001966 | SCOP2B (2022-06-29) |
Z [auth 3] | SCOP2 Family | Ribosomal protein L33p | 8075063 | 4000511 | SCOP2 (2022-06-29) |
Z [auth 3] | SCOP2 Superfamily | Zn-binding ribosomal proteins | 8075064 | 3001320 | SCOP2 (2022-06-29) |
BA [auth 5] | SCOP2B Superfamily | L35p-like | 8083340 | 3000790 | SCOP2B (2022-06-29) |
E | SCOP2B Superfamily | Translational proteins | 8089154 | 3000811 | SCOP2B (2022-06-29) |
F | SCOP2 Family | Ribosomal protein L4 | 8080707 | 4003628 | SCOP2 (2022-06-29) |
F | SCOP2 Superfamily | Ribosomal protein L4 | 8080708 | 3001146 | SCOP2 (2022-06-29) |
I | SCOP2B Superfamily | L9 N-domain-like | 8070581 | 3000338 | 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) |
---|---|---|---|---|---|---|---|---|
D | Ribosomal_L2_1 | e5mlcD1 | 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 | Ribosomal_L2_C | e5mlcD2 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: Ribosomal_L2_C | ECOD (1.6) |
G | Ribosomal_L5_C | e5mlcG1 | 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) |
Q [auth S] | Ribosomal_L20 | e5mlcS1 | A: alpha arrays | X: PABP domain-like | H: Ribosomal protein L20 (From Topology) | T: Ribosomal protein L20 | F: Ribosomal_L20 | ECOD (1.6) |
T [auth V] | Ribosomal_L23_1 | e5mlcV1 | 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_1 | ECOD (1.6) |
X [auth Z] | Ribosomal_L29 | e5mlcZ1 | A: alpha bundles | X: Long alpha-hairpin | H: Ribosomal protein L29 (L29p) (From Topology) | T: Ribosomal protein L29 (L29p) | F: Ribosomal_L29 | ECOD (1.6) |
CA [auth 6] | Ribosomal_L36 | e5mlc61 | A: few secondary structure elements | X: Ribosomal protein L36 (From Topology) | H: Ribosomal protein L36 (From Topology) | T: Ribosomal protein L36 | F: Ribosomal_L36 | ECOD (1.6) |
J [auth L] | Ribosomal_L13 | e5mlcL1 | 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) |
K [auth M] | Ribosomal_L14 | e5mlcM1 | 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) |
L [auth N] | Ribosomal_L27A | e5mlcN1 | 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_L27A | ECOD (1.6) |
M [auth O] | Ribosomal_L16 | e5mlcO1 | 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) |
N [auth P] | Ribosomal_L17_1 | e5mlcP1 | A: a+b two layers | X: Enolase-N/ribosomal protein | H: Prokaryotic ribosomal protein L17 (From Topology) | T: Prokaryotic ribosomal protein L17 | F: Ribosomal_L17_1 | ECOD (1.6) |
O [auth Q] | Ribosomal_L18p | e5mlcQ1 | A: mixed a+b and a/b | X: Ribonuclease H-like | H: Ribonuclease H-like (From Topology) | T: Ribonuclease H-like | F: Ribosomal_L18p | ECOD (1.6) |
P [auth R] | Ribosomal_L19 | e5mlcR1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: Ribosomal_L19 | ECOD (1.6) |
R [auth T] | Ribosomal_L21p | e5mlcT1 | A: beta barrels | X: Ribosomal protein L21p (From Topology) | H: Ribosomal protein L21p (From Topology) | T: Ribosomal protein L21p | F: Ribosomal_L21p | ECOD (1.6) |
S [auth U] | Ribosomal_L22 | e5mlcU1 | 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) |
U [auth W] | ribosomal_L24_1 | e5mlcW1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: ribosomal_L24_1 | ECOD (1.6) |
V [auth X] | Ribosomal_L27 | e5mlcX1 | A: a+b complex topology | X: alpha/beta-Hammerhead/Barrel-sandwich hybrid | H: alpha/beta-Hammerhead/Barrel-sandwich hybrid | T: Ribosomal L27 protein | F: Ribosomal_L27 | ECOD (1.6) |
W [auth Y] | Ribosomal_L28 | e5mlcY1 | A: few secondary structure elements | X: Ribosomal protein bL28-related (From Homology) | H: Ribosomal protein bL28-related | T: Ribosomal protein L28 | F: Ribosomal_L28 | ECOD (1.6) |
Y [auth 2] | UNK_F_TYPE | e5mlc21 | A: few secondary structure elements | X: Rubredoxin-like | H: Rubredoxin-related | T: Rubredoxin-related | F: UNK_F_TYPE | ECOD (1.6) |
Z [auth 3] | Ribosomal_L33_1 | e5mlc31 | A: few secondary structure elements | X: Rubredoxin-like | H: Rubredoxin-related | T: Rubredoxin-related | F: Ribosomal_L33_1 | ECOD (1.6) |
AA [auth 4] | Ribosomal_L34_1 | e5mlc41 | A: extended segments | X: 50S ribosomal protein L34 (From Topology) | H: 50S ribosomal protein L34 (From Topology) | T: 50S ribosomal protein L34 | F: Ribosomal_L34_1 | ECOD (1.6) |
BA [auth 5] | Ribosomal_L35p | e5mlc51 | A: a+b two layers | X: Ribosomal protein L35p (From Topology) | H: Ribosomal protein L35p (From Topology) | T: Ribosomal protein L35p | F: Ribosomal_L35p | ECOD (1.6) |
DA [auth 9] | RRF | e5mlc91 | A: a+b two layers | X: RRF/tRNA synthetase additional domain-like | H: Ribosome recycling factor, RRF (From Topology) | T: Ribosome recycling factor, RRF | F: RRF | ECOD (1.6) |
E | Ribosomal_L3 | e5mlcE1 | A: beta barrels | X: cradle loop barrel | H: RIFT-related | T: Alanine racemase-C | F: Ribosomal_L3 | ECOD (1.6) |
F | Ribosomal_L4 | e5mlcF1 | 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) |
H | Ribosomal_L6 | e5mlcH1 | 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) |
H | Ribosomal_L6_1 | e5mlcH2 | A: a+b two layers | X: Ribosomal protein L6 (From Topology) | H: Ribosomal protein L6 (From Topology) | T: Ribosomal protein L6 | F: Ribosomal_L6_1 | ECOD (1.6) |
I | Ribosomal_L9_N | e5mlcI1 | A: a+b two layers | X: L9 N-domain-like | H: L9 N-domain-like (From Topology) | T: L9 N-domain-like | F: Ribosomal_L9_N | ECOD (1.6) |
Domain Annotation: CATH CATH Database Homepage
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 | ||
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 | |
Q [auth S] | PF00453 | Ribosomal protein L20 (Ribosomal_L20) | Ribosomal protein L20 | - | Family |
T [auth V] | PF00276 | Ribosomal protein L23 (Ribosomal_L23) | Ribosomal protein L23 | - | Family |
X [auth Z] | PF00831 | Ribosomal L29 protein (Ribosomal_L29) | Ribosomal L29 protein | - | Family |
CA [auth 6] | PF00444 | Ribosomal protein L36 (Ribosomal_L36) | Ribosomal protein L36 | Domain | |
J [auth L] | PF00572 | Ribosomal protein L13 (Ribosomal_L13) | Ribosomal protein L13 | - | Family |
K [auth M] | PF00238 | Ribosomal protein L14p/L23e (Ribosomal_L14) | Ribosomal protein L14p/L23e | Domain | |
L [auth N] | 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 |
M [auth O] | PF00252 | Ribosomal protein L16p/L10e (Ribosomal_L16) | Ribosomal protein L16p/L10e | Domain | |
N [auth P] | PF01196 | Ribosomal protein L17 (Ribosomal_L17) | Ribosomal protein L17 | - | Family |
P [auth R] | PF01245 | Ribosomal protein L19 (Ribosomal_L19) | Ribosomal protein L19 | - | Family |
R [auth T] | PF00829 | Ribosomal prokaryotic L21 protein (Ribosomal_L21p) | Ribosomal prokaryotic L21 protein | - | Family |
S [auth U] | PF00237 | Ribosomal protein L22p/L17e (Ribosomal_L22) | Ribosomal protein L22p/L17e | This family includes L22 from prokaryotes and chloroplasts and L17 from eukaryotes. | Domain |
U [auth W] | PF17136 | Ribosomal proteins 50S L24/mitochondrial 39S L24 (ribosomal_L24) | Ribosomal proteins 50S L24/mitochondrial 39S L24 | - | Family |
U [auth W] | PF00467 | KOW motif (KOW) | KOW motif | - | Family |
W [auth Y] | PF00830 | Ribosomal L28 family (Ribosomal_L28) | Ribosomal L28 family | - | Family |
Z [auth 3] | PF00471 | Ribosomal protein L33 (Ribosomal_L33) | Ribosomal protein L33 | - | Family |
AA [auth 4] | PF00468 | Ribosomal protein L34 (Ribosomal_L34) | Ribosomal protein L34 | - | Family |
BA [auth 5] | PF01632 | Ribosomal protein L35 (Ribosomal_L35p) | Ribosomal protein L35 | - | Family |
DA [auth 9] | PF01765 | Ribosome recycling factor (RRF) | Ribosome recycling factor | The ribosome recycling factor (RRF / ribosome release factor) dissociates the ribosome from the mRNA after termination of translation, and is essential bacterial growth [1]. Thus ribosomes are "recycled" and ready for another round of protein synthe ... | Domain |
PF00297 | Ribosomal protein L3 (Ribosomal_L3) | Ribosomal protein L3 | - | Family | |
PF00573 | Ribosomal protein L4/L1 family (Ribosomal_L4) | Ribosomal protein L4/L1 family | - | Family | |
PF00347 | Ribosomal protein L6 (Ribosomal_L6) | Ribosomal protein L6 | Domain | ||
PF01281 | Ribosomal protein L9, N-terminal domain (Ribosomal_L9_N) | Ribosomal protein L9, N-terminal domain | Domain |