6AZ1
Cryo-EM structure of the small subunit of Leishmania ribosome bound to paromomycin
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
A | SCOP2B Superfamily | Ribosomal S3Ae-like | 8059220 | 3002166 | SCOP2B (2022-06-29) |
B | SCOP2 Family | Ribosomal protein S2-like | 8063813 | 4003744 | SCOP2 (2022-06-29) |
B | SCOP2 Superfamily | SIS domain/Ribosomal protein S2-like | 8063814 | 3001397 | SCOP2 (2022-06-29) |
H | SCOP2 Family | Ribosomal protein S7 | 8066018 | 4001112 | SCOP2 (2022-06-29) |
H | SCOP2 Superfamily | Ribosomal protein S7 | 8066019 | 3000799 | SCOP2 (2022-06-29) |
J | SCOP2B Superfamily | Ribosomal protein S8 | 8081971 | 3000709 | SCOP2B (2022-06-29) |
M | SCOP2B Superfamily | Ribosomal protein S10 | 8097706 | 3001336 | SCOP2B (2022-06-29) |
O | SCOP2 Family | Ribosomal protein L18p and S11 | 8097711 | 4000555 | SCOP2 (2022-06-29) |
O | SCOP2 Superfamily | Translational machinery components | 8097712 | 3000571 | SCOP2 (2022-06-29) |
Q | SCOP2 Family | L30e/L7ae ribosomal proteins | 8080817 | 4001513 | SCOP2 (2022-06-29) |
Q | SCOP2 Superfamily | L30e-like | 8080818 | 3001739 | SCOP2 (2022-06-29) |
R | SCOP2B Superfamily | S13-like H2TH domain | 8101421 | 3000053 | SCOP2B (2022-06-29) |
S | SCOP2 Family | Ribosomal protein S14p/S29e | 8059192 | 4003647 | SCOP2 (2022-06-29) |
S | SCOP2 Superfamily | Glucocorticoid receptor-like (DNA-binding domain) | 8059193 | 3000068 | SCOP2 (2022-06-29) |
W | SCOP2 Family | Ribosomal protein S19 | 8086071 | 4001081 | SCOP2 (2022-06-29) |
W | SCOP2 Superfamily | Ribosomal protein S19 | 8086072 | 3000686 | SCOP2 (2022-06-29) |
Y | SCOP2 Family | Ribosomal protein S21e | 8059210 | 4006215 | SCOP2 (2022-06-29) |
Y | SCOP2 Superfamily | Glucocorticoid receptor-like (DNA-binding domain) | 8059211 | 3000068 | SCOP2 (2022-06-29) |
AA [auth a] | SCOP2 Family | Ribosomal protein S25-like | 8097701 | 4007308 | SCOP2 (2022-06-29) |
AA [auth a] | SCOP2 Superfamily | Winged helix DNA-binding domain | 8097702 | 3000034 | SCOP2 (2022-06-29) |
BA [auth b] | SCOP2 Family | Ribosomal protein S26e | 8097707 | 4006236 | SCOP2 (2022-06-29) |
BA [auth b] | SCOP2 Superfamily | Glucocorticoid receptor-like (DNA-binding domain) | 8097708 | 3000068 | SCOP2 (2022-06-29) |
DA [auth d] | SCOP2 Family | Cold shock DNA-binding domain-like | 8097703 | 4001909 | SCOP2 (2022-06-29) |
DA [auth d] | SCOP2 Superfamily | Nucleic acid-binding proteins | 8097704 | 3000135 | SCOP2 (2022-06-29) |
EA [auth e] | SCOP2B Superfamily | Ribosomal protein S30e-like | 8059197 | 3002190 | SCOP2B (2022-06-29) |
N | SCOP2B Superfamily | Winged helix DNA-binding domain | 8059234 | 3000034 | 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) |
---|---|---|---|---|---|---|---|---|
A | Ribosomal_S3Ae_N | e6az1A2 | A: beta barrels | X: Ribosomal protein L25-like | H: 40S ribosomal protein S3A N-terminal domain (From Topology) | T: 40S ribosomal protein S3A N-terminal domain | F: Ribosomal_S3Ae_N | ECOD (1.6) |
A | Ribosomal_S3Ae_C | e6az1A1 | A: a+b two layers | X: T-fold | H: 40S ribosomal protein S3A C-terminal domain (From Topology) | T: 40S ribosomal protein S3A C-terminal domain | F: Ribosomal_S3Ae_C | ECOD (1.6) |
B | Ribosomal_S2_2 | e6az1B1 | A: a/b three-layered sandwiches | X: Flavodoxin-like | H: Ribosomal protein S2/SIS domain (From Topology) | T: Ribosomal protein S2/SIS domain | F: Ribosomal_S2_2 | ECOD (1.6) |
C | Ribosomal_S3_C | e6az1C1 | A: a+b two layers | X: T-fold | H: Ribosomal protein S3-C (From Topology) | T: Ribosomal protein S3-C | F: Ribosomal_S3_C | ECOD (1.6) |
C | KH_2_3 | e6az1C2 | A: a+b two layers | X: Alpha-lytic protease prodomain-like | H: KH-domains | T: Prokaryotic type KH domain (KH-domain type II) | F: KH_2_3 | ECOD (1.6) |
D | S4 | e6az1D1 | A: a+b two layers | X: beta-Grasp | H: Ubiquitin-related | T: Alpha-L RNA-binding motif | F: S4 | ECOD (1.6) |
E | Ribosomal_S4e | e6az1E2 | A: beta barrels | X: OB-fold | H: Nucleic acid-binding proteins (From Topology) | T: Nucleic acid-binding proteins | F: Ribosomal_S4e | ECOD (1.6) |
E | 40S_S4_C | e6az1E1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: 40S_S4_C | ECOD (1.6) |
E | RS4NT | e6az1E3 | A: a+b two layers | X: beta-Grasp | H: Ubiquitin-related | T: Alpha-L RNA-binding motif | F: RS4NT | ECOD (1.6) |
F | Ribosomal_S5_C_1 | e6az1F1 | A: a+b two layers | X: Ribosomal protein S5 domain 2-like (From Topology) | H: Ribosomal protein S5 domain 2-like (From Topology) | T: Ribosomal protein S5 domain 2-like | F: Ribosomal_S5_C_1 | ECOD (1.6) |
F | Ribosomal_S5_3 | e6az1F3 | A: a+b two layers | X: dsRBD-like | H: dsRNA-binding domain-like (From Topology) | T: dsRNA-binding domain-like | F: Ribosomal_S5_3 | ECOD (1.6) |
F | Ribosomal_S5_2 | e6az1F2 | A: extended segments | X: N-terminal region in 40S ribosomal protein rpS2 (S5p) (From Topology) | H: N-terminal region in 40S ribosomal protein rpS2 (S5p) (From Topology) | T: N-terminal region in 40S ribosomal protein rpS2 (S5p) | F: Ribosomal_S5_2 | ECOD (1.6) |
G | Ribosomal_S6e | e6az1G1 | A: beta barrels | X: Ribosomal protein L25-like | H: Ribosomal protein L25-like (From Topology) | T: Ribosomal protein L25-like | F: Ribosomal_S6e | ECOD (1.6) |
H | Ribosomal_S7_1 | e6az1H1 | A: alpha arrays | X: Ribosomal protein S7 (From Topology) | H: Ribosomal protein S7 (From Topology) | T: Ribosomal protein S7 | F: Ribosomal_S7_1 | ECOD (1.6) |
I | Ribosomal_S7e_C | e6az1I1 | A: a+b two layers | X: Alpha-lytic protease prodomain-like | H: 40S ribosomal protein S7-A (From Topology) | T: 40S ribosomal protein S7-A | F: Ribosomal_S7e_C | ECOD (1.6) |
I | Ribosomal_S7e_N | e6az1I2 | A: a+b two layers | X: Alpha-lytic protease prodomain-like | H: 40S ribosomal protein S7-A (From Topology) | T: 40S ribosomal protein S7-A | F: Ribosomal_S7e_N | ECOD (1.6) |
J | Ribosomal_S8_N_1 | e6az1J1 | A: a+b two layers | X: R3H domain-like | H: Ribosomal protein S8, N-terminal domain (From Topology) | T: Ribosomal protein S8, N-terminal domain | F: Ribosomal_S8_N_1 | ECOD (1.6) |
J | Ribosomal_S8_C_1 | e6az1J2 | A: a+b two layers | X: Ribosomal protein S8, C-terminal domain (From Topology) | H: Ribosomal protein S8, C-terminal domain (From Topology) | T: Ribosomal protein S8, C-terminal domain | F: Ribosomal_S8_C_1 | ECOD (1.6) |
K | Ribosomal_S8e | e6az1K1 | A: beta barrels | X: Ribosomal protein L14-like | H: Ribosomal protein L14-related (From Topology) | T: Ribosomal protein L14-related | F: Ribosomal_S8e | ECOD (1.6) |
L | Ribosomal_S9 | e6az1L1 | A: a+b two layers | X: Ribosomal protein S5 domain 2-like (From Topology) | H: Ribosomal protein S5 domain 2-like (From Topology) | T: Ribosomal protein S5 domain 2-like | F: Ribosomal_S9 | ECOD (1.6) |
M | Ribosomal_S10_1 | e6az1M1 | A: a+b two layers | X: Alpha-beta plaits | H: Ribosomal protein S10 (From Topology) | T: Ribosomal protein S10 | F: Ribosomal_S10_1 | ECOD (1.6) |
O | Ribosomal_S11 | e6az1O1 | A: mixed a+b and a/b | X: Ribonuclease H-like | H: Ribonuclease H-like (From Topology) | T: Ribonuclease H-like | F: Ribosomal_S11 | ECOD (1.6) |
P | Ribosom_S12_S23 | e6az1P1 | A: beta barrels | X: OB-fold | H: Nucleic acid-binding proteins (From Topology) | T: Nucleic acid-binding proteins | F: Ribosom_S12_S23 | ECOD (1.6) |
Q | Ribosomal_L7Ae | e6az1Q1 | A: a+b three layers | X: Bacillus chorismate mutase-like | H: L30e-like (From Topology) | T: L30e-like | F: Ribosomal_L7Ae | ECOD (1.6) |
R | Ribosomal_S13 | e6az1R1 | A: alpha arrays | X: HhH/H2TH | H: H2TH (From Topology) | T: H2TH | F: Ribosomal_S13 | ECOD (1.6) |
S | Ribosomal_S14_2 | e6az1S1 | A: few secondary structure elements | X: Glucocorticoid receptor-like | H: LIM domain-like | T: LIM domain-like | F: Ribosomal_S14_2 | ECOD (1.6) |
T | Ribosomal_S13_N_1 | e6az1T2 | A: alpha arrays | X: HTH | H: 40S ribosomal protein S13 N-terminal domain (From Topology) | T: 40S ribosomal protein S13 N-terminal domain | F: Ribosomal_S13_N_1 | ECOD (1.6) |
T | Ribosomal_S15_2 | e6az1T1 | A: alpha arrays | X: S15/NS1 RNA-binding domain (From Topology) | H: S15/NS1 RNA-binding domain (From Topology) | T: S15/NS1 RNA-binding domain | F: Ribosomal_S15_2 | ECOD (1.6) |
U | Ribosomal_S17_1 | e6az1U1 | A: beta barrels | X: OB-fold | H: Nucleic acid-binding proteins (From Topology) | T: Nucleic acid-binding proteins | F: Ribosomal_S17_1 | ECOD (1.6) |
W | Ribosomal_S19 | e6az1W1 | A: a+b two layers | X: Ribosomal protein S19 (From Topology) | H: Ribosomal protein S19 (From Topology) | T: Ribosomal protein S19 | F: Ribosomal_S19 | ECOD (1.6) |
X | Ribosomal_S19e | e6az1X1 | A: alpha arrays | X: HTH | H: HTH | T: winged | F: Ribosomal_S19e | ECOD (1.6) |
Y | Ribosomal_S21e | e6az1Y1 | A: a+b two layers | X: 40S ribosomal protein rpS21 (S21e) (From Topology) | H: 40S ribosomal protein rpS21 (S21e) (From Topology) | T: 40S ribosomal protein rpS21 (S21e) | F: Ribosomal_S21e | ECOD (1.6) |
Z | Ribosomal_S24e | e6az1Z1 | 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_S24e | ECOD (1.6) |
AA [auth a] | Ribosomal_S25 | e6az1a1 | A: alpha arrays | X: HTH | H: HTH | T: winged | F: Ribosomal_S25 | ECOD (1.6) |
BA [auth b] | Ribosomal_S26e | e6az1b1 | A: few secondary structure elements | X: Glucocorticoid receptor-like | H: LIM domain-like | T: LIM domain-like | F: Ribosomal_S26e | ECOD (1.6) |
CA [auth c] | Ribosomal_S27e | e6az1c1 | A: few secondary structure elements | X: Rubredoxin-like | H: Rubredoxin-related | T: Rubredoxin-related | F: Ribosomal_S27e | ECOD (1.6) |
DA [auth d] | Ribosomal_S28e | e6az1d1 | A: beta barrels | X: OB-fold | H: Nucleic acid-binding proteins (From Topology) | T: Nucleic acid-binding proteins | F: Ribosomal_S28e | ECOD (1.6) |
EA [auth e] | Ribosomal_S30 | e6az1e1 | A: extended segments | X: 40S ribosomal protein S30 (S30e) (From Topology) | H: 40S ribosomal protein S30 (S30e) (From Topology) | T: 40S ribosomal protein S30 (S30e) | F: Ribosomal_S30 | ECOD (1.6) |
FA [auth f] | Ribosomal_S27 | e6az1f1 | A: few secondary structure elements | X: Rubredoxin-like | H: Rubredoxin-related | T: Rubredoxin-related | F: Ribosomal_S27 | ECOD (1.6) |
GA [auth g] | ANAPC4_WD40_10 | e6az1g1 | A: beta duplicates or obligate multimers | X: beta-propeller-like | H: beta-propeller | T: 7-bladed | F: ANAPC4_WD40_10 | ECOD (1.6) |
N | S10_plectin | e6az1N1 | A: alpha arrays | X: HTH | H: HTH | T: winged | F: S10_plectin | ECOD (1.6) |
V | Ribosomal_S17e | e6az1V1 | A: alpha arrays | X: HTH | H: HTH | T: FF domain | F: Ribosomal_S17e | ECOD (1.6) |
Domain Annotation: CATH CATH Database Homepage
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
PF00318 | Ribosomal protein S2 (Ribosomal_S2) | Ribosomal protein S2 | - | Family | |
PF01667 | Ribosomal protein S27 (Ribosomal_S27e) | Ribosomal protein S27 | - | Family | |
PF07650 | KH domain (KH_2) | KH domain | - | Domain | |
PF00189 | Ribosomal protein S3, C-terminal domain (Ribosomal_S3_C) | Ribosomal protein S3, C-terminal domain | This family contains a central domain Pfam:PF00013, hence the amino and carboxyl terminal domains are stored separately. This is a minimal carboxyl-terminal domain. Some are much longer. | Domain | |
PF00163 | Ribosomal protein S4/S9 N-terminal domain (Ribosomal_S4) | Ribosomal protein S4/S9 N-terminal domain | - | Family | |
PF01479 | S4 domain (S4) | S4 domain | The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast pro ... | Domain | |
PF04758 | Ribosomal protein S30 (Ribosomal_S30) | Ribosomal protein S30 | - | Family | |
PF00900 | Ribosomal family S4e (Ribosomal_S4e) | Ribosomal family S4e | - | Family | |
PF16121 | 40S ribosomal protein S4 C-terminus (40S_S4_C) | 40S ribosomal protein S4 C-terminus | - | Family | |
PF08071 | RS4NT (NUC023) domain (RS4NT) | RS4NT (NUC023) domain | This is the N-terminal domain of Ribosomal S4 / S4e proteins. This domain is associated with S4 and KOW domains [1]. | Domain | |
PF01479 | S4 domain (S4) | S4 domain | The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast pro ... | Domain | |
PF00467 | KOW motif (KOW) | KOW motif | - | Family | |
PF03719 | Ribosomal protein S5, C-terminal domain (Ribosomal_S5_C) | Ribosomal protein S5, C-terminal domain | - | Domain | |
PF00333 | Ribosomal protein S5, N-terminal domain (Ribosomal_S5) | Ribosomal protein S5, N-terminal domain | - | Domain | |
PF01599 | Ribosomal protein S27a (Ribosomal_S27) | Ribosomal protein S27a | This family of ribosomal proteins consists mainly of the 40S ribosomal protein S27a which is synthesised as a C-terminal extension of ubiquitin (CEP). The S27a domain compromises the C-terminal half of the protein. The synthesis of ribosomal proteins ... | Domain | |
PF01092 | Ribosomal protein S6e (Ribosomal_S6e) | Ribosomal protein S6e | - | Family | |
PF00400 | WD domain, G-beta repeat (WD40) | WD domain, G-beta repeat | - | Repeat | |
PF00177 | Ribosomal protein S7p/S5e (Ribosomal_S7) | Ribosomal protein S7p/S5e | This family contains ribosomal protein S7 from prokaryotes and S5 from eukaryotes. | Domain | |
PF01251 | Ribosomal protein S7e (Ribosomal_S7e) | Ribosomal protein S7e | - | Family | |
PF00410 | Ribosomal protein S8 (Ribosomal_S8) | Ribosomal protein S8 | - | Domain | |
PF01201 | Ribosomal protein S8e (Ribosomal_S8e) | Ribosomal protein S8e | - | Family | |
PF00380 | Ribosomal protein S9/S16 (Ribosomal_S9) | Ribosomal protein S9/S16 | - | Family | |
PF00338 | Ribosomal protein S10p/S20e (Ribosomal_S10) | Ribosomal protein S10p/S20e | This family includes small ribosomal subunit S10 from prokaryotes and S20 from eukaryotes. | Domain | |
PF00411 | Ribosomal protein S11 (Ribosomal_S11) | Ribosomal protein S11 | - | Family | |
PF00164 | Ribosomal protein S12/S23 (Ribosom_S12_S23) | Ribosomal protein S12/S23 | - | Family | |
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 | |
PF00416 | Ribosomal protein S13/S18 (Ribosomal_S13) | Ribosomal protein S13/S18 | - | Family | |
PF00253 | Ribosomal protein S14p/S29e (Ribosomal_S14) | Ribosomal protein S14p/S29e | - | Family | |
PF00312 | Ribosomal protein S15 (Ribosomal_S15) | Ribosomal protein S15 | - | Domain | |
PF16205 | Ribosomal_S17 N-terminal (Ribosomal_S17_N) | Ribosomal_S17 N-terminal | - | Family | |
PF00366 | Ribosomal protein S17 (Ribosomal_S17) | Ribosomal protein S17 | - | Domain | |
PF00203 | Ribosomal protein S19 (Ribosomal_S19) | Ribosomal protein S19 | - | Domain | |
PF01090 | Ribosomal protein S19e (Ribosomal_S19e) | Ribosomal protein S19e | - | Family | |
PF01249 | Ribosomal protein S21e (Ribosomal_S21e) | Ribosomal protein S21e | - | Family | |
PF01282 | Ribosomal protein S24e (Ribosomal_S24e) | Ribosomal protein S24e | - | Family | |
PF03501 | Plectin/S10 domain (S10_plectin) | Plectin/S10 domain | This presumed domain is found at the N-terminus of some isoforms of the cytoskeletal muscle protein plectin as well as the ribosomal S10 protein. This domain may be involved in RNA binding. | Domain | |