6OKK
Cryo-EM structure of the Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine, small subunit
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
B | SCOP2B Superfamily | Ribosomal S3Ae-like | 8053207 | 3002166 | SCOP2B (2022-06-29) |
H | SCOP2B Superfamily | GS N-terminal domain-like | 8053165 | 3000408 | SCOP2B (2022-06-29) |
I | SCOP2B Superfamily | Ribosomal protein S7 | 8066011 | 3000799 | SCOP2B (2022-06-29) |
K | SCOP2B Superfamily | Ribosomal protein S8 | 8081977 | 3000709 | SCOP2B (2022-06-29) |
M | SCOP2 Family | Translational machinery components | 8096271 | 4000951 | SCOP2 (2022-06-29) |
M | SCOP2 Superfamily | Ribosomal protein S5 domain 2-like | 8096272 | 3000100 | SCOP2 (2022-06-29) |
N | SCOP2B Superfamily | Ribosomal protein S10 | 8100154 | 3001336 | SCOP2B (2022-06-29) |
O | SCOP2B Superfamily | Winged helix DNA-binding domain | 8055711 | 3000034 | SCOP2B (2022-06-29) |
S | SCOP2B Superfamily | S13-like H2TH domain | 8100146 | 3000053 | SCOP2B (2022-06-29) |
T | SCOP2B Superfamily | Glucocorticoid receptor-like (DNA-binding domain) | 8052571 | 3000068 | SCOP2B (2022-06-29) |
U | SCOP2B Superfamily | S15/NS1 RNA-binding domain | 8052965 | 3001284 | SCOP2B (2022-06-29) |
U | SCOP2B Superfamily | Homeodomain-like | 8052964 | 3000001 | SCOP2B (2022-06-29) |
V | SCOP2B Superfamily | Ribosomal S17 N-terminal domain-like | 8052724 | 3002138 | SCOP2B (2022-06-29) |
V | SCOP2B Superfamily | Nucleic acid-binding proteins | 8052726 | 3000135 | SCOP2B (2022-06-29) |
EA [auth e] | SCOP2B Superfamily | Nucleic acid-binding proteins | 8063420 | 3000135 | SCOP2B (2022-06-29) |
FA [auth f] | SCOP2B Superfamily | Ribosomal protein S30e-like | 8053452 | 3002190 | SCOP2B (2022-06-29) |
R | SCOP2B Superfamily | L30e-like | 8063972 | 3001739 | SCOP2B (2022-06-29) |
Z | SCOP2B Superfamily | Glucocorticoid receptor-like (DNA-binding domain) | 8053137 | 3000068 | SCOP2B (2022-06-29) |
CA [auth c] | SCOP2B Superfamily | Glucocorticoid receptor-like (DNA-binding domain) | 8053146 | 3000068 | SCOP2B (2022-06-29) |
C | SCOP2B Superfamily | SIS domain/Ribosomal protein S2-like | 8063816 | 3001397 | SCOP2B (2022-06-29) |
F | SCOP2B Superfamily | Nucleic acid-binding proteins | 8052749 | 3000135 | SCOP2B (2022-06-29) |
F | SCOP2B Superfamily | Alpha-L RNA-binding motif | 8052748 | 3001473 | SCOP2B (2022-06-29) |
F | SCOP2B Superfamily | Translation proteins SH3-like KOW motif containing domain | 8052750 | 3000334 | 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) |
---|---|---|---|---|---|---|---|---|
B | PF01015 | e6okkB1 | 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: PF01015 | ECOD (1.6) |
B | PF01015 | e6okkB2 | 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: PF01015 | ECOD (1.6) |
E | PF00163,PF01479 | e6okkE1 | A: a+b two layers | X: beta-Grasp | H: Ubiquitin-related | T: Alpha-L RNA-binding motif | F: PF00163,PF01479 | ECOD (1.6) |
G | PF03719 | e6okkG3 | 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: PF03719 | ECOD (1.6) |
G | PF00333 | e6okkG1 | A: a+b two layers | X: dsRBD-like | H: dsRNA-binding domain-like (From Topology) | T: dsRNA-binding domain-like | F: PF00333 | ECOD (1.6) |
G | PF00333 | e6okkG2 | 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: PF00333 | ECOD (1.6) |
H | PF01092 | e6okkH1 | A: beta barrels | X: Ribosomal protein L25-like | H: Ribosomal protein L25-like (From Topology) | T: Ribosomal protein L25-like | F: PF01092 | ECOD (1.6) |
I | PF00177 | e6okkI1 | A: alpha arrays | X: Ribosomal protein S7 (From Topology) | H: Ribosomal protein S7 (From Topology) | T: Ribosomal protein S7 | F: PF00177 | ECOD (1.6) |
J | PF01251 | e6okkJ2 | 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: PF01251 | ECOD (1.6) |
K | PF00410 | e6okkK1 | 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: PF00410 | ECOD (1.6) |
K | PF00410 | e6okkK2 | 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: PF00410 | ECOD (1.6) |
L | PF01201 | e6okkL1 | A: beta barrels | X: Ribosomal protein L14-like | H: Ribosomal protein L14-related (From Topology) | T: Ribosomal protein L14-related | F: PF01201 | ECOD (1.6) |
M | PF00380 | e6okkM1 | 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: PF00380 | ECOD (1.6) |
N | PF00338 | e6okkN1 | A: a+b two layers | X: Alpha-beta plaits | H: Ribosomal protein S10 (From Topology) | T: Ribosomal protein S10 | F: PF00338 | ECOD (1.6) |
O | PF03501 | e6okkO1 | A: alpha arrays | X: HTH | H: HTH | T: winged | F: PF03501 | ECOD (1.6) |
P | PF00411 | e6okkP1 | A: mixed a+b and a/b | X: Ribonuclease H-like | H: Ribonuclease H-like (From Topology) | T: Ribonuclease H-like | F: PF00411 | ECOD (1.6) |
S | PF00416 | e6okkS1 | A: alpha arrays | X: HhH/H2TH | H: H2TH (From Topology) | T: H2TH | F: PF00416 | ECOD (1.6) |
T | PF00253 | e6okkT1 | A: few secondary structure elements | X: Glucocorticoid receptor-like | H: LIM domain-like | T: LIM domain-like | F: PF00253 | ECOD (1.6) |
U | PF08069 | e6okkU2 | A: alpha arrays | X: HTH | H: 40S ribosomal protein S13 N-terminal domain (From Topology) | T: 40S ribosomal protein S13 N-terminal domain | F: PF08069 | ECOD (1.6) |
U | PF00312 | e6okkU1 | 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: PF00312 | ECOD (1.6) |
V | PF00366,PF16205 | e6okkV1 | A: beta barrels | X: OB-fold | H: Nucleic acid-binding proteins (From Topology) | T: Nucleic acid-binding proteins | F: PF00366,PF16205 | ECOD (1.6) |
W | PF00833 | e6okkW1 | A: alpha arrays | X: HTH | H: HTH | T: FF domain | F: PF00833 | ECOD (1.6) |
Y | PF01090 | e6okkY1 | A: alpha arrays | X: HTH | H: HTH | T: winged | F: PF01090 | ECOD (1.6) |
AA [auth a] | PF01282 | e6okka1 | 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: PF01282 | ECOD (1.6) |
BA [auth b] | PF03297 | e6okkb1 | A: alpha arrays | X: HTH | H: HTH | T: winged | F: PF03297 | ECOD (1.6) |
DA [auth d] | PF01667 | e6okkd1 | A: few secondary structure elements | X: Rubredoxin-like | H: Rubredoxin-related | T: Rubredoxin-related | F: PF01667 | ECOD (1.6) |
EA [auth e] | PF01200 | e6okke1 | A: beta barrels | X: OB-fold | H: Nucleic acid-binding proteins (From Topology) | T: Nucleic acid-binding proteins | F: PF01200 | ECOD (1.6) |
FA [auth f] | PF04758 | e6okkf1 | 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: PF04758 | ECOD (1.6) |
Q | PF00164 | e6okkQ1 | A: beta barrels | X: OB-fold | H: Nucleic acid-binding proteins (From Topology) | T: Nucleic acid-binding proteins | F: PF00164 | ECOD (1.6) |
R | PF01248 | e6okkR1 | A: a+b three layers | X: Bacillus chorismate mutase-like | H: L30e-like (From Topology) | T: L30e-like | F: PF01248 | ECOD (1.6) |
X | PF00203 | e6okkX1 | A: a+b two layers | X: Ribosomal protein S19 (From Topology) | H: Ribosomal protein S19 (From Topology) | T: Ribosomal protein S19 | F: PF00203 | ECOD (1.6) |
Z | PF01249 | e6okkZ1 | 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: PF01249 | ECOD (1.6) |
CA [auth c] | PF01283 | e6okkc1 | A: few secondary structure elements | X: Glucocorticoid receptor-like | H: LIM domain-like | T: LIM domain-like | F: PF01283 | ECOD (1.6) |
C | PF00318 | e6okkC1 | A: a/b three-layered sandwiches | X: Flavodoxin-like | H: Ribosomal protein S2/SIS domain (From Topology) | T: Ribosomal protein S2/SIS domain | F: PF00318 | ECOD (1.6) |
D | PF00189 | e6okkD2 | A: a+b two layers | X: T-fold | H: Ribosomal protein S3-C (From Topology) | T: Ribosomal protein S3-C | F: PF00189 | ECOD (1.6) |
D | F_UNCLASSIFIED | e6okkD1 | A: a+b two layers | X: Alpha-lytic protease prodomain-like | H: KH-domains | T: Prokaryotic type KH domain (KH-domain type II) | F: F_UNCLASSIFIED | ECOD (1.6) |
F | PF00900 | e6okkF2 | A: beta barrels | X: OB-fold | H: Nucleic acid-binding proteins (From Topology) | T: Nucleic acid-binding proteins | F: PF00900 | ECOD (1.6) |
F | PF00467,PF16121 | e6okkF3 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: PF00467,PF16121 | ECOD (1.6) |
F | PF00900,PF08071 | e6okkF1 | A: a+b two layers | X: beta-Grasp | H: Ubiquitin-related | T: Alpha-L RNA-binding motif | F: PF00900,PF08071 | ECOD (1.6) |
Domain Annotation: CATH CATH Database Homepage
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
PF01015 | Ribosomal S3Ae family (Ribosomal_S3Ae) | Ribosomal S3Ae family | - | Family | |
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 | |
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 | |
PF01092 | Ribosomal protein S6e (Ribosomal_S6e) | Ribosomal protein S6e | - | Family | |
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 | |
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 | |
PF00416 | Ribosomal protein S13/S18 (Ribosomal_S13) | Ribosomal protein S13/S18 | - | Family | |
PF00253 | Ribosomal protein S14p/S29e (Ribosomal_S14) | Ribosomal protein S14p/S29e | - | Family | |
PF08069 | Ribosomal S13/S15 N-terminal domain (Ribosomal_S13_N) | Ribosomal S13/S15 N-terminal domain | This domain is found at the N-terminus of ribosomal S13 and S15 proteins. This domain is also identified as NUC021 [1]. | Domain | |
PF00312 | Ribosomal protein S15 (Ribosomal_S15) | Ribosomal protein S15 | - | Domain | |
PF00366 | Ribosomal protein S17 (Ribosomal_S17) | Ribosomal protein S17 | - | Domain | |
PF16205 | Ribosomal_S17 N-terminal (Ribosomal_S17_N) | Ribosomal_S17 N-terminal | - | Family | |
PF00833 | Ribosomal S17 (Ribosomal_S17e) | Ribosomal S17 | - | Family | |
PF01090 | Ribosomal protein S19e (Ribosomal_S19e) | Ribosomal protein S19e | - | Family | |
AA [auth a] | PF01282 | Ribosomal protein S24e (Ribosomal_S24e) | Ribosomal protein S24e | - | Family |
BA [auth b] | PF03297 | S25 ribosomal protein (Ribosomal_S25) | S25 ribosomal protein | - | Family |
DA [auth d] | PF01667 | Ribosomal protein S27 (Ribosomal_S27e) | Ribosomal protein S27 | - | Family |
EA [auth e] | PF01200 | Ribosomal protein S28e (Ribosomal_S28e) | Ribosomal protein S28e | - | Family |
FA [auth f] | PF04758 | Ribosomal protein S30 (Ribosomal_S30) | Ribosomal protein S30 | - | 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 | |
PF00203 | Ribosomal protein S19 (Ribosomal_S19) | Ribosomal protein S19 | - | Domain | |
PF01249 | Ribosomal protein S21e (Ribosomal_S21e) | Ribosomal protein S21e | - | Family | |
CA [auth c] | PF01283 | Ribosomal protein S26e (Ribosomal_S26e) | Ribosomal protein S26e | - | Family |
PF00318 | Ribosomal protein S2 (Ribosomal_S2) | Ribosomal protein S2 | - | 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 | |
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 | |
PF00467 | KOW motif (KOW) | KOW motif | - | Family |