6ZMT
SARS-CoV-2 Nsp1 bound to a pre-40S-like ribosome complex
Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage
Chains | Domain Info | Class | Fold | Superfamily | Family | Domain | Species | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
FA [auth j] | d6zmtj_ | All beta proteins | 7-bladed beta-propeller | WD40 repeat-like | WD40-repeat | Guanine nucleotide-binding protein subunit beta-2-like 1 (GNB2L1 or RACK1) | (Homo sapiens ) [TaxId: 9606 ], | SCOPe (2.08) |
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
A [auth B] | SCOP2B Superfamily | SIS domain/Ribosomal protein S2-like | 8052791 | 3001397 | SCOP2B (2022-06-29) |
B [auth C] | SCOP2B Superfamily | Ribosomal S3Ae-like | 8053212 | 3002166 | SCOP2B (2022-06-29) |
E [auth F] | SCOP2B Superfamily | Prokaryotic type KH domain (KH-domain type II) | 8043545 | 3001043 | SCOP2B (2022-06-29) |
F [auth G] | SCOP2B Superfamily | GS N-terminal domain-like | 8053171 | 3000408 | SCOP2B (2022-06-29) |
H [auth I] | SCOP2B Superfamily | 50S Ribosomal protein L14-like | 8053077 | 3000433 | SCOP2B (2022-06-29) |
J [auth K] | SCOP2B Superfamily | Ribosomal protein S7 | 8066003 | 3000799 | SCOP2B (2022-06-29) |
K [auth L] | SCOP2B Superfamily | Nucleic acid-binding proteins | 8052717 | 3000135 | SCOP2B (2022-06-29) |
K [auth L] | SCOP2B Superfamily | Ribosomal S17 N-terminal domain-like | 8052715 | 3002138 | SCOP2B (2022-06-29) |
L [auth M] | SCOP2B Superfamily | Winged helix DNA-binding domain | 8055714 | 3000034 | SCOP2B (2022-06-29) |
M [auth N] | SCOP2B Superfamily | Homeodomain-like | 8052958 | 3000001 | SCOP2B (2022-06-29) |
M [auth N] | SCOP2B Superfamily | S15/NS1 RNA-binding domain | 8052959 | 3001284 | SCOP2B (2022-06-29) |
O [auth P] | SCOP2B Superfamily | Translational machinery components | 8098844 | 3000571 | SCOP2B (2022-06-29) |
Q [auth R] | SCOP2B Superfamily | Ribosomal protein S5 domain 2-like | 8082685 | 3000100 | SCOP2B (2022-06-29) |
U [auth V] | SCOP2B Superfamily | Ribosomal protein S10 | 8098806 | 3001336 | SCOP2B (2022-06-29) |
V [auth W] | SCOP2B Superfamily | Ribosomal protein S8 | 8095469 | 3000709 | SCOP2B (2022-06-29) |
Y [auth Z] | SCOP2B Superfamily | Glucocorticoid receptor-like (DNA-binding domain) | 8053139 | 3000068 | SCOP2B (2022-06-29) |
Z [auth a] | SCOP2B Superfamily | Winged helix DNA-binding domain | 8090992 | 3000034 | SCOP2B (2022-06-29) |
BA [auth d] | SCOP2B Superfamily | Nucleic acid-binding proteins | 8063426 | 3000135 | SCOP2B (2022-06-29) |
CA [auth e] | SCOP2B Superfamily | Ribosomal protein S30e-like | 8053453 | 3002190 | SCOP2B (2022-06-29) |
DA [auth f] | SCOP2B Superfamily | Glucocorticoid receptor-like (DNA-binding domain) | 8052572 | 3000068 | SCOP2B (2022-06-29) |
N [auth O] | SCOP2B Superfamily | L30e-like | 8063978 | 3001739 | SCOP2B (2022-06-29) |
S [auth T] | SCOP2B Superfamily | S13-like H2TH domain | 8101555 | 3000053 | SCOP2B (2022-06-29) |
T [auth U] | SCOP2B Superfamily | Winged helix DNA-binding domain | 8089318 | 3000034 | SCOP2B (2022-06-29) |
D [auth E] | SCOP2B Superfamily | Nucleic acid-binding proteins | 8052756 | 3000135 | SCOP2B (2022-06-29) |
D [auth E] | SCOP2B Superfamily | Alpha-L RNA-binding motif | 8052755 | 3001473 | SCOP2B (2022-06-29) |
D [auth E] | SCOP2B Superfamily | Translation proteins SH3-like KOW motif containing domain | 8052757 | 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) |
---|---|---|---|---|---|---|---|---|
A [auth B] | Ribosomal_S2_2 | e6zmtB1 | 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) |
B [auth C] | Ribosomal_S3Ae_N | e6zmtC2 | 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) |
B [auth C] | Ribosomal_S3Ae_C | e6zmtC1 | 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) |
C [auth D] | Ribosomal_S5_C_1 | e6zmtD1 | 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) |
C [auth D] | Ribosomal_S5_3 | e6zmtD3 | 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) |
C [auth D] | Ribosomal_S5_2 | e6zmtD2 | 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) |
E [auth F] | Ribosomal_S3_C | e6zmtF1 | 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) |
E [auth F] | KH_2_3 | e6zmtF2 | 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) |
F [auth G] | Ribosomal_S6e | e6zmtG1 | 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) |
G [auth H] | Ribosomal_S7e_N | e6zmtH1 | 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) |
G [auth H] | Ribosomal_S7e_C_1 | e6zmtH2 | 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_1 | ECOD (1.6) |
H [auth I] | Ribosomal_S8e | e6zmtI1 | 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) |
I [auth J] | S4 | e6zmtJ1 | A: a+b two layers | X: beta-Grasp | H: Ubiquitin-related | T: Alpha-L RNA-binding motif | F: S4 | ECOD (1.6) |
J [auth K] | Ribosomal_S7_1 | e6zmtK1 | 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) |
K [auth L] | Ribosomal_S17_1 | e6zmtL1 | 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) |
L [auth M] | S10_plectin | e6zmtM1 | A: alpha arrays | X: HTH | H: HTH | T: winged | F: S10_plectin | ECOD (1.6) |
M [auth N] | Ribosomal_S13_N | e6zmtN2 | 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 | ECOD (1.6) |
M [auth N] | Ribosomal_S15_2 | e6zmtN1 | 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) |
O [auth P] | Ribosomal_S11 | e6zmtP1 | 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 [auth Q] | Ribosomal_S19 | e6zmtQ1 | 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) |
Q [auth R] | Ribosomal_S9 | e6zmtR1 | 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) |
R [auth S] | Ribosomal_S17e | e6zmtS1 | A: alpha arrays | X: HTH | H: HTH | T: FF domain | F: Ribosomal_S17e | ECOD (1.6) |
U [auth V] | Ribosomal_S10_1 | e6zmtV1 | 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) |
V [auth W] | Ribosomal_S8_N_1 | e6zmtW1 | 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) |
V [auth W] | Ribosomal_S8_C_1 | e6zmtW2 | 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) |
W [auth X] | Ribosom_S12_S23 | e6zmtX1 | 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) |
X [auth Y] | Ribosomal_S24e | e6zmtY1 | 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) |
Y [auth Z] | Ribosomal_S21e | e6zmtZ1 | 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 [auth a] | Ribosomal_S25 | e6zmta1 | A: alpha arrays | X: HTH | H: HTH | T: winged | F: Ribosomal_S25 | ECOD (1.6) |
AA [auth b] | Ribosomal_S27e | e6zmtb1 | A: few secondary structure elements | X: Rubredoxin-like | H: Rubredoxin-related | T: Rubredoxin-related | F: Ribosomal_S27e | ECOD (1.6) |
BA [auth d] | Ribosomal_S28e | e6zmtd1 | A: beta barrels | X: OB-fold | H: Nucleic acid-binding proteins (From Topology) | T: Nucleic acid-binding proteins | F: Ribosomal_S28e | ECOD (1.6) |
CA [auth e] | Ribosomal_S30 | e6zmte1 | 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) |
DA [auth f] | Ribosomal_S14_2 | e6zmtf1 | A: few secondary structure elements | X: Glucocorticoid receptor-like | H: LIM domain-like | T: LIM domain-like | F: Ribosomal_S14_2 | ECOD (1.6) |
EA [auth g] | Ribosomal_S27 | e6zmtg1 | A: few secondary structure elements | X: Rubredoxin-like | H: Rubredoxin-related | T: Rubredoxin-related | F: Ribosomal_S27 | ECOD (1.6) |
FA [auth j] | DUF1899 | e6zmtj1 | A: beta duplicates or obligate multimers | X: beta-propeller-like | H: beta-propeller | T: 7-bladed | F: DUF1899 | ECOD (1.6) |
N [auth O] | Ribosomal_L7Ae | e6zmtO1 | A: a+b three layers | X: Bacillus chorismate mutase-like | H: L30e-like (From Topology) | T: L30e-like | F: Ribosomal_L7Ae | ECOD (1.6) |
S [auth T] | Ribosomal_S13 | e6zmtT1 | A: alpha arrays | X: HhH/H2TH | H: H2TH (From Topology) | T: H2TH | F: Ribosomal_S13 | ECOD (1.6) |
T [auth U] | Ribosomal_S19e | e6zmtU1 | A: alpha arrays | X: HTH | H: HTH | T: winged | F: Ribosomal_S19e | ECOD (1.6) |
D [auth E] | Ribosomal_S4e | e6zmtE3 | A: beta barrels | X: OB-fold | H: Nucleic acid-binding proteins (From Topology) | T: Nucleic acid-binding proteins | F: Ribosomal_S4e | ECOD (1.6) |
D [auth E] | 40S_S4_C | e6zmtE1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: 40S_S4_C | ECOD (1.6) |
D [auth E] | RS4NT | e6zmtE2 | A: a+b two layers | X: beta-Grasp | H: Ubiquitin-related | T: Alpha-L RNA-binding motif | F: RS4NT | ECOD (1.6) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
A [auth B] | PF01667 | Ribosomal protein S27 (Ribosomal_S27e) | Ribosomal protein S27 | - | Family |
A [auth B] | PF00318 | Ribosomal protein S2 (Ribosomal_S2) | Ribosomal protein S2 | - | Family |
A [auth B] | PF16122 | 40S ribosomal protein SA C-terminus (40S_SA_C) | 40S ribosomal protein SA C-terminus | - | Family |
C [auth D] | PF03719 | Ribosomal protein S5, C-terminal domain (Ribosomal_S5_C) | Ribosomal protein S5, C-terminal domain | - | Domain |
C [auth D] | PF00333 | Ribosomal protein S5, N-terminal domain (Ribosomal_S5) | Ribosomal protein S5, N-terminal domain | - | Domain |
E [auth F] | PF07650 | KH domain (KH_2) | KH domain | - | Domain |
E [auth F] | PF00253 | Ribosomal protein S14p/S29e (Ribosomal_S14) | Ribosomal protein S14p/S29e | - | Family |
E [auth F] | 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 |
F [auth G] | PF01092 | Ribosomal protein S6e (Ribosomal_S6e) | Ribosomal protein S6e | - | Family |
F [auth G] | 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 |
H [auth I] | PF01201 | Ribosomal protein S8e (Ribosomal_S8e) | Ribosomal protein S8e | - | Family |
I [auth J] | PF00163 | Ribosomal protein S4/S9 N-terminal domain (Ribosomal_S4) | Ribosomal protein S4/S9 N-terminal domain | - | Family |
I [auth J] | 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 |
I [auth J] | PF00400 | WD domain, G-beta repeat (WD40) | WD domain, G-beta repeat | - | Repeat |
J [auth K] | PF00177 | Ribosomal protein S7p/S5e (Ribosomal_S7) | Ribosomal protein S7p/S5e | This family contains ribosomal protein S7 from prokaryotes and S5 from eukaryotes. | Domain |
K [auth L] | PF16205 | Ribosomal_S17 N-terminal (Ribosomal_S17_N) | Ribosomal_S17 N-terminal | - | Family |
K [auth L] | PF00366 | Ribosomal protein S17 (Ribosomal_S17) | Ribosomal protein S17 | - | Domain |
L [auth M] | 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 |
M [auth N] | PF00312 | Ribosomal protein S15 (Ribosomal_S15) | Ribosomal protein S15 | - | Domain |
O [auth P] | PF00411 | Ribosomal protein S11 (Ribosomal_S11) | Ribosomal protein S11 | - | Family |
P [auth Q] | PF00203 | Ribosomal protein S19 (Ribosomal_S19) | Ribosomal protein S19 | - | Domain |
Q [auth R] | PF00380 | Ribosomal protein S9/S16 (Ribosomal_S9) | Ribosomal protein S9/S16 | - | Family |
U [auth V] | 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 |
V [auth W] | PF00410 | Ribosomal protein S8 (Ribosomal_S8) | Ribosomal protein S8 | - | Domain |
W [auth X] | PF00164 | Ribosomal protein S12/S23 (Ribosom_S12_S23) | Ribosomal protein S12/S23 | - | Family |
X [auth Y] | PF01282 | Ribosomal protein S24e (Ribosomal_S24e) | Ribosomal protein S24e | - | Family |
Y [auth Z] | PF01249 | Ribosomal protein S21e (Ribosomal_S21e) | Ribosomal protein S21e | - | Family |
N [auth O] | 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 |
S [auth T] | PF00416 | Ribosomal protein S13/S18 (Ribosomal_S13) | Ribosomal protein S13/S18 | - | Family |
T [auth U] | PF01090 | Ribosomal protein S19e (Ribosomal_S19e) | Ribosomal protein S19e | - | Family |
T [auth U] | PF22298 | Tsr1, G-like domain (Tsr1_G-like) | Tsr1, G-like domain | This entry represents the G-like (guanine nucleotide-binding domain) domain, found in Tsr1, a protein required for normal export of the pre-40S particles from the nucleus to the cytoplasm during 40S ribosomal subunit synthesis [1-5]. This domain adop ... | Domain |
D [auth E] | PF00900 | Ribosomal family S4e (Ribosomal_S4e) | Ribosomal family S4e | - | Family |
D [auth E] | PF16121 | 40S ribosomal protein S4 C-terminus (40S_S4_C) | 40S ribosomal protein S4 C-terminus | - | Family |
D [auth E] | 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 |
D [auth E] | PF00467 | KOW motif (KOW) | KOW motif | - | Family |