6EM1
State C (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
N [auth y] | SCOP2B Superfamily | Pentein | 8036230 | 3000640 | SCOP2B (2022-06-29) |
P [auth B] | SCOP2B Superfamily | Translational proteins | 8078363 | 3000811 | SCOP2B (2022-06-29) |
Q [auth C] | SCOP2B Superfamily | Ribosomal protein L4 | 8052816 | 3001146 | SCOP2B (2022-06-29) |
Q [auth C] | SCOP2B Superfamily | 60S ribosomal protein L4 C-terminal domain-like | 8052815 | 3002143 | SCOP2B (2022-06-29) |
S [auth E] | SCOP2B Superfamily | Translation proteins SH3-like KOW motif containing domain | 8053109 | 3000334 | SCOP2B (2022-06-29) |
B [auth F] | SCOP2B Superfamily | Ribosomal L30p/L7e protein, N-terminal domain-lke | 8052916 | 3002152 | SCOP2B (2022-06-29) |
B [auth F] | SCOP2B Superfamily | Ribosomal protein L30p/L7e | 8052917 | 3001378 | SCOP2B (2022-06-29) |
T [auth f] | SCOP2B Superfamily | Translational proteins | 8087451 | 3000811 | SCOP2B (2022-06-29) |
U [auth G] | SCOP2B Superfamily | L30e-like | 8063962 | 3001739 | SCOP2B (2022-06-29) |
BA [auth N] | SCOP2B Superfamily | Ribosomal proteins S24e, L23 and L15e | 8082481 | 3000210 | SCOP2B (2022-06-29) |
CA [auth O] | SCOP2B Superfamily | Ribosomal protein L13 | 8066053 | 3001134 | SCOP2B (2022-06-29) |
DA [auth P] | SCOP2B Superfamily | Ribosomal protein L22 | 8076708 | 3001078 | SCOP2B (2022-06-29) |
EA [auth Q] | SCOP2B Superfamily | Ribosomal proteins L15p and L18e | 8095970 | 3001045 | SCOP2B (2022-06-29) |
GA [auth V] | SCOP2B Superfamily | 50S Ribosomal protein L14-like | 8103364 | 3000433 | SCOP2B (2022-06-29) |
HA [auth Y] | SCOP2B Superfamily | Translation proteins SH3-like KOW motif containing domain | 8076760 | 3000334 | SCOP2B (2022-06-29) |
OA [auth o] | SCOP2B Superfamily | RNA-binding domain, RBD | 8061969 | 3000110 | 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) |
---|---|---|---|---|---|---|---|---|
M [auth W] | Ribosomal_L10 | e6em1W2 | A: a+b two layers | X: Alpha-beta plaits | H: Ribosomal protein L10-like (From Topology) | T: Ribosomal protein L10-like | F: Ribosomal_L10 | ECOD (1.6) |
M [auth W] | Ribosomal_P0_L10e | e6em1W1 | A: a+b two layers | X: Insertion domain in 60S ribosomal protein rpP0 (L10P) (From Topology) | H: Insertion domain in 60S ribosomal protein rpP0 (L10P) (From Topology) | T: Insertion domain in 60S ribosomal protein rpP0 (L10P) | F: Ribosomal_P0_L10e | ECOD (1.6) |
N [auth y] | eIF-6 | e6em1y1 | A: a+b duplicates or obligate multimers | X: Pentein (From Topology) | H: Pentein (From Topology) | T: Pentein | F: eIF-6 | ECOD (1.6) |
P [auth B] | Ribosomal_L3 | e6em1B1 | A: beta barrels | X: cradle loop barrel | H: RIFT-related | T: Alanine racemase-C | F: Ribosomal_L3 | ECOD (1.6) |
Q [auth C] | Ribosomal_L4 | e6em1C3 | 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) |
Q [auth C] | Ribos_L4_asso_C | e6em1C2 | A: extended segments | X: C-terminal helical region in 60S ribosomal protein L4 (L4p) (From Topology) | H: C-terminal helical region in 60S ribosomal protein L4 (L4p) (From Topology) | T: C-terminal helical region in 60S ribosomal protein L4 (L4p) | F: Ribos_L4_asso_C | ECOD (1.6) |
R [auth e] | Ribosomal_L32e | e6em1e1 | 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) |
S [auth E] | Ribosomal_L6e | e6em1E1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: Ribosomal_L6e | ECOD (1.6) |
B [auth F] | Ribosomal_L30_1 | e6em1F1 | 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) |
T [auth f] | Ribosomal_L35Ae | e6em1f1 | A: beta barrels | X: cradle loop barrel | H: RIFT-related | T: Alanine racemase-C | F: Ribosomal_L35Ae | ECOD (1.6) |
U [auth G] | Ribosomal_L7Ae_1 | e6em1G1 | 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) |
V [auth h] | Ribosomal_L29_2 | e6em1h1 | 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) |
W [auth H] | Ribosomal_L6_2 | e6em1H2 | 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) |
W [auth H] | Ribosomal_L6 | e6em1H1 | 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) |
X [auth i] | Ribosomal_L36e | e6em1i1 | A: alpha arrays | X: 60S ribosomal protein rpL36 (L36e) (From Topology) | H: 60S ribosomal protein rpL36 (L36e) (From Topology) | T: 60S ribosomal protein rpL36 (L36e) | F: Ribosomal_L36e | ECOD (1.6) |
Y [auth j] | Ribosomal_L37e | e6em1j1 | A: few secondary structure elements | X: Rubredoxin-like | H: Rubredoxin-related | T: Rubredoxin-related | F: Ribosomal_L37e | ECOD (1.6) |
Z [auth L] | Ribosomal_L13e | e6em1L1 | A: extended segments | X: RPL13 (From Topology) | H: RPL13 (From Topology) | T: RPL13 | F: Ribosomal_L13e | ECOD (1.6) |
AA [auth M] | Ribosomal_L14e | e6em1M1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: Ribosomal_L14e | ECOD (1.6) |
BA [auth N] | Ribosomal_L15e | e6em1N1 | 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) |
CA [auth O] | Ribosomal_L13 | e6em1O1 | 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) |
DA [auth P] | Ribosomal_L22 | e6em1P1 | 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) |
EA [auth Q] | Ribosomal_L18 | e6em1Q1 | 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) |
FA [auth S] | Ribosomal_L18A | e6em1S2 | A: a+b two layers | X: GP2-like | H: RplX-like (From Topology) | T: RplX-like | F: Ribosomal_L18A | ECOD (1.6) |
GA [auth V] | Ribosomal_L14 | e6em1V1 | 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) |
HA [auth Y] | Ribosomal_L26 | e6em1Y1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: Ribosomal_L26 | ECOD (1.6) |
LA [auth K] | Ribosomal_L1_2nd | e6em1K2 | A: a+b two layers | X: a+b domain in Ribosomal protein L1 (From Topology) | H: a+b domain in Ribosomal protein L1 (From Topology) | T: a+b domain in Ribosomal protein L1 | F: Ribosomal_L1_2nd | ECOD (1.6) |
LA [auth K] | Ribosomal_L1_1st_1 | e6em1K1 | A: a/b three-layered sandwiches | X: Flavodoxin-like | H: Rossmann-like domain in Ribosomal protein L1 (From Topology) | T: Rossmann-like domain in Ribosomal protein L1 | F: Ribosomal_L1_1st_1 | ECOD (1.6) |
D [auth 4] | UNK_F_TYPE | e6em141 | A: alpha superhelices | X: Repetitive alpha hairpins | H: ARM repeat (From Topology) | T: ARM repeat | F: UNK_F_TYPE | ECOD (1.6) |
NA [auth D] | UNK_F_TYPE | e6em1D2 | A: alpha duplicates or obligate multimers | X: RNA helicase Hera dimerization domain (From Topology) | H: RNA helicase Hera dimerization domain (From Topology) | T: RNA helicase Hera dimerization domain | F: UNK_F_TYPE | ECOD (1.6) |
NA [auth D] | Helicase_C_1 | e6em1D1 | A: a/b three-layered sandwiches | X: P-loop domains-like | H: P-loop domains-related | T: P-loop containing nucleoside triphosphate hydrolases | F: Helicase_C_1 | ECOD (1.6) |
QA [auth t] | Ribosomal_L30_1 | e6em1t1 | 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) |
E [auth 5] | ANAPC4_WD40_11 | e6em151 | A: beta duplicates or obligate multimers | X: beta-propeller-like | H: beta-propeller | T: 8-bladed | F: ANAPC4_WD40_11 | ECOD (1.6) |
F [auth A] | Brix | e6em1A1 | A: a/b three-layered sandwiches | X: Anticodon-binding domain of Class II aaRS (From Topology) | H: Anticodon-binding domain of Class II aaRS (From Topology) | T: Anticodon-binding domain of Class II aaRS | F: Brix | ECOD (1.6) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
M [auth W] | PF17777 | Insertion domain in 60S ribosomal protein L10P (RL10P_insert) | Insertion domain in 60S ribosomal protein L10P | This domain is found in prokaryotic and archaeal ribosomal L10 protein [1]. | Domain |
M [auth W] | PF00466 | Ribosomal protein L10 (Ribosomal_L10) | Ribosomal protein L10 | - | Family |
P [auth B] | PF17835 | NOG1 N-terminal helical domain (NOG1_N) | NOG1 N-terminal helical domain | This domain is found at the N-terminus of NOG1 GTPase proteins. | Domain |
P [auth B] | PF06858 | Nucleolar GTP-binding protein 1 (NOG1) (NOG1) | Nucleolar GTP-binding protein 1 (NOG1) | - | Family |
Q [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 |
Q [auth C] | PF00573 | Ribosomal protein L4/L1 family (Ribosomal_L4) | Ribosomal protein L4/L1 family | - | Family |
S [auth E] | PF01655 | Ribosomal protein L32 (Ribosomal_L32e) | Ribosomal protein L32 | - | Family |
S [auth E] | PF01159 | Ribosomal protein L6e (Ribosomal_L6e) | Ribosomal protein L6e | - | Family |
B [auth F] | PF08079 | Ribosomal L30 N-terminal domain (Ribosomal_L30_N) | Ribosomal L30 N-terminal domain | This presumed domain is found at the N-terminus of Ribosomal L30 proteins and has been termed RL30NT or NUC018 [1]. | Domain |
B [auth F] | PF00327 | Ribosomal protein L30p/L7e (Ribosomal_L30) | Ribosomal protein L30p/L7e | This family includes prokaryotic L30 and eukaryotic L7. | Domain |
B [auth F] | PF01247 | Ribosomal protein L35Ae (Ribosomal_L35Ae) | Ribosomal protein L35Ae | - | Domain |
U [auth G] | 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 |
W [auth H] | PF00831 | Ribosomal L29 protein (Ribosomal_L29) | Ribosomal L29 protein | - | Family |
W [auth H] | PF00347 | Ribosomal protein L6 (Ribosomal_L6) | Ribosomal protein L6 | - | Domain |
AA [auth M] | PF01929 | Ribosomal protein L14 (Ribosomal_L14e) | Ribosomal protein L14 | - | Family |
AA [auth M] | PF00467 | KOW motif (KOW) | KOW motif | - | Family |
BA [auth N] | PF00827 | Ribosomal L15 (Ribosomal_L15e) | Ribosomal L15 | - | Family |
CA [auth O] | PF00076 | RNA recognition motif (RRM_1) | RNA recognition motif | The RRM motif (a.k.a. RRM, RBD, or RNP domain) is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and pro ... | Domain |
CA [auth O] | PF00572 | Ribosomal protein L13 (Ribosomal_L13) | Ribosomal protein L13 | - | Family |
C [auth 3] | PF01778 | Ribosomal L28e protein family (Ribosomal_L28e) | Ribosomal L28e protein family | - | Family |
C [auth 3] | PF04874 | Mak16 protein C-terminal region (Mak16) | Mak16 protein C-terminal region | - | Family |
DA [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 |
FA [auth S] | PF08701 | GNL3L/Grn1 putative GTPase (GN3L_Grn1) | GNL3L/Grn1 putative GTPase | - | Family |
FA [auth S] | PF01775 | Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A (Ribosomal_L18A) | Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A | This family includes: archaeal 50S ribosomal protein L18Ae, often referred to as L20e or LX; fungal 60S ribosomal protein L20; and higher eukaryote 60S ribosomal protein L18A. | Domain |
GA [auth V] | PF00238 | Ribosomal protein L14p/L23e (Ribosomal_L14) | Ribosomal protein L14p/L23e | - | Domain |
GA [auth V] | PF09420 | Ribosome biogenesis protein Nop16 (Nop16) | Ribosome biogenesis protein Nop16 | - | Family |
HA [auth Y] | PF01912 | eIF-6 family (eIF-6) | eIF-6 family | - | Family |
HA [auth Y] | PF16906 | Ribosomal proteins L26 eukaryotic, L24P archaeal (Ribosomal_L26) | Ribosomal proteins L26 eukaryotic, L24P archaeal | - | Family |
HA [auth Y] | PF00467 | KOW motif (KOW) | KOW motif | - | Family |
LA [auth K] | PF00687 | Ribosomal protein L1p/L10e family (Ribosomal_L1) | Ribosomal protein L1p/L10e family | This family includes prokaryotic L1 and eukaryotic L10. | Domain |
NA [auth D] | PF13959 | Domain of unknown function (DUF4217) (DUF4217) | Domain of unknown function (DUF4217) | This short domain is found at the C-terminus of many helicase proteins. | Domain |
NA [auth D] | PF00271 | Helicase conserved C-terminal domain (Helicase_C) | Helicase conserved C-terminal domain | The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase. | Domain |
F [auth A] | PF04427 | Brix domain (Brix) | Brix domain | - | Domain |