5T6R
Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis: 60S-Nmd3 Complex
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
G | SCOP2B Superfamily | Translational machinery components | 8052875 | 3000571 | SCOP2B (2022-06-29) |
H | SCOP2B Superfamily | Translation proteins SH3-like KOW motif containing domain | 8053109 | 3000334 | SCOP2B (2022-06-29) |
I | SCOP2B Superfamily | Ribosomal protein L30p/L7e | 8052917 | 3001378 | SCOP2B (2022-06-29) |
I | SCOP2B Superfamily | Ribosomal L30p/L7e protein, N-terminal domain-lke | 8052916 | 3002152 | SCOP2B (2022-06-29) |
P [auth a] | SCOP2B Superfamily | Ribosomal proteins S24e, L23 and L15e | 8082481 | 3000210 | SCOP2B (2022-06-29) |
Q [auth b] | SCOP2B Superfamily | Ribosomal protein L13 | 8066053 | 3001134 | SCOP2B (2022-06-29) |
R [auth c] | SCOP2B Superfamily | Ribosomal protein L22 | 8076708 | 3001078 | SCOP2B (2022-06-29) |
KA [auth v] | SCOP2B Superfamily | Ribosomal protein L36e | 8053115 | 3002161 | SCOP2B (2022-06-29) |
LA [auth w] | SCOP2B Superfamily | Zn-binding ribosomal proteins | 8080044 | 3001320 | SCOP2B (2022-06-29) |
NA [auth y] | SCOP2B Superfamily | Ribosomal protein L39e | 8078549 | 3001756 | SCOP2B (2022-06-29) |
QA [auth R] | SCOP2B Superfamily | Zn-binding ribosomal proteins | 8103126 | 3001320 | SCOP2B (2022-06-29) |
J | SCOP2B Superfamily | L30e-like | 8063962 | 3001739 | SCOP2B (2022-06-29) |
L | SCOP2B Superfamily | Ribosomal protein L16p/L10e | 8079407 | 3000884 | SCOP2B (2022-06-29) |
M | SCOP2B Superfamily | RL5-like | 8073884 | 3001709 | SCOP2B (2022-06-29) |
N | SCOP2B Superfamily | Ribosomal protein L13e-like | 8053159 | 3002162 | SCOP2B (2022-06-29) |
S [auth d] | SCOP2B Superfamily | Ribosomal proteins L15p and L18e | 8095970 | 3001045 | SCOP2B (2022-06-29) |
T [auth e] | SCOP2B Superfamily | Ribosomal protein L19 (L19e) | 8077485 | 3000890 | SCOP2B (2022-06-29) |
W [auth h] | SCOP2B Superfamily | 60S Ribosomal protein L22e | 8053058 | 3002158 | SCOP2B (2022-06-29) |
X [auth i] | SCOP2B Superfamily | 50S Ribosomal protein L14-like | 8103364 | 3000433 | SCOP2B (2022-06-29) |
Z [auth k] | SCOP2B Superfamily | Ribosomal proteins S24e, L23 and L15e | 8095962 | 3000210 | SCOP2B (2022-06-29) |
AA [auth l] | SCOP2B Superfamily | Translation proteins SH3-like KOW motif containing domain | 8076760 | 3000334 | SCOP2B (2022-06-29) |
BA [auth m] | SCOP2B Superfamily | Translation proteins SH3-like KOW motif containing domain | 8053046 | 3000334 | SCOP2B (2022-06-29) |
CA [auth n] | SCOP2B Superfamily | Ribosomal proteins L15p and L18e | 8077127 | 3001045 | SCOP2B (2022-06-29) |
DA [auth o] | SCOP2B Superfamily | Ribosomal protein L29e | 8053045 | 3002157 | SCOP2B (2022-06-29) |
EA [auth p] | SCOP2B Superfamily | L30e-like | 8039862 | 3001739 | SCOP2B (2022-06-29) |
IA [auth t] | SCOP2B Superfamily | Ribosomal protein L34e-like | 8053547 | 3002203 | SCOP2B (2022-06-29) |
MA [auth x] | SCOP2B Superfamily | Ribosomal L38e protein-like | 8053562 | 3002206 | SCOP2B (2022-06-29) |
E | SCOP2B Superfamily | Translational proteins | 8078363 | 3000811 | SCOP2B (2022-06-29) |
F | SCOP2B Superfamily | 60S ribosomal protein L4 C-terminal domain-like | 8052815 | 3002143 | SCOP2B (2022-06-29) |
F | SCOP2B Superfamily | Ribosomal protein L4 | 8052816 | 3001146 | 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) |
---|---|---|---|---|---|---|---|---|
G | Ribosomal_L5e | e5t6rG1 | A: mixed a+b and a/b | X: Ribonuclease H-like | H: Ribonuclease H-like (From Topology) | T: Ribonuclease H-like | F: Ribosomal_L5e | ECOD (1.6) |
H | Ribosomal_L6e | e5t6rH1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: Ribosomal_L6e | ECOD (1.6) |
I | Ribosomal_L30_1 | e5t6rI1 | 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) |
K | Ribosomal_L6_2 | e5t6rK1 | 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) |
K | Ribosomal_L6 | e5t6rK2 | 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) |
P [auth a] | Ribosomal_L15e | e5t6ra1 | 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) |
Q [auth b] | Ribosomal_L13 | e5t6rb1 | 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) |
R [auth c] | Ribosomal_L22 | e5t6rc1 | 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) |
GA [auth r] | Ribosomal_L32e | e5t6rr1 | 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) |
KA [auth v] | Ribosomal_L36e | e5t6rv1 | 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) |
LA [auth w] | Ribosomal_L37e | e5t6rw1 | A: few secondary structure elements | X: Rubredoxin-like | H: Rubredoxin-related | T: Rubredoxin-related | F: Ribosomal_L37e | ECOD (1.6) |
NA [auth y] | Ribosomal_L39 | e5t6ry1 | A: extended segments | X: Ribosomal protein L39e (From Topology) | H: Ribosomal protein L39e (From Topology) | T: Ribosomal protein L39e | F: Ribosomal_L39 | ECOD (1.6) |
PA [auth Q] | Ribosomal_L44 | e5t6rQ1 | A: few secondary structure elements | X: Rubredoxin-like | H: Rubredoxin-related | T: Rubredoxin-related | F: Ribosomal_L44 | ECOD (1.6) |
QA [auth R] | Ribosomal_L37ae | e5t6rR1 | A: few secondary structure elements | X: Rubredoxin-like | H: Rubredoxin-related | T: Rubredoxin-related | F: Ribosomal_L37ae | ECOD (1.6) |
J | Ribosomal_L7Ae_1 | e5t6rJ1 | 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) |
L | Ribosomal_L16 | e5t6rL1 | 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) |
M | Ribosomal_L5_C | e5t6rM1 | 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) |
N | Ribosomal_L13e | e5t6rN1 | A: extended segments | X: RPL13 (From Topology) | H: RPL13 (From Topology) | T: RPL13 | F: Ribosomal_L13e | ECOD (1.6) |
O | Ribosomal_L14e | e5t6rO1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: Ribosomal_L14e | ECOD (1.6) |
S [auth d] | Ribosomal_L18 | e5t6rd1 | 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) |
T [auth e] | Ribosomal_L19e_N | e5t6re1 | A: alpha arrays | X: Ribosomal protein L19 (L19e) N-terminal domain (From Topology) | H: Ribosomal protein L19 (L19e) N-terminal domain (From Topology) | T: Ribosomal protein L19 (L19e) N-terminal domain | F: Ribosomal_L19e_N | ECOD (1.6) |
T [auth e] | Ribosomal_L19e_C | e5t6re2 | A: alpha bundles | X: Ribosomal protein L19 (L19e) C-terminal domain (From Topology) | H: Ribosomal protein L19 (L19e) C-terminal domain (From Topology) | T: Ribosomal protein L19 (L19e) C-terminal domain | F: Ribosomal_L19e_C | ECOD (1.6) |
U [auth f] | Ribosomal_L18A | e5t6rf1 | A: a+b two layers | X: GP2-like | H: RplX-like (From Topology) | T: RplX-like | F: Ribosomal_L18A | ECOD (1.6) |
V [auth g] | Ribosomal_L21e | e5t6rg1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: Ribosomal_L21e | ECOD (1.6) |
W [auth h] | Ribosomal_L22e | e5t6rh1 | A: a+b two layers | X: Ribosomal protein L22e (From Topology) | H: Ribosomal protein L22e (From Topology) | T: Ribosomal protein L22e | F: Ribosomal_L22e | ECOD (1.6) |
X [auth i] | Ribosomal_L14 | e5t6ri1 | 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) |
Y [auth j] | Ribosomal_L24e | e5t6rj1 | A: few secondary structure elements | X: Glucocorticoid receptor-like | H: LIM domain-like | T: LIM domain-like | F: Ribosomal_L24e | ECOD (1.6) |
Z [auth k] | Ribosomal_L23_3 | e5t6rk1 | 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_3 | ECOD (1.6) |
AA [auth l] | Ribosomal_L26 | e5t6rl1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: Ribosomal_L26 | ECOD (1.6) |
BA [auth m] | Ribosomal_L27e | e5t6rm1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: Ribosomal_L27e | ECOD (1.6) |
CA [auth n] | Ribosomal_L18 | e5t6rn1 | 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) |
DA [auth o] | Ribosomal_L29e | e5t6ro1 | A: extended segments | X: RPL29 (From Topology) | H: RPL29 (From Topology) | T: RPL29 | F: Ribosomal_L29e | ECOD (1.6) |
EA [auth p] | Ribosomal_L7Ae | e5t6rp1 | A: a+b three layers | X: Bacillus chorismate mutase-like | H: L30e-like (From Topology) | T: L30e-like | F: Ribosomal_L7Ae | ECOD (1.6) |
FA [auth q] | Ribosomal_L31e | e5t6rq1 | A: a+b two layers | X: Ribosomal protein L31e-like | H: Ribosomal protein L31e/gp120 outer domain (From Topology) | T: Ribosomal protein L31e/gp120 outer domain | F: Ribosomal_L31e | ECOD (1.6) |
IA [auth t] | Ribosomal_L34e | e5t6rt1 | A: few secondary structure elements | X: Glucocorticoid receptor-like | H: RPL34 (From Topology) | T: RPL34 | F: Ribosomal_L34e | ECOD (1.6) |
JA [auth u] | Ribosomal_L29_2 | e5t6ru1 | 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) |
MA [auth x] | Ribosomal_L38e | e5t6rx1 | A: a+b two layers | X: SRP9/14-like | H: Signal recognition particle alu RNA binding heterodimer SRP9/14-related (From Topology) | T: Signal recognition particle alu RNA binding heterodimer SRP9/14-related | F: Ribosomal_L38e | ECOD (1.6) |
D | Ribosomal_L2_1 | e5t6rD2 | 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_2 | e5t6rD1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: Ribosomal_L2_C_2 | ECOD (1.6) |
OA [auth z] | Ribosomal_L40e | e5t6rz1 | A: few secondary structure elements | X: Rubredoxin-like | H: Rubredoxin-related | T: Rubredoxin-related | F: Ribosomal_L40e | ECOD (1.6) |
SA [auth V] | KOG2613_2nd | e5t6rV2 | A: beta barrels | X: OB-fold | H: Nucleic acid-binding proteins (From Topology) | T: Nucleic acid-binding proteins | F: KOG2613_2nd | ECOD (1.6) |
SA [auth V] | KOG2613_1st | e5t6rV3 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: KOG2613_1st | ECOD (1.6) |
SA [auth V] | NMD3 | e5t6rV1 | A: a+b two layers | X: 60S ribosomal export protein NMD3 a+b domain (From Topology) | H: 60S ribosomal export protein NMD3 a+b domain (From Topology) | T: 60S ribosomal export protein NMD3 a+b domain | F: NMD3 | ECOD (1.6) |
E | Ribosomal_L3 | e5t6rE1 | A: beta barrels | X: cradle loop barrel | H: RIFT-related | T: Alanine racemase-C | F: Ribosomal_L3 | ECOD (1.6) |
F | Ribosomal_L4 | e5t6rF1 | 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) |
F | Ribos_L4_asso_C | e5t6rF2 | 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) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
PF00827 | Ribosomal L15 (Ribosomal_L15e) | Ribosomal L15 | - | Family | |
PF17144 | Ribosomal large subunit proteins 60S L5, and 50S L18 (Ribosomal_L5e) | Ribosomal large subunit proteins 60S L5, and 50S L18 | - | Family | |
PF14204 | Ribosomal L18 C-terminal region (Ribosomal_L18_c) | Ribosomal L18 C-terminal region | This domain is the C-terminal end of ribosomal L18/L5 proteins. | Domain | |
PF01776 | Ribosomal L22e protein family (Ribosomal_L22e) | Ribosomal L22e protein family | - | Family | |
PF01159 | Ribosomal protein L6e (Ribosomal_L6e) | Ribosomal protein L6e | - | Family | |
PF00238 | Ribosomal protein L14p/L23e (Ribosomal_L14) | Ribosomal protein L14p/L23e | - | Domain | |
PF00327 | Ribosomal protein L30p/L7e (Ribosomal_L30) | Ribosomal protein L30p/L7e | This family includes prokaryotic L30 and eukaryotic L7. | Domain | |
PF00347 | Ribosomal protein L6 (Ribosomal_L6) | Ribosomal protein L6 | - | Domain | |
PF00276 | Ribosomal protein L23 (Ribosomal_L23) | Ribosomal protein L23 | - | Family | |
PA [auth Q] | PF00935 | Ribosomal protein L44 (Ribosomal_L44) | Ribosomal protein L44 | - | Family |
PA [auth Q] | PF01198 | Ribosomal protein L31e (Ribosomal_L31e) | Ribosomal protein L31e | - | Family |
QA [auth R] | PF01780 | Ribosomal L37ae protein family (Ribosomal_L37ae) | Ribosomal L37ae protein family | - | Family |
QA [auth R] | PF01655 | Ribosomal protein L32 (Ribosomal_L32e) | Ribosomal protein L32 | - | Family |
PF01246 | Ribosomal protein L24e (Ribosomal_L24e) | Ribosomal protein L24e | - | Domain | |
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 | |
PF16906 | Ribosomal proteins L26 eukaryotic, L24P archaeal (Ribosomal_L26) | Ribosomal proteins L26 eukaryotic, L24P archaeal | - | Family | |
PF00252 | Ribosomal protein L16p/L10e (Ribosomal_L16) | Ribosomal protein L16p/L10e | - | Domain | |
PF00467 | KOW motif (KOW) | KOW motif | - | Family | |
PF01777 | Ribosomal L27e protein family (Ribosomal_L27e) | Ribosomal L27e protein family | - | Family | |
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 | |
PF01294 | Ribosomal protein L13e (Ribosomal_L13e) | Ribosomal protein L13e | - | Family | |
PF00828 | Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A (Ribosomal_L27A) | Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A | - | Family | |
PF01779 | Ribosomal L29e protein family (Ribosomal_L29e) | Ribosomal L29e protein family | - | Family | |
PF01929 | Ribosomal protein L14 (Ribosomal_L14e) | Ribosomal protein L14 | - | Family | |
PF00467 | KOW motif (KOW) | KOW motif | - | Family | |
PF00572 | Ribosomal protein L13 (Ribosomal_L13) | Ribosomal protein L13 | - | Family | |
PF00237 | Ribosomal protein L22p/L17e (Ribosomal_L22) | Ribosomal protein L22p/L17e | This family includes L22 from prokaryotes and chloroplasts and L17 from eukaryotes. | Domain | |
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 | |
PF17135 | Ribosomal protein 60S L18 and 50S L18e (Ribosomal_L18) | Ribosomal protein 60S L18 and 50S L18e | - | Family | |
RA [auth S] | PF01247 | Ribosomal protein L35Ae (Ribosomal_L35Ae) | Ribosomal protein L35Ae | - | Domain |
SA [auth V] | PF21192 | NMD3 OB-fold domain (NMD3_OB) | NMD3 OB-fold domain | A key step in ribosome biogenesis is the nuclear export of pre-ribosomal particles. Nmd3, a highly conserved protein in eukaryotes, is a specific adaptor required for the export of pre-60S particles. This entry represents the third domain in NMD3 whi ... | Domain |
SA [auth V] | PF21193 | NMD3 SH3 domain (NMD_SH3) | NMD3 SH3 domain | A key step in ribosome biogenesis is the nuclear export of pre-ribosomal particles. Nmd3, a highly conserved protein in eukaryotes, is a specific adaptor required for the export of pre-60S particles. This entry represents the second domain in NMD3 wh ... | Domain |
SA [auth V] | PF01158 | Ribosomal protein L36e (Ribosomal_L36e) | Ribosomal protein L36e | - | Family |
PF01280 | Ribosomal protein L19e (Ribosomal_L19e) | Ribosomal protein L19e | - | Family | |
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 | |
PF00573 | Ribosomal protein L4/L1 family (Ribosomal_L4) | Ribosomal protein L4/L1 family | - | Family | |
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 |