6AHD
The Cryo-EM Structure of Human Pre-catalytic Spliceosome (B complex) at 3.8 angstrom resolution
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
A | SCOP2B Superfamily | Ribonuclease H-like | 8041105 | 3000143 | SCOP2B (2022-06-29) |
A | SCOP2B Superfamily | JAB1/MPN domain-like | 8053277 | 3001105 | SCOP2B (2022-06-29) |
J [auth L] | SCOP2B Superfamily | Nop domain | 8033305 | 3001551 | SCOP2B (2022-06-29) |
BB [auth V] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8041748 | 3000419 | SCOP2B (2022-06-29) |
EA [auth j] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8041748 | 3000419 | SCOP2B (2022-06-29) |
N [auth b] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8041748 | 3000419 | SCOP2B (2022-06-29) |
O [auth c] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8041749 | 3000419 | SCOP2B (2022-06-29) |
FA [auth k] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8041749 | 3000419 | SCOP2B (2022-06-29) |
VA [auth P] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8041749 | 3000419 | SCOP2B (2022-06-29) |
IA [auth n] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8063468 | 3000419 | SCOP2B (2022-06-29) |
R [auth f] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8063468 | 3000419 | SCOP2B (2022-06-29) |
YA [auth S] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8063468 | 3000419 | SCOP2B (2022-06-29) |
S [auth g] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8041751 | 3000419 | SCOP2B (2022-06-29) |
CA [auth h] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8041751 | 3000419 | SCOP2B (2022-06-29) |
ZA [auth T] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8041751 | 3000419 | SCOP2B (2022-06-29) |
V [auth W] | SCOP2B Superfamily | Cyclophilin-like | 8042789 | 3000168 | SCOP2B (2022-06-29) |
W [auth A0] | SCOP2B Superfamily | Ubiquitin-like | 8038047 | 3000157 | SCOP2B (2022-06-29) |
Y [auth Z] | SCOP2B Superfamily | PRP38-like | 8055808 | 3002318 | SCOP2B (2022-06-29) |
JA [auth o] | SCOP2B Superfamily | L domain-like | 8043993 | 3001010 | SCOP2B (2022-06-29) |
KA [auth p] | SCOP2B Superfamily | RNA-binding domain, RBD | 8035327 | 3000110 | SCOP2B (2022-06-29) |
PA [auth r] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8063456 | 3000419 | SCOP2B (2022-06-29) |
QA [auth s] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8063488 | 3000419 | SCOP2B (2022-06-29) |
RA [auth t] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8063472 | 3000419 | SCOP2B (2022-06-29) |
SA [auth x] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8063442 | 3000419 | SCOP2B (2022-06-29) |
TA [auth y] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8063466 | 3000419 | SCOP2B (2022-06-29) |
UA [auth z] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8063492 | 3000419 | SCOP2B (2022-06-29) |
EB [auth 3] | SCOP2B Superfamily | WD40 repeat-like | 8052534 | 3001694 | SCOP2B (2022-06-29) |
EB [auth 3] | SCOP2B Superfamily | WD40 repeat-like | 8052535 | 3001694 | SCOP2B (2022-06-29) |
EB [auth 3] | SCOP2B Superfamily | WD40 repeat-like | 8051197 | 3001694 | SCOP2B (2022-06-29) |
EB [auth 3] | SCOP2B Superfamily | WD40 repeat-like | 8052534 | 3001694 | SCOP2B (2022-06-29) |
FB [auth 5] | SCOP2B Superfamily | RNA-binding domain, RBD | 8040695 | 3000110 | SCOP2B (2022-06-29) |
GB [auth 6] | SCOP2B Superfamily | Triquetra zinc finger motif | 8051848 | 3002040 | SCOP2B (2022-06-29) |
JB [auth 4] | SCOP2B Superfamily | RNA-binding domain, RBD | 8090834 | 3000110 | SCOP2B (2022-06-29) |
KB [auth D] | SCOP2B Superfamily | Brl domain-like | 8036193 | 3000115 | SCOP2B (2022-06-29) |
KB [auth D] | SCOP2B Superfamily | E set domains | 8055093 | 3000070 | SCOP2B (2022-06-29) |
F [auth O] | SCOP2B Superfamily | Thioredoxin-like | 8044390 | 3000031 | SCOP2B (2022-06-29) |
I [auth M] | SCOP2B Superfamily | L30e-like | 8043738 | 3001739 | 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 [auth C] | GTP_EFTU_D2_2 | e6ahdC2 | A: beta barrels | X: cradle loop barrel | H: RIFT-related | T: Alanine racemase-C | F: GTP_EFTU_D2_2 | ECOD (1.6) |
G [auth C] | EFG_IV | e6ahdC5 | 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: EFG_IV | ECOD (1.6) |
G [auth C] | EFG_C | e6ahdC1 | A: a+b two layers | X: Alpha-beta plaits | H: EF-G C-terminal domain-like (From Topology) | T: EF-G C-terminal domain-like | F: EFG_C | ECOD (1.6) |
G [auth C] | EFG_II | e6ahdC4 | A: a+b two layers | X: Alpha-beta plaits | H: EF-G C-terminal domain-like (From Topology) | T: EF-G C-terminal domain-like | F: EFG_II | ECOD (1.6) |
G [auth C] | MnmE_helical_2nd | e6ahdC3 | A: a/b three-layered sandwiches | X: P-loop domains-like | H: P-loop domains-related | T: P-loop containing nucleoside triphosphate hydrolases | F: MnmE_helical_2nd | ECOD (1.6) |
A | U5_2-snRNA_bdg | e6ahdA6 | A: alpha bundles | X: helical bundle domain in reverse transcriptase-like polymerases (From Topology) | H: helical bundle domain in reverse transcriptase-like polymerases (From Topology) | T: helical bundle domain in reverse transcriptase-like polymerases | F: U5_2-snRNA_bdg | ECOD (1.6) |
A | PROCN_C,PROCN_N | e6ahdA3 | A: alpha complex topology | X: Pre-mRNA-splicing factor 8 N-terminal domain (From Topology) | H: Pre-mRNA-splicing factor 8 N-terminal domain (From Topology) | T: Pre-mRNA-splicing factor 8 N-terminal domain | F: PROCN_C,PROCN_N | ECOD (1.6) |
A | RRM_4 | e6ahdA5 | A: a+b two layers | X: Alpha-beta plaits | H: Adenylyl and guanylyl cyclase catalytic domain-like | T: Adenylyl and guanylyl cyclase catalytic domain-like | F: RRM_4 | ECOD (1.6) |
A | PROCT | e6ahdA2 | A: a+b three layers | X: Cytidine deaminase-like (From Topology) | H: Cytidine deaminase-like (From Topology) | T: Cytidine deaminase-like | F: PROCT | ECOD (1.6) |
A | U6-snRNA_bdg | e6ahdA4 | A: a/b three-layered sandwiches | X: Restriction endonuclease-like | H: Restriction endonuclease-like (From Topology) | T: Restriction endonuclease-like | F: U6-snRNA_bdg | ECOD (1.6) |
A | PRP8_domainIV | e6ahdA1 | A: mixed a+b and a/b | X: Ribonuclease H-like | H: Ribonuclease H-like (From Topology) | T: Ribonuclease H-like | F: PRP8_domainIV | ECOD (1.6) |
J [auth L] | Nop_C | e6ahdL2 | A: alpha arrays | X: HhH/H2TH | H: SAM/DNA-glycosylase | T: Nop C-terminal domain | F: Nop_C | ECOD (1.6) |
J [auth L] | Nop_N | e6ahdL1 | A: alpha complex topology | X: Nop N-terminal domain (From Topology) | H: Nop N-terminal domain (From Topology) | T: Nop N-terminal domain | F: Nop_N | ECOD (1.6) |
J [auth L] | Prp31_C | e6ahdL3 | A: extended segments | X: Pre-mRNA-processing factor 31 C-terminal region (From Topology) | H: Pre-mRNA-processing factor 31 C-terminal region (From Topology) | T: Pre-mRNA-processing factor 31 C-terminal region | F: Prp31_C | ECOD (1.6) |
L [auth J] | DUF1115 | e6ahdJ1 | A: a+b two layers | X: Alpha-beta plaits | H: Acylphosphatase-like (From Topology) | T: Acylphosphatase-like | F: DUF1115 | ECOD (1.6) |
L [auth J] | PRP3 | e6ahdJ2 | A: extended segments | X: U4/U6 small nuclear ribonucleoprotein PRP3 N-terminal region (From Topology) | H: U4/U6 small nuclear ribonucleoprotein PRP3 N-terminal region (From Topology) | T: U4/U6 small nuclear ribonucleoprotein PRP3 N-terminal region | F: PRP3 | ECOD (1.6) |
AB [auth U] | LSM | e6ahdU1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: LSM | ECOD (1.6) |
DA [auth i] | LSM | e6ahdi1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: LSM | ECOD (1.6) |
M [auth a] | LSM | e6ahda1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: LSM | ECOD (1.6) |
BB [auth V] | LSM | e6ahdV1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: LSM | ECOD (1.6) |
EA [auth j] | LSM | e6ahdj1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: LSM | ECOD (1.6) |
N [auth b] | LSM | e6ahdb1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: LSM | ECOD (1.6) |
O [auth c] | LSM | e6ahdc1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: LSM | ECOD (1.6) |
FA [auth k] | LSM | e6ahdk1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: LSM | ECOD (1.6) |
VA [auth P] | LSM | e6ahdP1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: LSM | ECOD (1.6) |
GA [auth l] | LSM | e6ahdl1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: LSM | ECOD (1.6) |
P [auth d] | LSM | e6ahdd1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: LSM | ECOD (1.6) |
WA [auth Q] | LSM | e6ahdQ1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: LSM | ECOD (1.6) |
HA [auth m] | LSM | e6ahdm1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: LSM | ECOD (1.6) |
Q [auth e] | LSM | e6ahde1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: LSM | ECOD (1.6) |
XA [auth R] | LSM | e6ahdR1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: LSM | ECOD (1.6) |
IA [auth n] | LSM | e6ahdn1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: LSM | ECOD (1.6) |
R [auth f] | LSM | e6ahdf1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: LSM | ECOD (1.6) |
YA [auth S] | LSM | e6ahdS1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: LSM | ECOD (1.6) |
S [auth g] | LSM | e6ahdg1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: LSM | ECOD (1.6) |
CA [auth h] | LSM | e6ahdh1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: LSM | ECOD (1.6) |
ZA [auth T] | LSM | e6ahdT1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: LSM | ECOD (1.6) |
T [auth E] | ANAPC4_WD40_7 | e6ahdE1 | A: beta duplicates or obligate multimers | X: beta-propeller-like | H: beta-propeller | T: 7-bladed | F: ANAPC4_WD40_7 | ECOD (1.6) |
U [auth X] | zf-U1 | e6ahdX1 | A: few secondary structure elements | X: beta-beta-alpha zinc fingers | H: beta-beta-alpha zinc fingers (From Topology) | T: beta-beta-alpha zinc fingers | F: zf-U1 | ECOD (1.6) |
V [auth W] | Pro_isomerase | e6ahdW1 | A: beta barrels | X: Cyclophilin-like (From Topology) | H: Cyclophilin-like (From Topology) | T: Cyclophilin-like | F: Pro_isomerase | ECOD (1.6) |
W [auth A0] | ubiquitin_4 | e6ahdA01 | A: a+b two layers | X: beta-Grasp | H: Ubiquitin-related | T: Ubiquitin-like | F: ubiquitin_4 | ECOD (1.6) |
Y [auth Z] | PRP38 | e6ahdZ1 | A: alpha superhelices | X: Repetitive alpha hairpins | H: Pre-mRNA-splicing factor 38A (From Topology) | T: Pre-mRNA-splicing factor 38A | F: PRP38 | ECOD (1.6) |
Z [auth 8] | PRP9_N | e6ahd81 | A: few secondary structure elements | X: beta-beta-alpha zinc fingers | H: beta-beta-alpha zinc fingers (From Topology) | T: beta-beta-alpha zinc fingers | F: PRP9_N | ECOD (1.6) |
AA [auth Y] | ANAPC4_WD40_6 | e6ahdY1 | A: beta duplicates or obligate multimers | X: beta-propeller-like | H: beta-propeller | T: 7-bladed | F: ANAPC4_WD40_6 | ECOD (1.6) |
AA [auth Y] | LisH_1 | e6ahdY2 | A: alpha duplicates or obligate multimers | X: Lis-homology dimerization domain (From Topology) | H: Lis-homology dimerization domain (From Topology) | T: Lis-homology dimerization domain | F: LisH_1 | ECOD (1.6) |
JA [auth o] | LRR_9 | e6ahdo1 | A: beta duplicates or obligate multimers | X: Single-stranded right-handed beta-helix | H: Leucine-rich repeats (From Topology) | T: Leucine-rich repeats | F: LRR_9 | ECOD (1.6) |
KA [auth p] | RRM_1_2 | e6ahdp1 | A: a+b two layers | X: Alpha-beta plaits | H: RNA-binding domain, RBD (From Topology) | T: RNA-binding domain, RBD | F: RRM_1_2 | ECOD (1.6) |
LA [auth u] | Surp | e6ahdu1 | A: alpha bundles | X: Surp module (SWAP domain) (From Topology) | H: Surp module (SWAP domain) (From Topology) | T: Surp module (SWAP domain) | F: Surp | ECOD (1.6) |
MA [auth v] | SF3A2 | e6ahdv1 | A: beta sandwiches | X: HSP20-like | H: Pre-mRNA-splicing factor PRP11 C-terminal domain (From Topology) | T: Pre-mRNA-splicing factor PRP11 C-terminal domain | F: SF3A2 | ECOD (1.6) |
OA [auth q] | LSM | e6ahdq1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: LSM | ECOD (1.6) |
PA [auth r] | LSM | e6ahdr1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: LSM | ECOD (1.6) |
QA [auth s] | LSM | e6ahds1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: LSM | ECOD (1.6) |
RA [auth t] | LSM | e6ahdt1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: LSM | ECOD (1.6) |
SA [auth x] | LSM | e6ahdx1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: LSM | ECOD (1.6) |
TA [auth y] | LSM | e6ahdy1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: LSM | ECOD (1.6) |
UA [auth z] | LSM | e6ahdz1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: LSM | ECOD (1.6) |
EB [auth 3] | CPSF_A_N | e6ahd34 | A: beta duplicates or obligate multimers | X: beta-propeller-like | H: beta-propeller | T: 7-bladed | F: CPSF_A_N | ECOD (1.6) |
EB [auth 3] | MMS1_N_C | e6ahd33 | A: beta duplicates or obligate multimers | X: beta-propeller-like | H: beta-propeller | T: 7-bladed | F: MMS1_N_C | ECOD (1.6) |
EB [auth 3] | MMS1_N_N | e6ahd32 | A: beta duplicates or obligate multimers | X: beta-propeller-like | H: beta-propeller | T: 7-bladed | F: MMS1_N_N | ECOD (1.6) |
EB [auth 3] | CPSF_A_C | e6ahd31 | A: alpha arrays | X: HTH | H: HTH | T: tri-helical | F: CPSF_A_C | ECOD (1.6) |
FB [auth 5] | RRM_1_2 | e6ahd51 | A: a+b two layers | X: Alpha-beta plaits | H: RNA-binding domain, RBD (From Topology) | T: RNA-binding domain, RBD | F: RRM_1_2 | ECOD (1.6) |
GB [auth 6] | PHF5 | e6ahd61 | A: few secondary structure elements | X: Glucocorticoid receptor-like | H: LIM domain-like | T: PHD finger-like domain-containing protein 5A | F: PHF5 | ECOD (1.6) |
HB [auth 7] | SF3b10 | e6ahd71 | A: alpha arrays | X: RDS3 complex subunit 10 (From Topology) | H: RDS3 complex subunit 10 (From Topology) | T: RDS3 complex subunit 10 | F: SF3b10 | ECOD (1.6) |
JB [auth 4] | RRM_1_1 | e6ahd41 | A: a+b two layers | X: Alpha-beta plaits | H: RNA-binding domain, RBD (From Topology) | T: RNA-binding domain, RBD | F: RRM_1_1 | ECOD (1.6) |
KB [auth D] | Sec63_3rd | e6ahdD3 | A: beta sandwiches | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: Sec63_3rd | ECOD (1.6) |
KB [auth D] | KOG0952 | e6ahdD5 | A: alpha arrays | X: HTH | H: HTH | T: winged | F: KOG0952 | ECOD (1.6) |
KB [auth D] | Sec63_2nd_1 | e6ahdD1 | A: alpha arrays | X: HhH/H2TH | H: SAM-like subdomain in Sec63-like proteins (From Topology) | T: SAM-like subdomain in Sec63-like proteins | F: Sec63_2nd_1 | ECOD (1.6) |
KB [auth D] | Sec63_2nd | e6ahdD6 | A: alpha arrays | X: HhH/H2TH | H: SAM-like subdomain in Sec63-like proteins (From Topology) | T: SAM-like subdomain in Sec63-like proteins | F: Sec63_2nd | ECOD (1.6) |
KB [auth D] | Sec63_1st | e6ahdD12 | A: alpha arrays | X: Sec63 N-terminal subdomain-like (From Topology) | H: Sec63 N-terminal subdomain-like (From Topology) | T: Sec63 N-terminal subdomain-like | F: Sec63_1st | ECOD (1.6) |
KB [auth D] | DEAD_1 | e6ahdD11 | A: a/b three-layered sandwiches | X: P-loop domains-like | H: P-loop domains-related | T: P-loop containing nucleoside triphosphate hydrolases | F: DEAD_1 | ECOD (1.6) |
KB [auth D] | Helicase_C_5 | e6ahdD2 | 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_5 | ECOD (1.6) |
KB [auth D] | DEAD_1,KOG0951_2nd | e6ahdD8 | A: a/b three-layered sandwiches | X: P-loop domains-like | H: P-loop domains-related | T: P-loop containing nucleoside triphosphate hydrolases | F: DEAD_1,KOG0951_2nd | ECOD (1.6) |
F [auth O] | DIM1 | e6ahdO1 | A: a+b three layers | X: Thioredoxin-like | H: Thioredoxin-like (From Topology) | T: Thioredoxin-like | F: DIM1 | ECOD (1.6) |
I [auth M] | Ribosomal_L7Ae_1 | e6ahdM1 | 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) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
G [auth C] | PF00679 | Elongation factor G C-terminus (EFG_C) | Elongation factor G C-terminus | This domain includes the carboxyl terminal regions of Elongation factor G, elongation factor 2 and some tetracycline resistance proteins and adopt a ferredoxin-like fold. | Domain |
G [auth C] | PF00009 | Elongation factor Tu GTP binding domain (GTP_EFTU) | Elongation factor Tu GTP binding domain | This domain contains a P-loop motif, also found in several other families such as Pfam:PF00071, Pfam:PF00025 and Pfam:PF00063. Elongation factor Tu consists of three structural domains, this plus two C-terminal beta barrel domains. | Domain |
G [auth C] | PF14492 | Elongation Factor G, domain III (EFG_III) | Elongation Factor G, domain III | This domain is found in Elongation Factor G. It shares a similar structure with domain V (Pfam:PF00679). Structural studies in drosophila indicate this is domain 3 [1]. | Domain |
G [auth C] | PF03144 | Elongation factor Tu domain 2 (GTP_EFTU_D2) | Elongation factor Tu domain 2 | Elongation factor Tu consists of three structural domains, this is the second domain. This domain adopts a beta barrel structure. This the second domain is involved in binding to charged tRNA [1]. This domain is also found in other proteins such as e ... | Domain |
G [auth C] | PF03764 | Elongation factor G, domain IV (EFG_IV) | Elongation factor G, domain IV | This domain is found in elongation factor G, elongation factor 2 and some tetracycline resistance proteins and adopts a ribosomal protein S5 domain 2-like fold. | Domain |
G [auth C] | PF01423 | LSM domain (LSM) | LSM domain | The LSM domain contains Sm proteins as well as other related LSM (Like Sm) proteins. The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F and G) i ... | Domain |
BA [auth H] | PF01423 | LSM domain (LSM) | LSM domain | The LSM domain contains Sm proteins as well as other related LSM (Like Sm) proteins. The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F and G) i ... | Domain |
PF10597 | U5-snRNA binding site 2 of PrP8 (U5_2-snRNA_bdg) | U5-snRNA binding site 2 of PrP8 | The essential spliceosomal protein Prp8 interacts with U5 and U6 snRNAs and with specific pre-mRNA sequences that participate in catalysis [1]. This close association with crucial RNA sequences, together with extensive genetic evidence, suggests that ... | Domain | |
PF10598 | RNA recognition motif of the spliceosomal PrP8 (RRM_4) | RNA recognition motif of the spliceosomal PrP8 | The large RNA-protein complex of the spliceosome catalyses pre-mRNA splicing. One of the most conserved core proteins is PrP8 which occupies a central position in the catalytic core of the spliceosome, and has been implicated in several crucial molec ... | Domain | |
PF10596 | U6-snRNA interacting domain of PrP8 (U6-snRNA_bdg) | U6-snRNA interacting domain of PrP8 | This domain incorporates the interacting site for the U6-snRNA as part of the U4/U6.U5 tri-snRNPs complex of the spliceosome, and is the prime candidate for the role of cofactor for the spliceosome's RNA core. The essential spliceosomal protein Prp8 ... | Domain | |
PF12134 | PRP8 domain IV core (PRP8_domainIV) | PRP8 domain IV core | This domain is found in eukaryotes, and is about 20 amino acids in length. It is found associated with Pfam:PF10597, Pfam:PF10596, Pfam:PF10598, Pfam:PF08083, Pfam:PF08082, Pfam:PF01398, Pfam:PF08084. There is a conserved LILR sequence motif. The dom ... | Domain | |
PF08082 | PRO8NT (NUC069), PrP8 N-terminal domain (PRO8NT) | PRO8NT (NUC069), PrP8 N-terminal domain | The PRO8NT domain is found at the N-terminus of pre-mRNA splicing factors of PRO8 family [1]. The NLS or nuclear localisation signal for these spliceosome proteins begins at the start and runs for 60 residues. N-terminal to this domain is a highly va ... | Domain | |
PF08083 | PROCN (NUC071) domain (PROCN) | PROCN (NUC071) domain | The PROCN domain is the central domain in pre-mRNA splicing factors of PRO8 family [1]. | Domain | |
PF08084 | PROCT (NUC072) domain (PROCT) | PROCT (NUC072) domain | The PROCT domain is the C-terminal domain in pre-mRNA splicing factors of PRO8 family [1]. | Domain | |
PF01398 | JAB1/Mov34/MPN/PAD-1 ubiquitin protease (JAB) | JAB1/Mov34/MPN/PAD-1 ubiquitin protease | - | Family | |
J [auth L] | PF09785 | Prp31 C terminal domain (Prp31_C) | Prp31 C terminal domain | - | Family |
J [auth L] | PF01798 | snoRNA binding domain, fibrillarin (Nop) | snoRNA binding domain, fibrillarin | - | Family |
K [auth 9] | PF03343 | SART-1 family (SART-1) | SART-1 family | - | Family |
L [auth J] | PF06544 | Small nuclear ribonucleoprotein Prp3, C-terminal domain (Prp3_C) | Small nuclear ribonucleoprotein Prp3, C-terminal domain | This domain is found at the C-terminal end of U4/U6 and U4/U5/U6- small nuclear ribonucleoprotein Prp3, part of the tri-RNA complex that form the spliceosome. Prp3 plays a key role in the recognition of the snRNA duplex. This binding domain, highly c ... | Domain |
L [auth J] | PF01423 | LSM domain (LSM) | LSM domain | The LSM domain contains Sm proteins as well as other related LSM (Like Sm) proteins. The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F and G) i ... | Domain |
AB [auth U], DA [auth i], M [auth a] | PF01805 | Surp module (Surp) | Surp module | - | Family |
BB [auth V], EA [auth j], N [auth b] | PF01423 | LSM domain (LSM) | LSM domain | The LSM domain contains Sm proteins as well as other related LSM (Like Sm) proteins. The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F and G) i ... | Domain |
FA [auth k], O [auth c], VA [auth P] | 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 |
FA [auth k], O [auth c], VA [auth P] | PF01423 | LSM domain (LSM) | LSM domain | The LSM domain contains Sm proteins as well as other related LSM (Like Sm) proteins. The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F and G) i ... | Domain |
GA [auth l], P [auth d], WA [auth Q] | PF01423 | LSM domain (LSM) | LSM domain | The LSM domain contains Sm proteins as well as other related LSM (Like Sm) proteins. The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F and G) i ... | Domain |
HA [auth m], Q [auth e], XA [auth R] | PF01423 | LSM domain (LSM) | LSM domain | The LSM domain contains Sm proteins as well as other related LSM (Like Sm) proteins. The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F and G) i ... | Domain |
IA [auth n], R [auth f], YA [auth S] | PF01423 | LSM domain (LSM) | LSM domain | The LSM domain contains Sm proteins as well as other related LSM (Like Sm) proteins. The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F and G) i ... | Domain |
CA [auth h], S [auth g], ZA [auth T] | PF01423 | LSM domain (LSM) | LSM domain | The LSM domain contains Sm proteins as well as other related LSM (Like Sm) proteins. The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F and G) i ... | Domain |
T [auth E] | PF00400 | WD domain, G-beta repeat (WD40) | WD domain, G-beta repeat | - | Repeat |
U [auth X] | PF06220 | U1 zinc finger (zf-U1) | U1 zinc finger | This family consists of several U1 small nuclear ribonucleoprotein C (U1-C) proteins. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site (ss) at early stages of spliceosome assembly. Recruitment of U1 to a class o ... | Domain |
U [auth X] | PF01423 | LSM domain (LSM) | LSM domain | The LSM domain contains Sm proteins as well as other related LSM (Like Sm) proteins. The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F and G) i ... | Domain |
V [auth W] | PF16837 | Pre-mRNA-splicing factor SF3A3, of SF3a complex, Prp9 (SF3A3) | Pre-mRNA-splicing factor SF3A3, of SF3a complex, Prp9 | SF3A3 is one of the components of the SF3a splicing factor complex of the mature U2 snRNP (small nuclear ribonucleoprotein particle). In yeast, SF3a shows a bifurcated assembly structure of three subunits, Prp9 (subunit 3), Prp11 (subunit 2) and Prp2 ... | Domain |
V [auth W] | PF00160 | Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD (Pro_isomerase) | Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD | The peptidyl-prolyl cis-trans isomerases, also known as cyclophilins, share this domain of about 109 amino acids. Cyclophilins have been found in all organisms studied so far and catalyse peptidyl-prolyl isomerisation during which the peptide bond pr ... | Domain |
V [auth W] | PF12108 | Splicing factor SF3a60 binding domain (SF3a60_bindingd) | Splicing factor SF3a60 binding domain | This domain is found in eukaryotes. This domain is about 30 amino acids in length. This domain has a single completely conserved residue Y that may be functionally important. SF3a60 makes up the SF3a complex with SF3a66 and SF3a120. This domain is th ... | Domain |
W [auth A0] | PF00240 | Ubiquitin family (ubiquitin) | Ubiquitin family | This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry ... | Domain |
Y [auth Z] | PF03371 | PRP38 family (PRP38) | PRP38 family | - | Family |
Z [auth 8] | PF12171 | Zinc-finger double-stranded RNA-binding (zf-C2H2_jaz) | Zinc-finger double-stranded RNA-binding | - | Family |
AA [auth Y] | PF17814 | LisH-like dimerisation domain (LisH_TPL) | LisH-like dimerisation domain | TOPLESS (TPL) proteins have a highly conserved N-terminal domain containing a lissencephaly homologous (LisH) dimerization motif [1]. | Domain |
AA [auth Y] | PF00400 | WD domain, G-beta repeat (WD40) | WD domain, G-beta repeat | - | Repeat |
AA [auth Y] | PF01423 | LSM domain (LSM) | LSM domain | The LSM domain contains Sm proteins as well as other related LSM (Like Sm) proteins. The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F and G) i ... | Domain |
C [auth B] | PF01423 | LSM domain (LSM) | LSM domain | The LSM domain contains Sm proteins as well as other related LSM (Like Sm) proteins. The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F and G) i ... | Domain |
D [auth F] | PF01423 | LSM domain (LSM) | LSM domain | The LSM domain contains Sm proteins as well as other related LSM (Like Sm) proteins. The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F and G) i ... | Domain |
CB [auth K] | PF08799 | pre-mRNA processing factor 4 (PRP4) like (PRP4) | pre-mRNA processing factor 4 (PRP4) like | This small domain is found on PRP4 ribonuleoproteins. PRP4 is a U4/U6 small nuclear ribonucleoprotein that is involved in pre-mRNA processing. | Domain |
CB [auth K] | PF00400 | WD domain, G-beta repeat (WD40) | WD domain, G-beta repeat | - | Repeat |
CB [auth K] | PF01423 | LSM domain (LSM) | LSM domain | The LSM domain contains Sm proteins as well as other related LSM (Like Sm) proteins. The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F and G) i ... | Domain |
DB [auth 1] | PF22646 | PPP2R1A-like HEAT repeat (PPP2R1A-like_HEAT) | PPP2R1A-like HEAT repeat | - | Repeat |
EB [auth 3] | PF10433 | Mono-functional DNA-alkylating methyl methanesulfonate N-term (MMS1_N) | Mono-functional DNA-alkylating methyl methanesulfonate N-term | - | Repeat |
EB [auth 3] | PF03178 | CPSF A subunit region (CPSF_A) | CPSF A subunit region | - | Repeat |
FB [auth 5] | 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 |
IB [auth 2] | PF04037 | Domain of unknown function (DUF382) (DUF382) | Domain of unknown function (DUF382) | - | Family |
IB [auth 2] | PF04046 | PSP (PSP) | PSP | - | Family |
JB [auth 4] | 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 |
KB [auth D] | PF02889 | Sec63 Brl domain (Sec63) | Sec63 Brl domain | - | Family |
KB [auth D] | PF00270 | DEAD/DEAH box helicase (DEAD) | DEAD/DEAH box helicase | Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome ... | Domain |
KB [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 |
E [auth G] | PF01423 | LSM domain (LSM) | LSM domain | The LSM domain contains Sm proteins as well as other related LSM (Like Sm) proteins. The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F and G) i ... | Domain |
F [auth O] | PF02966 | Mitosis protein DIM1 (DIM1) | Mitosis protein DIM1 | - | Domain |
H [auth N] | PF14559 | Tetratricopeptide repeat (TPR_19) | Tetratricopeptide repeat | - | Repeat |
H [auth N] | PF06424 | PRP1 splicing factor, N-terminal (PRP1_N) | PRP1 splicing factor, N-terminal | This domain is specific to the N-terminal part of the prp1 splicing factor, which is involved in mRNA splicing (and possibly also poly(A)+ RNA nuclear export and cell cycle progression). This domain is specific to the N terminus of the RNA splicing f ... | Domain |
H [auth N] | PF13432 | Tetratricopeptide repeat (TPR_16) | Tetratricopeptide repeat | - | Repeat |
H [auth N] | PF01423 | LSM domain (LSM) | LSM domain | The LSM domain contains Sm proteins as well as other related LSM (Like Sm) proteins. The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F and G) i ... | Domain |
I [auth M] | 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 |