5LJ3
Structure of the core of the yeast spliceosome immediately after branching
Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage
Chains | Domain Info | Class | Fold | Superfamily | Family | Domain | Species | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
P [auth N] | d5lj3n1 | Alpha and beta proteins (a+b) | Ferredoxin-like | RNA-binding domain, RBD, aka RNA recognition motif (RRM) | Canonical RBD | Pre-mRNA splicing factor Cwf5 / Ecm2 / Stl11, RRM domain | (Saccharomyces cerevisiae ) [TaxId: 4932 ], | SCOPe (2.08) |
P [auth N] | d5lj3n2 | Small proteins | Pre-mRNA splicing factor Cwf5-like | Pre-mRNA splicing factor Cwf5-like | Pre-mRNA splicing factor Cwf5-like | Pre-mRNA splicing factor Cwf5 / Ecm2 / Stl11, Zn-binding domain | (Saccharomyces cerevisiae ) [TaxId: 4932 ], | SCOPe (2.08) |
S [auth R] | d5lj3r_ | Peptides | Pre-mRNA splicing factor Cwc21 fragment | Pre-mRNA splicing factor Cwc21 fragment | Pre-mRNA splicing factor Cwc21 fragment | Pre-mRNA splicing factor Cwc21 fragment | (Saccharomyces cerevisiae ) [TaxId: 4932 ], | SCOPe (2.08) |
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
F [auth A] | SCOP2B Superfamily | Ribonuclease H-like | 8040983 | 3000143 | SCOP2B (2022-06-29) |
M [auth K] | SCOP2B Superfamily | Pre-mRNA-processing protein 45-like | 8092739 | 3002618 | SCOP2B (2022-06-29) |
O [auth M] | SCOP2B Superfamily | CCCH zinc finger-like | 8051791 | 3001741 | SCOP2B (2022-06-29) |
O [auth M] | SCOP2B Superfamily | RNA-binding domain RBD | 8051796 | 3000110 | SCOP2B (2022-06-29) |
EA [auth k] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8077613 | 3000419 | SCOP2B (2022-06-29) |
V [auth b] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8077613 | 3000419 | SCOP2B (2022-06-29) |
HA [auth n] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8098694 | 3000419 | SCOP2B (2022-06-29) |
W [auth d] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8098694 | 3000419 | SCOP2B (2022-06-29) |
JA [auth q] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8043703 | 3000419 | SCOP2B (2022-06-29) |
Y [auth f] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8043703 | 3000419 | SCOP2B (2022-06-29) |
BA [auth j] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8063490 | 3000419 | SCOP2B (2022-06-29) |
GA [auth m] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8063490 | 3000419 | SCOP2B (2022-06-29) |
DA [auth Y] | SCOP2 Family | Canonical RBD | 8073744 | 4000236 | SCOP2 (2022-06-29) |
DA [auth Y] | SCOP2 Superfamily | RNA-binding domain RBD | 8073745 | 3000110 | SCOP2 (2022-06-29) |
KA [auth r] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8098668 | 3000419 | SCOP2B (2022-06-29) |
Z [auth g] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8098668 | 3000419 | 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) |
---|---|---|---|---|---|---|---|---|
F [auth A] | U5_2-snRNA_bdg | e5lj3A3 | 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) |
F [auth A] | PROCN_C,PROCN_N | e5lj3A1 | 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) |
F [auth A] | RRM_4 | e5lj3A2 | 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) |
F [auth A] | U6-snRNA_bdg | e5lj3A5 | 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) |
F [auth A] | PRP8_domainIV | e5lj3A4 | 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) |
I [auth C] | GTP_EFTU_D2_2 | e5lj3C5 | A: beta barrels | X: cradle loop barrel | H: RIFT-related | T: Alanine racemase-C | F: GTP_EFTU_D2_2 | ECOD (1.6) |
I [auth C] | EFG_IV | e5lj3C2 | 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) |
I [auth C] | EFG_C | e5lj3C4 | 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) |
I [auth C] | EFG_II | e5lj3C3 | 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) |
I [auth C] | MnmE_helical_2nd | e5lj3C1 | 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) |
J [auth G] | Isy1 | e5lj3G1 | A: alpha bundles | X: Long alpha-hairpin | H: ISY1 N-terminal domain-like (From Topology) | T: ISY1 N-terminal domain-like | F: Isy1 | ECOD (1.6) |
K [auth H] | MIF4G | e5lj3H1 | A: alpha superhelices | X: Repetitive alpha hairpins | H: ARM repeat (From Topology) | T: ARM repeat | F: MIF4G | ECOD (1.6) |
K [auth H] | MA3 | e5lj3H2 | A: alpha superhelices | X: Repetitive alpha hairpins | H: ARM repeat (From Topology) | T: ARM repeat | F: MA3 | ECOD (1.6) |
L [auth J] | ANAPC4_WD40_9 | e5lj3J1 | A: beta duplicates or obligate multimers | X: beta-propeller-like | H: beta-propeller | T: 7-bladed | F: ANAPC4_WD40_9 | ECOD (1.6) |
N [auth L] | G10 | e5lj3L1 | A: few secondary structure elements | X: Pre-mRNA-splicing factor BUD31 (From Topology) | H: Pre-mRNA-splicing factor BUD31 (From Topology) | T: Pre-mRNA-splicing factor BUD31 | F: G10 | ECOD (1.6) |
O [auth M] | RRM_1_6 | e5lj3M2 | A: a+b two layers | X: Alpha-beta plaits | H: RNA-binding domain, RBD (From Topology) | T: RNA-binding domain, RBD | F: RRM_1_6 | ECOD (1.6) |
O [auth M] | Torus | e5lj3M1 | A: few secondary structure elements | X: CCCH zinc finger | H: CCCH zinc finger (From Topology) | T: CCCH zinc finger | F: Torus | ECOD (1.6) |
P [auth N] | RRM_1_7 | e5lj3N1 | A: a+b two layers | X: Alpha-beta plaits | H: RNA-binding domain, RBD (From Topology) | T: RNA-binding domain, RBD | F: RRM_1_7 | ECOD (1.6) |
P [auth N] | KOG0153 | e5lj3N2 | A: few secondary structure elements | X: RING/U-box-like | H: RING/U-box-like | T: FYVE/PHD zinc finger | F: KOG0153 | ECOD (1.6) |
Q [auth O] | Myb_DNA-binding_1 | e5lj3O1 | A: alpha arrays | X: HTH | H: HTH | T: tri-helical | F: Myb_DNA-binding_1 | ECOD (1.6) |
S [auth R] | cwf21 | e5lj3R1 | A: alpha duplicates or obligate multimers | X: cwf21 domain (From Topology) | H: cwf21 domain (From Topology) | T: cwf21 domain | F: cwf21 | ECOD (1.6) |
T [auth S] | TPR_15 | e5lj3S1 | A: alpha superhelices | X: Repetitive alpha hairpins | H: ARM repeat (From Topology) | T: ARM repeat | F: TPR_15 | ECOD (1.6) |
U [auth T] | Suf | e5lj3T1 | A: alpha superhelices | X: Repetitive alpha hairpins | H: ARM repeat (From Topology) | T: ARM repeat | F: Suf | ECOD (1.6) |
EA [auth k] | LSM | e5lj3k1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: LSM | ECOD (1.6) |
V [auth b] | LSM | e5lj3b1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: LSM | ECOD (1.6) |
HA [auth n] | LSM | e5lj3n1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: LSM | ECOD (1.6) |
W [auth d] | LSM | e5lj3d1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: LSM | ECOD (1.6) |
IA [auth p] | LSM | e5lj3p1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: LSM | ECOD (1.6) |
X [auth e] | LSM | e5lj3e1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: LSM | ECOD (1.6) |
JA [auth q] | LSM | e5lj3q1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: LSM | ECOD (1.6) |
Y [auth f] | LSM | e5lj3f1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: LSM | ECOD (1.6) |
AA [auth h] | LSM | e5lj3h1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: LSM | ECOD (1.6) |
FA [auth l] | LSM | e5lj3l1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: LSM | ECOD (1.6) |
BA [auth j] | LSM | e5lj3j1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: LSM | ECOD (1.6) |
GA [auth m] | LSM | e5lj3m1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: LSM | ECOD (1.6) |
CA [auth W] | LRR_9 | e5lj3W1 | 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) |
DA [auth Y] | RRM_1_2 | e5lj3Y1 | 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) |
KA [auth r] | LSM | e5lj3r1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: LSM | ECOD (1.6) |
Z [auth g] | LSM | e5lj3g1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: LSM | ECOD (1.6) |
Domain Annotation: CATH CATH Database Homepage
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
F [auth A] | 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 |
F [auth A] | 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 |
F [auth A] | 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 |
F [auth A] | 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 |
F [auth A] | 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 |
G [auth D] | PF04502 | Saf4/Yju2 protein (Saf4_Yju2) | Saf4/Yju2 protein | - | Family |
H [auth F] | PF10197 | N-terminal domain of CBF1 interacting co-repressor CIR (Cir_N) | N-terminal domain of CBF1 interacting co-repressor CIR | This is a 45 residue conserved region at the N-terminal end of a family of proteins referred to as CIRs (CBF1-interacting co-repressors). CBF1 (centromere-binding factor 1) acts as a transcription factor that causes repression by binding specifically ... | Domain |
I [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 |
I [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 |
I [auth C] | PF16004 | 116 kDa U5 small nuclear ribonucleoprotein component N-terminus (EFTUD2) | 116 kDa U5 small nuclear ribonucleoprotein component N-terminus | - | Family |
J [auth G] | PF06246 | Isy1-like splicing family (Isy1) | Isy1-like splicing family | - | Family |
L [auth J] | PF00400 | WD domain, G-beta repeat (WD40) | WD domain, G-beta repeat | - | Repeat |
N [auth L] | PF01125 | Pre-mRNA-splicing factor BUD31 (BUD31) | Pre-mRNA-splicing factor BUD31 | This entry includes Pre-mRNA-splicing factor BUD31, also known as G10 protein, and its homologues. BUD31 is involved in the pre-mRNA splicing process [1-3] and it is highly conserved in a wide range of eukaryotic species. Human BUD31 may play a role ... | Domain |
O [auth M] | PF16131 | Torus domain (Torus) | Torus domain | This domain is found in pre-mRNA-splicing factor CWC2. It includes a CCCH-type zinc finger [1]. | Domain |
O [auth M] | 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 |
P [auth N] | PF21369 | STL11, N-terminal (STL11_N) | STL11, N-terminal | This entry represents the N-terminal domain of STL11 from yeast and its homologues [1-4], such as RBM22 from human. This domain comprises a zinc finger, FYVE/PHD type. Members of this entry are involved in pre-mRNA splicing. | Domain |
Q [auth O] | PF00249 | Myb-like DNA-binding domain (Myb_DNA-binding) | Myb-like DNA-binding domain | This family contains the DNA binding domains from Myb proteins, as well as the SANT domain family [1]. | Domain |
R [auth P] | PF04889 | Cwf15/Cwc15 cell cycle control protein (Cwf_Cwc_15) | Cwf15/Cwc15 cell cycle control protein | - | Family |
S [auth R] | PF08312 | cwf21 domain (cwf21) | cwf21 domain | The cwf21 family is involved in mRNA splicing. It has been isolated as a subcomplex of the splicosome in Schizosaccharomyces pombe [1]. The function of the cwf21 domain is to bind directly to the spliceosomal protein Prp8. Mutations in the cwf21 dom ... | Domain |
T [auth S] | PF02184 | HAT (Half-A-TPR) repeat (HAT) | HAT (Half-A-TPR) repeat | - | Repeat |
EA [auth k], V [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 |
HA [auth n], W [auth d] | 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 p], X [auth e] | 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 |
JA [auth q], Y [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 |
AA [auth h], FA [auth l] | 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 j], GA [auth m] | 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 W] | PF14580 | Leucine-rich repeat (LRR_9) | Leucine-rich repeat | - | Repeat |
DA [auth Y] | PF13893 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) (RRM_5) | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | The RRM motif 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 protein components of snRNPs. The mo ... | Domain |
KA [auth r], Z [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 |