5WSG
Cryo-EM structure of the Catalytic Step II spliceosome (C* complex) at 4.0 angstrom resolution
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
EA [auth l] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8098694 | 3000419 | SCOP2B (2022-06-29) |
LA [auth U] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8098694 | 3000419 | SCOP2B (2022-06-29) |
GA [auth g] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8063490 | 3000419 | SCOP2B (2022-06-29) |
A | SCOP2B Superfamily | Ribonuclease H-like | 8040983 | 3000143 | SCOP2B (2022-06-29) |
V [auth o] | SCOP2B Superfamily | RING/U-box like | 8037831 | 3000160 | SCOP2B (2022-06-29) |
W [auth p] | SCOP2B Superfamily | RING/U-box like | 8037831 | 3000160 | SCOP2B (2022-06-29) |
X [auth q] | SCOP2B Superfamily | RING/U-box like | 8037831 | 3000160 | SCOP2B (2022-06-29) |
Y [auth r] | SCOP2B Superfamily | RING/U-box like | 8037831 | 3000160 | SCOP2B (2022-06-29) |
AA [auth k] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8077613 | 3000419 | SCOP2B (2022-06-29) |
HA [auth F] | SCOP2 Family | Sm motif of small nuclear ribonucleoproteins, SNRNP | 8077612 | 4001809 | SCOP2 (2022-06-29) |
HA [auth F] | SCOP2 Superfamily | Sm-like ribonucleoproteins | 8077613 | 3000419 | SCOP2 (2022-06-29) |
CA [auth h] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8043703 | 3000419 | SCOP2B (2022-06-29) |
JA [auth H] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8043703 | 3000419 | SCOP2B (2022-06-29) |
DA [auth j] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8098668 | 3000419 | SCOP2B (2022-06-29) |
KA [auth K] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8098668 | 3000419 | SCOP2B (2022-06-29) |
OA [auth X] | SCOP2B Superfamily | RNA-binding domain, RBD | 8073745 | 3000110 | SCOP2B (2022-06-29) |
SA [auth f] | SCOP2B Superfamily | Functional domain of the splicing factor Prp18 | 8037866 | 3000735 | SCOP2B (2022-06-29) |
E [auth P] | SCOP2B Superfamily | Pre-mRNA-processing protein 45-like | 8092739 | 3002618 | SCOP2B (2022-06-29) |
G [auth R] | SCOP2B Superfamily | CCCH zinc finger-like | 8051791 | 3001741 | SCOP2B (2022-06-29) |
G [auth R] | SCOP2B Superfamily | RNA-binding domain, RBD | 8051796 | 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) |
---|---|---|---|---|---|---|---|---|
D [auth O] | ANAPC4_WD40_2 | e5wsgO1 | A: beta duplicates or obligate multimers | X: beta-propeller-like | H: beta-propeller | T: 7-bladed | F: ANAPC4_WD40_2 | ECOD (1.6) |
T [auth v] | UNK_F_TYPE | e5wsgv1 | A: alpha superhelices | X: Repetitive alpha hairpins | H: ARM repeat (From Topology) | T: ARM repeat | F: UNK_F_TYPE | ECOD (1.6) |
EA [auth l] | LSM | e5wsgl1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: LSM | ECOD (1.6) |
LA [auth U] | LSM | e5wsgU1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: LSM | ECOD (1.6) |
GA [auth g] | LSM | e5wsgg1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: LSM | ECOD (1.6) |
NA [auth W] | LSM | e5wsgW1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: LSM | ECOD (1.6) |
PA [auth Y] | LRR_9 | e5wsgY1 | 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) |
A | U5_2-snRNA_bdg | e5wsgA3 | 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 | e5wsgA1 | 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 | e5wsgA2 | 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 | U6-snRNA_bdg | e5wsgA4 | 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 | e5wsgA5 | 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 Z] | MIF4G | e5wsgZ1 | A: alpha superhelices | X: Repetitive alpha hairpins | H: ARM repeat (From Topology) | T: ARM repeat | F: MIF4G | ECOD (1.6) |
J [auth Z] | MA3 | e5wsgZ2 | A: alpha superhelices | X: Repetitive alpha hairpins | H: ARM repeat (From Topology) | T: ARM repeat | F: MA3 | ECOD (1.6) |
Q [auth c] | Myb_DNA-binding_1 | e5wsgc2 | A: alpha arrays | X: HTH | H: HTH | T: tri-helical | F: Myb_DNA-binding_1 | ECOD (1.6) |
R [auth d] | TPR_15 | e5wsgd1 | A: alpha superhelices | X: Repetitive alpha hairpins | H: ARM repeat (From Topology) | T: ARM repeat | F: TPR_15 | ECOD (1.6) |
B [auth C] | GTP_EFTU_D2_2 | e5wsgC5 | A: beta barrels | X: cradle loop barrel | H: RIFT-related | T: Alanine racemase-C | F: GTP_EFTU_D2_2 | ECOD (1.6) |
B [auth C] | EFG_IV | e5wsgC2 | 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) |
B [auth C] | EFG_C | e5wsgC4 | 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) |
B [auth C] | EFG_II | e5wsgC3 | 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) |
B [auth C] | MnmE_helical_2nd | e5wsgC1 | 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) |
U [auth n] | ANAPC4_WD40_2 | e5wsgn1 | A: beta duplicates or obligate multimers | X: beta-propeller-like | H: beta-propeller | T: 7-bladed | F: ANAPC4_WD40_2 | ECOD (1.6) |
X [auth q] | ANAPC4_WD40_14 | e5wsgq1 | A: beta duplicates or obligate multimers | X: beta-propeller-like | H: beta-propeller | T: 8-bladed | F: ANAPC4_WD40_14 | ECOD (1.6) |
X [auth q] | U-box | e5wsgq2 | A: few secondary structure elements | X: RING/U-box-like | H: RING/U-box-like | T: RING/U-box | F: U-box | ECOD (1.6) |
Y [auth r] | U-box | e5wsgr1 | A: few secondary structure elements | X: RING/U-box-like | H: RING/U-box-like | T: RING/U-box | F: U-box | ECOD (1.6) |
AA [auth k] | LSM | e5wsgk1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: LSM | ECOD (1.6) |
HA [auth F] | LSM | e5wsgF1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: LSM | ECOD (1.6) |
BA [auth i] | LSM | e5wsgi1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: LSM | ECOD (1.6) |
IA [auth G] | LSM | e5wsgG1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: LSM | ECOD (1.6) |
CA [auth h] | LSM | e5wsgh1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: LSM | ECOD (1.6) |
JA [auth H] | LSM | e5wsgH1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: LSM | ECOD (1.6) |
DA [auth j] | LSM | e5wsgj1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: LSM | ECOD (1.6) |
KA [auth K] | LSM | e5wsgK1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: LSM | ECOD (1.6) |
FA [auth m] | LSM | e5wsgm1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: LSM | ECOD (1.6) |
MA [auth V] | LSM | e5wsgV1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: LSM | ECOD (1.6) |
OA [auth X] | RRM_1_2 | e5wsgX1 | 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) |
RA [auth e] | OB_NTP_bind | e5wsge4 | A: beta barrels | X: OB-fold | H: Nucleic acid-binding proteins (From Topology) | T: Nucleic acid-binding proteins | F: OB_NTP_bind | ECOD (1.6) |
RA [auth e] | HA2_N,HA2_C | e5wsge2 | 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: HA2_N,HA2_C | ECOD (1.6) |
RA [auth e] | Helicase_C_7 | e5wsge3 | 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_7 | ECOD (1.6) |
RA [auth e] | HA2_N,DEAD_3 | e5wsge1 | A: a/b three-layered sandwiches | X: P-loop domains-like | H: P-loop domains-related | T: P-loop containing nucleoside triphosphate hydrolases | F: HA2_N,DEAD_3 | ECOD (1.6) |
SA [auth f] | Prp18 | e5wsgf1 | A: alpha bundles | X: Functional domain of the splicing factor Prp18 (From Topology) | H: Functional domain of the splicing factor Prp18 (From Topology) | T: Functional domain of the splicing factor Prp18 | F: Prp18 | ECOD (1.6) |
F [auth Q] | RRM_1_7 | e5wsgQ1 | 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) |
F [auth Q] | KOG0153 | e5wsgQ2 | 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) |
G [auth R] | RRM_1_6 | e5wsgR1 | 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) |
G [auth R] | Torus | e5wsgR2 | A: few secondary structure elements | X: CCCH zinc finger | H: CCCH zinc finger (From Topology) | T: CCCH zinc finger | F: Torus | ECOD (1.6) |
I [auth T] | G10 | e5wsgT1 | 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) |
Domain Annotation: CATH CATH Database Homepage
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
D [auth O] | PF00400 | WD domain, G-beta repeat (WD40) | WD domain, G-beta repeat | - | Repeat |
O [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 |
EA [auth l], LA [auth U] | 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 |
PA [auth Y] | PF14580 | Leucine-rich repeat (LRR_9) | Leucine-rich repeat | - | Repeat |
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 | |
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 | |
J [auth Z] | PF02847 | MA3 domain (MA3) | MA3 domain | - | Repeat |
S [auth I] | 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 |
B [auth C] | 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 |
B [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 |
B [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 |
B [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 |
AA [auth k], HA [auth F] | PF02840 | Prp18 domain (Prp18) | Prp18 domain | - | Family |
AA [auth k], HA [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 |
BA [auth i], IA [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 |
CA [auth h], JA [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 |
DA [auth j], KA [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 |
FA [auth m], MA [auth V] | 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 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 |
E [auth P] | PF02731 | SKIP/SNW domain (SKIP_SNW) | SKIP/SNW domain | - | Family |
F [auth Q] | 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 |
G [auth R] | 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 |
G [auth R] | 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 |
I [auth T] | 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 |