5WSG | pdb_00005wsg

Cryo-EM structure of the Catalytic Step II spliceosome (C* complex) at 4.0 angstrom resolution

External Resource: Annotation


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
G [auth R]SCOP2B SuperfamilyCCCH zinc finger-like 8051791 3001741 SCOP2B (2022-06-29)
G [auth R]SCOP2B SuperfamilyRNA-binding domain, RBD 8051796 3000110 SCOP2B (2022-06-29)
E [auth P]SCOP2B SuperfamilyPre-mRNA-processing protein 45-like 8092739 3002618 SCOP2B (2022-06-29)
SA [auth f]SCOP2B SuperfamilyFunctional domain of the splicing factor Prp18 8037866 3000735 SCOP2B (2022-06-29)
OA [auth X]SCOP2B SuperfamilyRNA-binding domain, RBD 8073745 3000110 SCOP2B (2022-06-29)
GA [auth g]SCOP2B SuperfamilySm-like ribonucleoproteins 8063490 3000419 SCOP2B (2022-06-29)
LA [auth U]SCOP2B SuperfamilySm-like ribonucleoproteins 8098694 3000419 SCOP2B (2022-06-29)
EA [auth l]SCOP2B SuperfamilySm-like ribonucleoproteins 8098694 3000419 SCOP2B (2022-06-29)
KA [auth K]SCOP2B SuperfamilySm-like ribonucleoproteins 8098668 3000419 SCOP2B (2022-06-29)
DA [auth j]SCOP2B SuperfamilySm-like ribonucleoproteins 8098668 3000419 SCOP2B (2022-06-29)
JA [auth H]SCOP2B SuperfamilySm-like ribonucleoproteins 8043703 3000419 SCOP2B (2022-06-29)
CA [auth h]SCOP2B SuperfamilySm-like ribonucleoproteins 8043703 3000419 SCOP2B (2022-06-29)
HA [auth F]SCOP2 FamilySm motif of small nuclear ribonucleoproteins, SNRNP 8077612 4001809 SCOP2 (2022-06-29)
HA [auth F]SCOP2 SuperfamilySm-like ribonucleoproteins 8077613 3000419 SCOP2 (2022-06-29)
AA [auth k]SCOP2B SuperfamilySm-like ribonucleoproteins 8077613 3000419 SCOP2B (2022-06-29)
Y [auth r]SCOP2B SuperfamilyRING/U-box like 8037831 3000160 SCOP2B (2022-06-29)
X [auth q]SCOP2B SuperfamilyRING/U-box like 8037831 3000160 SCOP2B (2022-06-29)
W [auth p]SCOP2B SuperfamilyRING/U-box like 8037831 3000160 SCOP2B (2022-06-29)
V [auth o]SCOP2B SuperfamilyRING/U-box like 8037831 3000160 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyRibonuclease H-like 8040983 3000143 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
G [auth R]AP_endonuc_2e5wsgR1 A: a/b three-layered sandwichesX: Cytochrome P450H: Cytochrome P450T: Cytochrome P450F: AP_endonuc_2ECOD (v294.1)
RA [auth e]Ribosomal_L10e5wsge1 A: a/b three-layered sandwichesX: SH3H: SH3T: SH3F: Ribosomal_L10ECOD (v294.1)
I [auth T]Ribosomal_L10e5wsgT1 A: a/b three-layered sandwichesX: SH3H: SH3T: SH3F: Ribosomal_L10ECOD (v294.1)
F [auth Q]Ribosomal_L10e5wsgQ1 A: a/b three-layered sandwichesX: SH3H: SH3T: SH3F: Ribosomal_L10ECOD (v294.1)
D [auth O]Ribosomal_L10e5wsgO1 A: a/b three-layered sandwichesX: SH3H: SH3T: SH3F: Ribosomal_L10ECOD (v294.1)
SA [auth f]Ribosomal_L10e5wsgf1 A: a/b three-layered sandwichesX: SH3H: SH3T: SH3F: Ribosomal_L10ECOD (v294.1)
PA [auth Y]Ribosomal_L10e5wsgY1 A: a/b three-layered sandwichesX: SH3H: SH3T: SH3F: Ribosomal_L10ECOD (v294.1)
OA [auth X]Ribosomal_L10e5wsgX1 A: a/b three-layered sandwichesX: SH3H: SH3T: SH3F: Ribosomal_L10ECOD (v294.1)
NA [auth W]Ribosomal_L10e5wsgW1 A: a/b three-layered sandwichesX: SH3H: SH3T: SH3F: Ribosomal_L10ECOD (v294.1)
GA [auth g]Ribosomal_L10e5wsgg1 A: a/b three-layered sandwichesX: SH3H: SH3T: SH3F: Ribosomal_L10ECOD (v294.1)
MA [auth V]Ribosomal_L10e5wsgV1 A: a/b three-layered sandwichesX: SH3H: SH3T: SH3F: Ribosomal_L10ECOD (v294.1)
FA [auth m]Ribosomal_L10e5wsgm1 A: a/b three-layered sandwichesX: SH3H: SH3T: SH3F: Ribosomal_L10ECOD (v294.1)
LA [auth U]Ribosomal_L10e5wsgU1 A: a/b three-layered sandwichesX: SH3H: SH3T: SH3F: Ribosomal_L10ECOD (v294.1)
EA [auth l]Ribosomal_L10e5wsgl1 A: a/b three-layered sandwichesX: SH3H: SH3T: SH3F: Ribosomal_L10ECOD (v294.1)
KA [auth K]Ribosomal_L10e5wsgK1 A: a/b three-layered sandwichesX: SH3H: SH3T: SH3F: Ribosomal_L10ECOD (v294.1)
DA [auth j]Ribosomal_L10e5wsgj1 A: a/b three-layered sandwichesX: SH3H: SH3T: SH3F: Ribosomal_L10ECOD (v294.1)
JA [auth H]Ribosomal_L10e5wsgH1 A: a/b three-layered sandwichesX: SH3H: SH3T: SH3F: Ribosomal_L10ECOD (v294.1)
CA [auth h]Ribosomal_L10e5wsgh1 A: a/b three-layered sandwichesX: SH3H: SH3T: SH3F: Ribosomal_L10ECOD (v294.1)
IA [auth G]Ribosomal_L10e5wsgG1 A: a/b three-layered sandwichesX: SH3H: SH3T: SH3F: Ribosomal_L10ECOD (v294.1)
BA [auth i]Ribosomal_L10e5wsgi1 A: a/b three-layered sandwichesX: SH3H: SH3T: SH3F: Ribosomal_L10ECOD (v294.1)
HA [auth F]Ribosomal_L10e5wsgF1 A: a/b three-layered sandwichesX: SH3H: SH3T: SH3F: Ribosomal_L10ECOD (v294.1)
AA [auth k]Ribosomal_L10e5wsgk1 A: a/b three-layered sandwichesX: SH3H: SH3T: SH3F: Ribosomal_L10ECOD (v294.1)
Y [auth r]FATCe5wsgr1 A: a/b three-layered sandwichesX: HAD domain-likeH: Rubredoxin-relatedT: Rubredoxin-relatedF: FATCECOD (v294.1)
X [auth q]U-boxe5wsgq1 A: a/b three-layered sandwichesX: MocoBD/DmpA-relatedH: Protein kinase/SAICAR synthase/ATP-graspT: Protein kinaseF: U-boxECOD (v294.1)
U [auth n]Ribosomal_L10e5wsgn1 A: a/b three-layered sandwichesX: SH3H: SH3T: SH3F: Ribosomal_L10ECOD (v294.1)
T [auth v]U-boxe5wsgv1 A: a/b three-layered sandwichesX: MocoBD/DmpA-relatedH: Protein kinase/SAICAR synthase/ATP-graspT: Protein kinaseF: U-boxECOD (v294.1)
B [auth C]AP_endonuc_2e5wsgC1 A: a/b three-layered sandwichesX: Cytochrome P450H: Cytochrome P450T: Cytochrome P450F: AP_endonuc_2ECOD (v294.1)
R [auth d]U-boxe5wsgd1 A: a/b three-layered sandwichesX: MocoBD/DmpA-relatedH: Protein kinase/SAICAR synthase/ATP-graspT: Protein kinaseF: U-boxECOD (v294.1)
Q [auth c]AARP2CNe5wsgc1 A: a/b three-layered sandwichesX: Spectrin repeat-likeH: Spectrin repeatT: Spectrin repeatF: AARP2CNECOD (v294.1)
J [auth Z]U-boxe5wsgZ1 A: a/b three-layered sandwichesX: MocoBD/DmpA-relatedH: Protein kinase/SAICAR synthase/ATP-graspT: Protein kinaseF: U-boxECOD (v294.1)
ARibosomal_L10e5wsgA1 A: a/b three-layered sandwichesX: SH3H: SH3T: SH3F: Ribosomal_L10ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
D [auth O]2.130.10.10 Mainly Beta 7 Propeller Methylamine Dehydrogenase Chain HCATH (4.3.0)
SA [auth f]1.20.940.10 Mainly Alpha Up-down Bundle RNA Binding Protein, Prp18 Chain ACATH (4.3.0)
OA [auth X]3.30.70.330 Alpha Beta 2-Layer Sandwich Alpha-Beta Plaits RRM (RNA recognition motif) domainCATH (4.3.0)
NA [auth W]2.30.30.100 Mainly Beta Roll SH3 type barrels. CATH (4.3.0)
GA [auth g]2.30.30.100 Mainly Beta Roll SH3 type barrels. CATH (4.3.0)
MA [auth V]2.30.30.100 Mainly Beta Roll SH3 type barrels. CATH (4.3.0)
FA [auth m]2.30.30.100 Mainly Beta Roll SH3 type barrels. CATH (4.3.0)
LA [auth U]2.30.30.100 Mainly Beta Roll SH3 type barrels. CATH (4.3.0)
EA [auth l]2.30.30.100 Mainly Beta Roll SH3 type barrels. CATH (4.3.0)
KA [auth K]2.30.30.100 Mainly Beta Roll SH3 type barrels. CATH (4.3.0)
DA [auth j]2.30.30.100 Mainly Beta Roll SH3 type barrels. CATH (4.3.0)
JA [auth H]2.30.30.100 Mainly Beta Roll SH3 type barrels. CATH (4.3.0)
CA [auth h]2.30.30.100 Mainly Beta Roll SH3 type barrels. CATH (4.3.0)
IA [auth G]2.30.30.100 Mainly Beta Roll SH3 type barrels. CATH (4.3.0)
BA [auth i]2.30.30.100 Mainly Beta Roll SH3 type barrels. CATH (4.3.0)
Y [auth r]3.30.40.10 Alpha Beta 2-Layer Sandwich Herpes Virus-1 Zinc/RING finger domain, C3HC4 (zinc finger)CATH (utative)
X [auth q]2.130.10.10 Mainly Beta 7 Propeller Methylamine Dehydrogenase Chain HCATH (utative)
W [auth p]3.30.40.10 Alpha Beta 2-Layer Sandwich Herpes Virus-1 Zinc/RING finger domain, C3HC4 (zinc finger)CATH (utative)
J [auth Z]1.25.40.180 Mainly Alpha Alpha Horseshoe Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat CATH (utative)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
C [auth J]PF01423LSM domain (LSM)LSM domainThe 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 ...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) in common, which assemble around the Sm site present in four of the major spliceosomal small nuclear RNAs. The U6 snRNP binds to the LSM (Like Sm) proteins [3]. Sm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Sm proteins. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. This family also includes the bacterial Hfq (host factor Q) proteins. Hfq are also RNA-binding proteins, that form hexameric rings.
Domain
G [auth R]PF16131Torus domain (Torus)Torus domainThis domain is found in pre-mRNA-splicing factor CWC2. It includes a CCCH-type zinc finger [1]. Domain
G [auth R]PF00076RNA recognition motif (RRM_1)RNA recognition motifThe 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 ...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 protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins (Swiss:P05455) have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteristic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins (Swiss:P05455) are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.
Domain
O [auth L]PF01423LSM domain (LSM)LSM domainThe 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 ...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) in common, which assemble around the Sm site present in four of the major spliceosomal small nuclear RNAs. The U6 snRNP binds to the LSM (Like Sm) proteins [3]. Sm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Sm proteins. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. This family also includes the bacterial Hfq (host factor Q) proteins. Hfq are also RNA-binding proteins, that form hexameric rings.
Domain
I [auth T]PF01125Pre-mRNA-splicing factor BUD31 (BUD31)Pre-mRNA-splicing factor BUD31This 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 ...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 as a regulator of androgen receptor (AR) transcriptional activity, probably increasing the AR transcriptional activity [4].
Domain
F [auth Q]PF21369STL11, N-terminal (STL11_N)STL11, N-terminalThis 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
E [auth P]PF02731SKIP/SNW domain (SKIP_SNW)SKIP/SNW domain- Family
D [auth O]PF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat
PA [auth Y]PF14580Leucine-rich repeat (LRR_9)Leucine-rich repeat- Repeat
FA [auth m],
MA [auth V]		PF01423LSM domain (LSM)LSM domainThe 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 ...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) in common, which assemble around the Sm site present in four of the major spliceosomal small nuclear RNAs. The U6 snRNP binds to the LSM (Like Sm) proteins [3]. Sm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Sm proteins. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. This family also includes the bacterial Hfq (host factor Q) proteins. Hfq are also RNA-binding proteins, that form hexameric rings.
Domain
EA [auth l],
LA [auth U]		PF01423LSM domain (LSM)LSM domainThe 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 ...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) in common, which assemble around the Sm site present in four of the major spliceosomal small nuclear RNAs. The U6 snRNP binds to the LSM (Like Sm) proteins [3]. Sm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Sm proteins. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. This family also includes the bacterial Hfq (host factor Q) proteins. Hfq are also RNA-binding proteins, that form hexameric rings.
Domain
DA [auth j],
KA [auth K]		PF01423LSM domain (LSM)LSM domainThe 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 ...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) in common, which assemble around the Sm site present in four of the major spliceosomal small nuclear RNAs. The U6 snRNP binds to the LSM (Like Sm) proteins [3]. Sm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Sm proteins. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. This family also includes the bacterial Hfq (host factor Q) proteins. Hfq are also RNA-binding proteins, that form hexameric rings.
Domain
CA [auth h],
JA [auth H]		PF01423LSM domain (LSM)LSM domainThe 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 ...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) in common, which assemble around the Sm site present in four of the major spliceosomal small nuclear RNAs. The U6 snRNP binds to the LSM (Like Sm) proteins [3]. Sm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Sm proteins. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. This family also includes the bacterial Hfq (host factor Q) proteins. Hfq are also RNA-binding proteins, that form hexameric rings.
Domain
BA [auth i],
IA [auth G]		PF01423LSM domain (LSM)LSM domainThe 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 ...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) in common, which assemble around the Sm site present in four of the major spliceosomal small nuclear RNAs. The U6 snRNP binds to the LSM (Like Sm) proteins [3]. Sm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Sm proteins. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. This family also includes the bacterial Hfq (host factor Q) proteins. Hfq are also RNA-binding proteins, that form hexameric rings.
Domain
AA [auth k],
HA [auth F]		PF02840Prp18 domain (Prp18)Prp18 domain- Family
AA [auth k],
HA [auth F]		PF01423LSM domain (LSM)LSM domainThe 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 ...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) in common, which assemble around the Sm site present in four of the major spliceosomal small nuclear RNAs. The U6 snRNP binds to the LSM (Like Sm) proteins [3]. Sm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Sm proteins. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. This family also includes the bacterial Hfq (host factor Q) proteins. Hfq are also RNA-binding proteins, that form hexameric rings.
Domain
B [auth C]PF00249Myb-like DNA-binding domain (Myb_DNA-binding)Myb-like DNA-binding domainThis family contains the DNA binding domains from Myb proteins, as well as the SANT domain family [1]. Domain
B [auth C]PF00679Elongation factor G C-terminus (EFG_C)Elongation factor G C-terminusThis 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]PF00009Elongation factor Tu GTP binding domain (GTP_EFTU)Elongation factor Tu GTP binding domainThis 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]PF03764Elongation factor G, domain IV (EFG_IV)Elongation factor G, domain IVThis 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
S [auth I]PF01423LSM domain (LSM)LSM domainThe 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 ...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) in common, which assemble around the Sm site present in four of the major spliceosomal small nuclear RNAs. The U6 snRNP binds to the LSM (Like Sm) proteins [3]. Sm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Sm proteins. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. This family also includes the bacterial Hfq (host factor Q) proteins. Hfq are also RNA-binding proteins, that form hexameric rings.
Domain
M [auth D]PF23233Pre-mRNA-splicing factor Syf1/CNRKL1 N-terminal HAT repeat (HAT_Syf1_CNRKL1_N)Pre-mRNA-splicing factor Syf1/CNRKL1 N-terminal HAT repeat- Repeat
J [auth Z]PF02847MA3 domain (MA3)MA3 domain- Repeat
PF10597U5-snRNA binding site 2 of PrP8 (U5_2-snRNA_bdg)U5-snRNA binding site 2 of PrP8The 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 ...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 Prp8 could directly affect the function of the catalytic core, perhaps acting as a splicing cofactor [2].
Domain
PF10598RNA recognition motif of the spliceosomal PrP8 (RRM_4)RNA recognition motif of the spliceosomal PrP8The 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 ...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 molecular rearrangements that occur there, and has recently come under the spotlight for its role in the inherited human disease, Retinitis Pigmentosa [1]. The RNA-recognition motif of PrP8 is highly conserved and provides a possible RNA binding centre for the 5-prime SS, BP, or 3-prime SS of pre-mRNA which are known to contact with Prp8. The most conserved regions of an RRM are defined as the RNP1 and RNP2 sequences. Recognition of RNA targets can also be modulated by a number of other factors, most notably the two loops beta1-alpha1, beta2-beta3 and the amino acid residues C-terminal to the RNP2 domain [2].
Domain
PF10596U6-snRNA interacting domain of PrP8 (U6-snRNA_bdg)U6-snRNA interacting domain of PrP8This 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 ...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 interacts with U5 and U6 snRNAs and with specific pre-mRNA sequences that participate in catalysis. This close association with crucial RNA sequences, together with extensive genetic evidence, suggests that Prp8 could directly affect the function of the catalytic core, perhaps acting as a splicing cofactor [1].
Domain
PF08082PRO8NT (NUC069), PrP8 N-terminal domain (PRO8NT)PRO8NT (NUC069), PrP8 N-terminal domainThe 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 ...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 variable proline-rich region [4].
Domain
PF08083PROCN (NUC071) domain (PROCN)PROCN (NUC071) domainThe PROCN domain is the central domain in pre-mRNA splicing factors of PRO8 family [1]. Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
C [auth J]Pre-mRNA-splicing factor CWC21-
G [auth R]Pre-mRNA-splicing factor CWC2
O [auth L]RNA (91-MER)---
RA [auth e]Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16
I [auth T]Pre-mRNA-splicing factor BUD31-
H [auth S]Pre-mRNA-splicing factor CWC15
F [auth Q]Pre-mRNA-splicing factor SLT11
E [auth P]Pre-mRNA-processing protein 45-
D [auth O]Pre-mRNA-splicing factor PRP46-
SA [auth f]Pre-mRNA-splicing factor 18-
QA [auth b]3'-exon-intron---
PA [auth Y]U2 small nuclear ribonucleoprotein A'
OA [auth X]U2 small nuclear ribonucleoprotein B''
GA [auth g],
NA [auth W]		Small nuclear ribonucleoprotein Sm D2
FA [auth m],
MA [auth V]		Small nuclear ribonucleoprotein Sm D1
EA [auth l],
LA [auth U]		Small nuclear ribonucleoprotein Sm D3
DA [auth j],
KA [auth K]		Small nuclear ribonucleoprotein G
CA [auth h],
JA [auth H]		Small nuclear ribonucleoprotein F
BA [auth i],
IA [auth G]		Small nuclear ribonucleoprotein E
AA [auth k],
HA [auth F]		Small nuclear ribonucleoprotein-associated protein B
Z [auth t]Pre-mRNA-splicing factor SNT309-
V [auth o],
W [auth p],
X [auth q],
Y [auth r]		Pre-mRNA-processing factor 19
U [auth n]Pre-mRNA-processing factor 17
T [auth v]Syf1,Pre-mRNA-splicing factor SYF1,Syf1,Pre-mRNA-splicing factor SYF1,Syf1,Pre-mRNA-splicing factor SYF1,Syf1-
B [auth C]Pre-mRNA-splicing factor SNU114
S [auth I]Pre-mRNA-splicing factor SYF2-
R [auth d]Pre-mRNA-splicing factor CLF1,Pre-mRNA-splicing factor CLF1,Clf1
Q [auth c]Pre-mRNA-splicing factor CEF1,Pre-mRNA-splicing factor CEF1,Cef1,Pre-mRNA-splicing factor CEF1
P [auth M]3'-intron-lariat---
N [auth E]Saccharomyces cerevisiae S288c SNR6 snRNA---
M [auth D]U5 snRNA---
L [auth N]5'-intron-lariat---
K [auth B]5'-exon---
J [auth Z]Pre-mRNA-splicing factor CWC22
Pre-mRNA-splicing factor 8

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
C [auth J]IPR013170mRNA splicing factor Cwf21 domainDomain
C [auth J]IPR051372Pre-mRNA-splicing factor CWC21Family
G [auth R]IPR039171Pre-mRNA-splicing factor Cwc2/Slt11Family
G [auth R]IPR034181Pre-mRNA-splicing factor Cwc2, RNA recognition motifDomain
G [auth R]IPR000504RNA recognition motif domainDomain
G [auth R]IPR032297Torus domainDomain
G [auth R]IPR000571Zinc finger, CCCH-typeDomain
G [auth R]IPR012677Nucleotide-binding alpha-beta plait domain superfamilyHomologous Superfamily
G [auth R]IPR035979RNA-binding domain superfamilyHomologous Superfamily
RA [auth e]IPR011709DEAD-box helicase, OB foldDomain
RA [auth e]IPR001650Helicase, C-terminal domain-likeDomain
RA [auth e]IPR014001Helicase superfamily 1/2, ATP-binding domainDomain
RA [auth e]IPR048333Helicase associated domain (HA2), winged-helix domainDomain
RA [auth e]IPR002464DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved siteConserved Site
RA [auth e]IPR007502Helicase-associated domainDomain
RA [auth e]IPR011545DEAD/DEAH-box helicase domainDomain
RA [auth e]IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily
I [auth T]IPR001748Pre-mRNA-splicing factor BUD31Family
I [auth T]IPR018230BUD31/G10-related, conserved siteConserved Site
H [auth S]IPR006973Pre-mRNA-splicing factor Cwf15/Cwc15Family
F [auth Q]IPR039171Pre-mRNA-splicing factor Cwc2/Slt11Family
F [auth Q]IPR034356Slt11, RNA recognition motifDomain
F [auth Q]IPR048995STL11/RBM22-like, N-terminal domainDomain
E [auth P]IPR017862SKI-interacting protein, SKIPFamily
E [auth P]IPR004015SKI-interacting protein SKIP, SNW domainDomain
D [auth O]IPR045241WD repeat Prp46/PLRG1-likeFamily
D [auth O]IPR020472PAC1/LIS1-like, WD-40 repeatRepeat
D [auth O]IPR001680WD40 repeatRepeat
D [auth O]IPR019775WD40 repeat, conserved siteConserved Site
D [auth O]IPR036322WD40-repeat-containing domain superfamilyHomologous Superfamily
D [auth O]IPR015943WD40/YVTN repeat-like-containing domain superfamilyHomologous Superfamily
SA [auth f]IPR039979Pre-mRNA-splicing factor 18Family
SA [auth f]IPR004098Prp18Domain
PA [auth Y]IPR001611Leucine-rich repeatRepeat
PA [auth Y]IPR003603U2A'/phosphoprotein 32 family A, C-terminalDomain
PA [auth Y]IPR032675Leucine-rich repeat domain superfamilyHomologous Superfamily
PA [auth Y]IPR044640U2 small nuclear ribonucleoprotein A'Family
OA [auth X]IPR012677Nucleotide-binding alpha-beta plait domain superfamilyHomologous Superfamily
OA [auth X]IPR000504RNA recognition motif domainDomain
OA [auth X]IPR035979RNA-binding domain superfamilyHomologous Superfamily
GA [auth g],
NA [auth W]		IPR001163Sm domain, eukaryotic/archaea-typeDomain
GA [auth g],
NA [auth W]		IPR047575Sm domainDomain
GA [auth g],
NA [auth W]		IPR027248Small nuclear ribonucleoprotein Sm D2Family
GA [auth g],
NA [auth W]		IPR010920LSM domain superfamilyHomologous Superfamily
FA [auth m],
MA [auth V]		IPR027141Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3Family
FA [auth m],
MA [auth V]		IPR001163Sm domain, eukaryotic/archaea-typeDomain
FA [auth m],
MA [auth V]		IPR047575Sm domainDomain
FA [auth m],
MA [auth V]		IPR010920LSM domain superfamilyHomologous Superfamily
EA [auth l],
LA [auth U]		IPR027141Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3Family
EA [auth l],
LA [auth U]		IPR034099Small nuclear ribonucleoprotein Sm D3Family
EA [auth l],
LA [auth U]		IPR001163Sm domain, eukaryotic/archaea-typeDomain
EA [auth l],
LA [auth U]		IPR047575Sm domainDomain
EA [auth l],
LA [auth U]		IPR010920LSM domain superfamilyHomologous Superfamily
DA [auth j],
KA [auth K]		IPR044641Sm-like protein Lsm7/SmGFamily
DA [auth j],
KA [auth K]		IPR034098Small nuclear ribonucleoprotein GFamily
DA [auth j],
KA [auth K]		IPR001163Sm domain, eukaryotic/archaea-typeDomain
DA [auth j],
KA [auth K]		IPR047575Sm domainDomain
DA [auth j],
KA [auth K]		IPR010920LSM domain superfamilyHomologous Superfamily
CA [auth h],
JA [auth H]		IPR016487Sm-like protein Lsm6/SmFFamily
CA [auth h],
JA [auth H]		IPR034100Small nuclear ribonucleoprotein FFamily
CA [auth h],
JA [auth H]		IPR001163Sm domain, eukaryotic/archaea-typeDomain
CA [auth h],
JA [auth H]		IPR047575Sm domainDomain
CA [auth h],
JA [auth H]		IPR010920LSM domain superfamilyHomologous Superfamily
BA [auth i],
IA [auth G]		IPR027078Small nuclear ribonucleoprotein EFamily
BA [auth i],
IA [auth G]		IPR001163Sm domain, eukaryotic/archaea-typeDomain
BA [auth i],
IA [auth G]		IPR047575Sm domainDomain
BA [auth i],
IA [auth G]		IPR010920LSM domain superfamilyHomologous Superfamily
AA [auth k],
HA [auth F]		IPR050914Small nuclear ribonucleoprotein-associated SmB/NAA38-likeFamily
AA [auth k],
HA [auth F]		IPR001163Sm domain, eukaryotic/archaea-typeDomain
AA [auth k],
HA [auth F]		IPR047575Sm domainDomain
AA [auth k],
HA [auth F]		IPR010920LSM domain superfamilyHomologous Superfamily
V [auth o],
W [auth p],
X [auth q],
Y [auth r]		IPR003613U-box domainDomain
V [auth o],
W [auth p],
X [auth q],
Y [auth r]		IPR038959Prp19Family
V [auth o],
W [auth p],
X [auth q],
Y [auth r]		IPR013083Zinc finger, RING/FYVE/PHD-typeHomologous Superfamily
V [auth o],
W [auth p],
X [auth q],
Y [auth r]		IPR011047Quinoprotein alcohol dehydrogenase-like superfamilyHomologous Superfamily
V [auth o],
W [auth p],
X [auth q],
Y [auth r]		IPR013915Prp19, coiled-coil regionDomain
V [auth o],
W [auth p],
X [auth q],
Y [auth r]		IPR055340Pre-mRNA-processing factor 19, U-box domainDomain
V [auth o],
W [auth p],
X [auth q],
Y [auth r]		IPR015943WD40/YVTN repeat-like-containing domain superfamilyHomologous Superfamily
U [auth n]IPR032847Pre-mRNA-processing factor 17Family
U [auth n]IPR036322WD40-repeat-containing domain superfamilyHomologous Superfamily
U [auth n]IPR020472PAC1/LIS1-like, WD-40 repeatRepeat
U [auth n]IPR001680WD40 repeatRepeat
U [auth n]IPR015943WD40/YVTN repeat-like-containing domain superfamilyHomologous Superfamily
T [auth v]IPR011990Tetratricopeptide-like helical domain superfamilyHomologous Superfamily
T [auth v]IPR055430Pre-mRNA-splicing factor Syf1/CRNKL1-like, C-terminal HAT-repeats domainDomain
T [auth v]IPR003107HAT (Half-A-TPR) repeatRepeat
T [auth v]IPR045075Pre-mRNA-splicing factor Syf1-likeFamily
T [auth v]IPR056350Pre-mRNA-splicing factor SYF1, central HAT repeats domainDomain
T [auth v]IPR055433Pre-mRNA-splicing factor Syf1-like, N-terminal HAT-repeats domainDomain
B [auth C]IPR005517Translation elongation factor EFG/EF2, domain IVDomain
B [auth C]IPR000795Translational (tr)-type GTP-binding domainDomain
B [auth C]IPR035647EF-G domain III/V-likeHomologous Superfamily
B [auth C]IPR035655116kDa U5 small nuclear ribonucleoprotein component, C-terminalDomain
B [auth C]IPR009000Translation protein, beta-barrel domain superfamilyHomologous Superfamily
B [auth C]IPR020568Ribosomal protein uS5 domain 2-type superfamilyHomologous Superfamily
B [auth C]IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily
B [auth C]IPR014721Small ribosomal subunit protein uS5 domain 2-type fold, subgroupHomologous Superfamily
B [auth C]IPR031950116kDa U5 small nuclear ribonucleoprotein component, N-terminalDomain
B [auth C]IPR000640Elongation factor EFG, domain V-likeDomain
B [auth C]IPR044121Snu114, GTP-binding domainDomain
S [auth I]IPR013260mRNA splicing factor SYF2Family
R [auth d]IPR011990Tetratricopeptide-like helical domain superfamilyHomologous Superfamily
R [auth d]IPR003107HAT (Half-A-TPR) repeatRepeat
R [auth d]IPR045075Pre-mRNA-splicing factor Syf1-likeFamily
R [auth d]IPR055433Pre-mRNA-splicing factor Syf1-like, N-terminal HAT-repeats domainDomain
Q [auth c]IPR009057Homedomain-like superfamilyHomologous Superfamily
Q [auth c]IPR047240Pre-mRNA splicing factor component CDC5L/Cef1, second SANT/myb-like domainDomain
Q [auth c]IPR017930Myb domainDomain
Q [auth c]IPR047242Pre-mRNA splicing factor component CDC5L/Cef1Family
Q [auth c]IPR001005SANT/Myb domainDomain
Q [auth c]IPR021786Pre-mRNA splicing factor component Cdc5p/Cef1, C-terminalDomain
J [auth Z]IPR050781Pre-mRNA-splicing factor CWC22Family
J [auth Z]IPR003891Initiation factor eIF-4 gamma, MA3Domain
J [auth Z]IPR003890MIF4G-like, type 3Domain
J [auth Z]IPR016024Armadillo-type foldHomologous Superfamily
IPR012984PROCT domainDomain
IPR012591PRO8NT domainDomain
IPR019580Pre-mRNA-processing-splicing factor 8, U6-snRNA-bindingDomain
IPR027652Pre-mRNA-processing-splicing factor 8Family
IPR043172Prp8 RNase domain IV, palm regionHomologous Superfamily
IPR012592PROCN domainDomain
IPR012337Ribonuclease H-like superfamilyHomologous Superfamily
IPR043173Prp8 RNase domain IV, fingers regionHomologous Superfamily
IPR021983PRP8 domain IV coreDomain
IPR019581Pre-mRNA-processing-splicing factor 8, U5-snRNA-bindingDomain
IPR037518MPN domainDomain
IPR019582RNA recognition motif, spliceosomal PrP8Domain
IPR042516Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding domain superfamilyHomologous Superfamily
IPR000555JAB1/MPN/MOV34 metalloenzyme domainDomain