5GMK

Cryo-EM structure of the Catalytic Step I spliceosome (C complex) at 3.4 angstrom resolution

External Resource: Annotation


Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

ChainsDomain InfoClassFoldSuperfamilyFamilyDomainSpeciesProvenance Source (Version)
R [auth d]d5gmkd_ All alpha proteins alpha-alpha superhelix TPR-like HAT/Suf repeat Pre-mRNA splicing factor Clf1 (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ], (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ], SCOPe (2.08)
S [auth F]d5gmkf_ Alpha and beta proteins (a+b) Pre-mRNA splicing factor Cwc16-like Pre-mRNA splicing factor Cwc16-like Pre-mRNA splicing factor Cwc16-like Pre-mRNA splicing factor Cwc16 / Yju2 (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ], SCOPe (2.08)
T [auth G]d5gmkg_ Peptides Pre-mRNA splicing factor Cwc25-like Pre-mRNA splicing factor Cwc25-like Pre-mRNA splicing factor Cwc25-like Pre-mRNA splicing factor Cwc25 (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ], SCOPe (2.08)
U [auth H]d5gmkh_ All alpha proteins Long alpha-hairpin ISY1 domain-like ISY1 N-terminal domain-like Pre-mRNA splicing factor Isl1 (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ], SCOPe (2.08)
V [auth I]d5gmki_ Peptides Pre-mRNA splicing factor Syf2-like Pre-mRNA splicing factor Syf2-like Pre-mRNA splicing factor Syf2-like Pre-mRNA splicing factor Syf2 (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ], SCOPe (2.08)
W [auth v]d5gmkv_ All alpha proteins alpha-alpha superhelix TPR-like HAT/Suf repeat Pre-mRNA splicing factor Cwf3 / Syf1 (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ], (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ], (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ], SCOPe (2.08)
X [auth n]d5gmkn1 All beta proteins 7-bladed beta-propeller WD40 repeat-like WD40-repeat Pre-mRNA splicing factor Prp17, WD40 domain (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ], SCOPe (2.08)
X [auth n]d5gmkn2 Peptides Pre-mRNA splicing factor Prp17-like Pre-mRNA splicing factor Prp17-like Pre-mRNA splicing factor Prp17-like Pre-mRNA splicing factor Prp17, extended domain (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ], SCOPe (2.08)
RA [auth a]d5gmka_ Alpha and beta proteins (a+b) Ferredoxin-like RNA-binding domain, RBD, aka RNA recognition motif (RRM) Canonical RBD Spliceosomal U2 small nuclear ribonucleoprotein B' / U2B' / Msl1 protein (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ], SCOPe (2.08)
SA [auth b]d5gmkb_ Alpha and beta proteins (a/b) Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) L domain-like U2A'-like Spliceosomal U2 small nuclear ribonucleoprotein A' / U2A' / Lea1 protein (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ], SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
ASCOP2B SuperfamilyRibonuclease H-like8040983 3000143 SCOP2B (2022-06-29)
K [auth P]SCOP2B SuperfamilyPre-mRNA-processing protein 45-like8092739 3002618 SCOP2B (2022-06-29)
M [auth R]SCOP2B SuperfamilyRNA-binding domain RBD8051796 3000110 SCOP2B (2022-06-29)
M [auth R]SCOP2B SuperfamilyCCCH zinc finger-like8051791 3001741 SCOP2B (2022-06-29)
N [auth S]SCOP2 FamilyCwf15/Cwc15-like8046625 4005200 SCOP2 (2022-06-29)
N [auth S]SCOP2 SuperfamilyCwf15/Cwc15-like8103703 3002807 SCOP2 (2022-06-29)
AA [auth q]SCOP2B SuperfamilyRING/U-box like8037831 3000160 SCOP2B (2022-06-29)
BA [auth r]SCOP2B SuperfamilyRING/U-box like8037831 3000160 SCOP2B (2022-06-29)
Y [auth o]SCOP2B SuperfamilyRING/U-box like8037831 3000160 SCOP2B (2022-06-29)
Z [auth p]SCOP2B SuperfamilyRING/U-box like8037831 3000160 SCOP2B (2022-06-29)
DA [auth k]SCOP2B SuperfamilySm-like ribonucleoproteins8077613 3000419 SCOP2B (2022-06-29)
KA [auth s]SCOP2B SuperfamilySm-like ribonucleoproteins8077613 3000419 SCOP2B (2022-06-29)
FA [auth h]SCOP2B SuperfamilySm-like ribonucleoproteins8043703 3000419 SCOP2B (2022-06-29)
MA [auth w]SCOP2B SuperfamilySm-like ribonucleoproteins8043703 3000419 SCOP2B (2022-06-29)
GA [auth j]SCOP2B SuperfamilySm-like ribonucleoproteins8098668 3000419 SCOP2B (2022-06-29)
NA [auth x]SCOP2B SuperfamilySm-like ribonucleoproteins8098668 3000419 SCOP2B (2022-06-29)
HA [auth l]SCOP2B SuperfamilySm-like ribonucleoproteins8098694 3000419 SCOP2B (2022-06-29)
OA [auth y]SCOP2B SuperfamilySm-like ribonucleoproteins8098694 3000419 SCOP2B (2022-06-29)
JA [auth g]SCOP2B SuperfamilySm-like ribonucleoproteins8063490 3000419 SCOP2B (2022-06-29)
RA [auth a]SCOP2B SuperfamilyRNA-binding domain RBD8073745 3000110 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
APF10596,PF10597e5gmkA5 A: alpha bundlesX: 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 polymerasesF: PF10596,PF10597ECOD (1.6)
APF08082,PF08083e5gmkA1 A: alpha complex topologyX: 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 domainF: PF08082,PF08083ECOD (1.6)
APF10598e5gmkA2 A: a+b two layersX: Alpha-beta plaitsH: Adenylyl and guanylyl cyclase catalytic domain-likeT: Adenylyl and guanylyl cyclase catalytic domain-likeF: PF10598ECOD (1.6)
APF10596e5gmkA4 A: a/b three-layered sandwichesX: Restriction endonuclease-likeH: Restriction endonuclease-like (From Topology)T: Restriction endonuclease-likeF: PF10596ECOD (1.6)
APF12134e5gmkA3 A: mixed a+b and a/bX: Ribonuclease H-likeH: Ribonuclease H-like (From Topology)T: Ribonuclease H-likeF: PF12134ECOD (1.6)
J [auth O]PF00400e5gmkO1 A: beta duplicates or obligate multimersX: beta-propeller-likeH: beta-propellerT: 7-bladedF: PF00400ECOD (1.6)
L [auth Q]F_UNCLASSIFIEDe5gmkQ2 A: a+b two layersX: Alpha-beta plaitsH: RNA-binding domain, RBD (From Topology)T: RNA-binding domain, RBDF: F_UNCLASSIFIEDECOD (1.6)
L [auth Q]PF21369e5gmkQ1 A: few secondary structure elementsX: RING/U-box-likeH: RING/U-box-likeT: FYVE/PHD zinc fingerF: PF21369ECOD (1.6)
O [auth T]PF01125e5gmkT1 A: few secondary structure elementsX: Pre-mRNA-splicing factor BUD31 (From Topology)H: Pre-mRNA-splicing factor BUD31 (From Topology)T: Pre-mRNA-splicing factor BUD31F: PF01125ECOD (1.6)
Q [auth c]PF00249e5gmkc1 A: alpha arraysX: HTHH: HTHT: tri-helicalF: PF00249ECOD (1.6)
R [auth d]PF02184,PF05843e5gmkd1 A: alpha superhelicesX: Repetitive alpha hairpinsH: ARM repeat (From Topology)T: ARM repeatF: PF02184,PF05843ECOD (1.6)
U [auth H]PF06246e5gmkH1 A: alpha bundlesX: Long alpha-hairpinH: ISY1 N-terminal domain-like (From Topology)T: ISY1 N-terminal domain-likeF: PF06246ECOD (1.6)
W [auth v]F_UNCLASSIFIEDe5gmkv1 A: alpha superhelicesX: Repetitive alpha hairpinsH: ARM repeat (From Topology)T: ARM repeatF: F_UNCLASSIFIEDECOD (1.6)
X [auth n]PF00400e5gmkn1 A: beta duplicates or obligate multimersX: beta-propeller-likeH: beta-propellerT: 7-bladedF: PF00400ECOD (1.6)
AA [auth q]F_UNCLASSIFIEDe5gmkq1 A: beta duplicates or obligate multimersX: beta-propeller-likeH: beta-propellerT: 8-bladedF: F_UNCLASSIFIEDECOD (1.6)
AA [auth q]PF04564e5gmkq2 A: few secondary structure elementsX: RING/U-box-likeH: RING/U-box-likeT: RING/U-boxF: PF04564ECOD (1.6)
BA [auth r]PF04564e5gmkr1 A: few secondary structure elementsX: RING/U-box-likeH: RING/U-box-likeT: RING/U-boxF: PF04564ECOD (1.6)
Y [auth o]PF04564e5gmko1 A: few secondary structure elementsX: RING/U-box-likeH: RING/U-box-likeT: RING/U-boxF: PF04564ECOD (1.6)
Z [auth p]PF04564e5gmkp1 A: few secondary structure elementsX: RING/U-box-likeH: RING/U-box-likeT: RING/U-boxF: PF04564ECOD (1.6)
DA [auth k]PF01423e5gmkk1 A: beta barrelsX: SH3H: SH3T: SH3F: PF01423ECOD (1.6)
KA [auth s]PF01423e5gmks1 A: beta barrelsX: SH3H: SH3T: SH3F: PF01423ECOD (1.6)
EA [auth i]PF01423e5gmki1 A: beta barrelsX: SH3H: SH3T: SH3F: PF01423ECOD (1.6)
LA [auth u]PF01423e5gmku1 A: beta barrelsX: SH3H: SH3T: SH3F: PF01423ECOD (1.6)
FA [auth h]PF01423e5gmkh1 A: beta barrelsX: SH3H: SH3T: SH3F: PF01423ECOD (1.6)
MA [auth w]PF01423e5gmkw1 A: beta barrelsX: SH3H: SH3T: SH3F: PF01423ECOD (1.6)
GA [auth j]PF01423e5gmkj1 A: beta barrelsX: SH3H: SH3T: SH3F: PF01423ECOD (1.6)
NA [auth x]PF01423e5gmkx1 A: beta barrelsX: SH3H: SH3T: SH3F: PF01423ECOD (1.6)
HA [auth l]PF01423e5gmkl1 A: beta barrelsX: SH3H: SH3T: SH3F: PF01423ECOD (1.6)
OA [auth y]PF01423e5gmky1 A: beta barrelsX: SH3H: SH3T: SH3F: PF01423ECOD (1.6)
PA [auth z]PF01423e5gmkz1 A: beta barrelsX: SH3H: SH3T: SH3F: PF01423ECOD (1.6)
IA [auth m]PF01423e5gmkm1 A: beta barrelsX: SH3H: SH3T: SH3F: PF01423ECOD (1.6)
JA [auth g]PF01423e5gmkg1 A: beta barrelsX: SH3H: SH3T: SH3F: PF01423ECOD (1.6)
QA [auth e]PF01423e5gmke1 A: beta barrelsX: SH3H: SH3T: SH3F: PF01423ECOD (1.6)
RA [auth a]PF13893e5gmka1 A: a+b two layersX: Alpha-beta plaitsH: RNA-binding domain, RBD (From Topology)T: RNA-binding domain, RBDF: PF13893ECOD (1.6)
SA [auth b]PF14580e5gmkb1 A: beta duplicates or obligate multimersX: Single-stranded right-handed beta-helixH: Leucine-rich repeats (From Topology)T: Leucine-rich repeatsF: PF14580ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
J [auth O]2.130.10.10 Mainly Beta 7 Propeller Methylamine Dehydrogenase Chain HCATH (4.3.0)
X [auth n]2.130.10.10 Mainly Beta 7 Propeller Methylamine Dehydrogenase Chain HCATH (4.3.0)
AA [auth q]3.30.40.10 Alpha Beta 2-Layer Sandwich Herpes Virus-1 Zinc/RING finger domain, C3HC4 (zinc finger)CATH (4.3.0)
BA [auth r]3.30.40.10 Alpha Beta 2-Layer Sandwich Herpes Virus-1 Zinc/RING finger domain, C3HC4 (zinc finger)CATH (utative)
Z [auth p]3.30.40.10 Alpha Beta 2-Layer Sandwich Herpes Virus-1 Zinc/RING finger domain, C3HC4 (zinc finger)CATH (utative)
EA [auth i]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)
FA [auth h]2.30.30.100 Mainly Beta Roll SH3 type barrels. CATH (4.3.0)
MA [auth w]2.30.30.100 Mainly Beta Roll SH3 type barrels. CATH (4.3.0)
GA [auth j]2.30.30.100 Mainly Beta Roll SH3 type barrels. CATH (4.3.0)
NA [auth x]2.30.30.100 Mainly Beta Roll SH3 type barrels. CATH (4.3.0)
HA [auth l]2.30.30.100 Mainly Beta Roll SH3 type barrels. CATH (4.3.0)
OA [auth y]2.30.30.100 Mainly Beta Roll SH3 type barrels. CATH (4.3.0)
PA [auth z]2.30.30.100 Mainly Beta Roll SH3 type barrels. CATH (4.3.0)
IA [auth m]2.30.30.100 Mainly Beta Roll SH3 type barrels. CATH (4.3.0)
JA [auth g]2.30.30.100 Mainly Beta Roll SH3 type barrels. CATH (4.3.0)
QA [auth e]2.30.30.100 Mainly Beta Roll SH3 type barrels. CATH (4.3.0)
RA [auth a]3.30.70.330 Alpha Beta 2-Layer Sandwich Alpha-Beta Plaits RRM (RNA recognition motif) domainCATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
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
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]PF16004116 kDa U5 small nuclear ribonucleoprotein component N-terminus (EFTUD2)116 kDa U5 small nuclear ribonucleoprotein component N-terminus- Family
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
J [auth O]PF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat
K [auth P]PF02731SKIP/SNW domain (SKIP_SNW)SKIP/SNW domain- Family
L [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
M [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
M [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 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
P [auth Z]PF02847MA3 domain (MA3)MA3 domain- Repeat
Q [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
Q [auth c]PF11831pre-mRNA splicing factor component (Myb_Cef)pre-mRNA splicing factor component- Family
R [auth d]PF02184HAT (Half-A-TPR) repeat (HAT)HAT (Half-A-TPR) repeat- Repeat
S [auth F]PF04502Saf4/Yju2 protein (Saf4_Yju2)Saf4/Yju2 protein- Family
T [auth G]PF10197N-terminal domain of CBF1 interacting co-repressor CIR (Cir_N)N-terminal domain of CBF1 interacting co-repressor CIRThis 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 ...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 to GTGGGAA motifs in responsive promoters, and it requires CIR as a co-repressor. CIR binds to histone deacetylase and to SAP30 and serves as a linker between CBF1 and the histone deacetylase complex [1].
Domain
U [auth H]PF06246Isy1-like splicing family (Isy1)Isy1-like splicing family- Family
V [auth I]PF08231SYF2 splicing factor (SYF2)SYF2 splicing factorProteins in this family are involved in cell cycle progression and pre-mRNA splicing [1] [2].Domain
X [auth n]PF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat
DA [auth k],
KA [auth s]		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 i],
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
FA [auth h],
MA [auth w]		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
GA [auth j],
NA [auth x]		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
HA [auth l],
OA [auth y]		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
IA [auth m],
PA [auth z]		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
JA [auth g],
QA [auth e]		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
RA [auth a]PF13893RNA 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 ...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 motif also appears in a few single stranded DNA binding proteins.
Domain
SA [auth b]PF14580Leucine-rich repeat (LRR_9)Leucine-rich repeat- Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
Pre-mRNA-splicing factor 8
B [auth C]Pre-mRNA-splicing factor SNU114
C [auth D]U5 snRNA---
D [auth E]U6 snRNA---
E [auth L]U2 snRNA---
F [auth M]Intron_BPS---
G [auth B]5'-Exon---
H [auth N]5'-Splicing Site---
I [auth J]Pre-mRNA-splicing factor CWC21-
J [auth O]Pre-mRNA-splicing factor PRP46-
K [auth P]Pre-mRNA-processing protein 45-
L [auth Q]Pre-mRNA-splicing factor SLT11
M [auth R]Pre-mRNA-splicing factor CWC2
N [auth S]Pre-mRNA-splicing factor CWC15
O [auth T]Pre-mRNA-splicing factor BUD31-
P [auth Z]Pre-mRNA-splicing factor CWC22
Q [auth c]Pre-mRNA-splicing factor CEF1
R [auth d]Pre-mRNA-splicing factor CLF1
S [auth F]Protein CWC16
T [auth G]Pre-mRNA-splicing factor CWC25-
U [auth H]Pre-mRNA-splicing factor ISY1-
V [auth I]Pre-mRNA-splicing factor SYF2-
W [auth v]Pre-mRNA-splicing factor SYF1-
X [auth n]Pre-mRNA-processing factor 17
AA [auth q],
BA [auth r],
Y [auth o],
Z [auth p]		Pre-mRNA-processing factor 19
CA [auth t]Pre-mRNA-splicing factor SNT309-
DA [auth k],
KA [auth s]		Small nuclear ribonucleoprotein-associated protein B
EA [auth i],
LA [auth u]		Small nuclear ribonucleoprotein E
FA [auth h],
MA [auth w]		Small nuclear ribonucleoprotein F
GA [auth j],
NA [auth x]		Small nuclear ribonucleoprotein G
HA [auth l],
OA [auth y]		Small nuclear ribonucleoprotein Sm D3
IA [auth m],
PA [auth z]		Small nuclear ribonucleoprotein Sm D1
JA [auth g],
QA [auth e]		Small nuclear ribonucleoprotein Sm D2
RA [auth a]U2 small nuclear ribonucleoprotein B''
SA [auth b]U2 small nuclear ribonucleoprotein A'

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
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
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
I [auth J]IPR013170mRNA splicing factor Cwf21 domainDomain
J [auth O]IPR045241WD repeat Prp46/PLRG1-likeFamily
J [auth O]IPR001680WD40 repeatRepeat
J [auth O]IPR019775WD40 repeat, conserved siteConserved Site
J [auth O]IPR020472G-protein beta WD-40 repeatRepeat
J [auth O]IPR036322WD40-repeat-containing domain superfamilyHomologous Superfamily
J [auth O]IPR015943WD40/YVTN repeat-like-containing domain superfamilyHomologous Superfamily
K [auth P]IPR017862SKI-interacting protein, SKIPFamily
K [auth P]IPR004015SKI-interacting protein SKIP, SNW domainDomain
L [auth Q]IPR039171Pre-mRNA-splicing factor Cwc2/Slt11Family
L [auth Q]IPR034356Slt11, RNA recognition motifDomain
L [auth Q]IPR048995STL11/RBM22-like, N-terminal domainDomain
M [auth R]IPR039171Pre-mRNA-splicing factor Cwc2/Slt11Family
M [auth R]IPR034181Pre-mRNA-splicing factor Cwc2, RNA recognition motifDomain
M [auth R]IPR000504RNA recognition motif domainDomain
M [auth R]IPR032297Torus domainDomain
M [auth R]IPR000571Zinc finger, CCCH-typeDomain
M [auth R]IPR012677Nucleotide-binding alpha-beta plait domain superfamilyHomologous Superfamily
M [auth R]IPR035979RNA-binding domain superfamilyHomologous Superfamily
N [auth S]IPR006973Pre-mRNA-splicing factor Cwf15/Cwc15Family
O [auth T]IPR001748Pre-mRNA-splicing factor BUD31Family
O [auth T]IPR018230BUD31/G10-related, conserved siteConserved Site
P [auth Z]IPR003891Initiation factor eIF-4 gamma, MA3Domain
P [auth Z]IPR003890MIF4G-like, type 3Domain
P [auth Z]IPR016024Armadillo-type foldHomologous Superfamily
Q [auth c]IPR047240Pre-mRNA splicing factor component CDC5L/Cef1, second SANT/myb-like domainDomain
Q [auth c]IPR017930Myb domainDomain
Q [auth c]IPR009057Homeobox-like domain superfamilyHomologous Superfamily
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
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
S [auth F]IPR043701Splicing factor Yju2Family
S [auth F]IPR007590Saf4/Yju2 proteinFamily
T [auth G]IPR019339CBF1-interacting co-repressor CIR, N-terminal domainDomain
T [auth G]IPR022209Pre-mRNA splicing factorFamily
U [auth H]IPR029012Helix hairpin bin domain superfamilyHomologous Superfamily
U [auth H]IPR009360Pre-mRNA-splicing factor Isy1Family
U [auth H]IPR037200Pre-mRNA-splicing factor Isy1 superfamilyHomologous Superfamily
V [auth I]IPR013260mRNA splicing factor SYF2Family
W [auth v]IPR011990Tetratricopeptide-like helical domain superfamilyHomologous Superfamily
W [auth v]IPR003107HAT (Half-A-TPR) repeatRepeat
W [auth v]IPR045075Pre-mRNA-splicing factor Syf1-likeFamily
X [auth n]IPR032847Pre-mRNA-processing factor 17Family
X [auth n]IPR036322WD40-repeat-containing domain superfamilyHomologous Superfamily
X [auth n]IPR001680WD40 repeatRepeat
X [auth n]IPR020472G-protein beta WD-40 repeatRepeat
X [auth n]IPR015943WD40/YVTN repeat-like-containing domain superfamilyHomologous Superfamily
AA [auth q],
BA [auth r],
Y [auth o],
Z [auth p]		IPR003613U-box domainDomain
AA [auth q],
BA [auth r],
Y [auth o],
Z [auth p]		IPR013915Pre-mRNA-splicing factor 19Domain
AA [auth q],
BA [auth r],
Y [auth o],
Z [auth p]		IPR013083Zinc finger, RING/FYVE/PHD-typeHomologous Superfamily
AA [auth q],
BA [auth r],
Y [auth o],
Z [auth p]		IPR011047Quinoprotein alcohol dehydrogenase-like superfamilyHomologous Superfamily
AA [auth q],
BA [auth r],
Y [auth o],
Z [auth p]		IPR015943WD40/YVTN repeat-like-containing domain superfamilyHomologous Superfamily
AA [auth q],
BA [auth r],
Y [auth o],
Z [auth p]		IPR038959Pre-mRNA-processing factor 19Family
DA [auth k],
KA [auth s]		IPR001163Sm domain, eukaryotic/archaea-typeDomain
DA [auth k],
KA [auth s]		IPR047575Sm domainDomain
DA [auth k],
KA [auth s]		IPR010920LSM domain superfamilyHomologous Superfamily
EA [auth i],
LA [auth u]		IPR027078Small nuclear ribonucleoprotein EFamily
EA [auth i],
LA [auth u]		IPR001163Sm domain, eukaryotic/archaea-typeDomain
EA [auth i],
LA [auth u]		IPR047575Sm domainDomain
EA [auth i],
LA [auth u]		IPR010920LSM domain superfamilyHomologous Superfamily
FA [auth h],
MA [auth w]		IPR016487Sm-like protein Lsm6/SmFFamily
FA [auth h],
MA [auth w]		IPR034100Small nuclear ribonucleoprotein FFamily
FA [auth h],
MA [auth w]		IPR001163Sm domain, eukaryotic/archaea-typeDomain
FA [auth h],
MA [auth w]		IPR047575Sm domainDomain
FA [auth h],
MA [auth w]		IPR010920LSM domain superfamilyHomologous Superfamily
GA [auth j],
NA [auth x]		IPR044641Sm-like protein Lsm7/SmGFamily
GA [auth j],
NA [auth x]		IPR034098Small nuclear ribonucleoprotein GFamily
GA [auth j],
NA [auth x]		IPR001163Sm domain, eukaryotic/archaea-typeDomain
GA [auth j],
NA [auth x]		IPR047575Sm domainDomain
GA [auth j],
NA [auth x]		IPR010920LSM domain superfamilyHomologous Superfamily
HA [auth l],
OA [auth y]		IPR027141Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3Family
HA [auth l],
OA [auth y]		IPR034099Small nuclear ribonucleoprotein Sm D3Family
HA [auth l],
OA [auth y]		IPR001163Sm domain, eukaryotic/archaea-typeDomain
HA [auth l],
OA [auth y]		IPR047575Sm domainDomain
HA [auth l],
OA [auth y]		IPR010920LSM domain superfamilyHomologous Superfamily
IA [auth m],
PA [auth z]		IPR027141Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3Family
IA [auth m],
PA [auth z]		IPR001163Sm domain, eukaryotic/archaea-typeDomain
IA [auth m],
PA [auth z]		IPR047575Sm domainDomain
IA [auth m],
PA [auth z]		IPR010920LSM domain superfamilyHomologous Superfamily
JA [auth g],
QA [auth e]		IPR001163Sm domain, eukaryotic/archaea-typeDomain
JA [auth g],
QA [auth e]		IPR047575Sm domainDomain
JA [auth g],
QA [auth e]		IPR027248Small nuclear ribonucleoprotein Sm D2Family
JA [auth g],
QA [auth e]		IPR010920LSM domain superfamilyHomologous Superfamily
RA [auth a]IPR012677Nucleotide-binding alpha-beta plait domain superfamilyHomologous Superfamily
RA [auth a]IPR000504RNA recognition motif domainDomain
RA [auth a]IPR035979RNA-binding domain superfamilyHomologous Superfamily
SA [auth b]IPR032675Leucine-rich repeat domain superfamilyHomologous Superfamily
SA [auth b]IPR001611Leucine-rich repeatRepeat
SA [auth b]IPR003603U2A'/phosphoprotein 32 family A, C-terminalDomain