5YLZ

Cryo-EM Structure of the Post-catalytic Spliceosome from Saccharomyces cerevisiae at 3.6 angstrom

External Resource: Annotation


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
ASCOP2B SuperfamilyRibonuclease H-like8040983 3000143 SCOP2B (2022-06-29)
O [auth N]SCOP2B SuperfamilyCCCH zinc finger-like8051791 3001741 SCOP2B (2022-06-29)
O [auth N]SCOP2B SuperfamilyRNA-binding domain RBD8051796 3000110 SCOP2B (2022-06-29)
R [auth Q]SCOP2B SuperfamilyPre-mRNA-processing protein 45-like8092739 3002618 SCOP2B (2022-06-29)
USCOP2B SuperfamilyFunctional domain of the splicing factor Prp188037866 3000735 SCOP2B (2022-06-29)
EA [auth h]SCOP2B SuperfamilySm-like ribonucleoproteins8077613 3000419 SCOP2B (2022-06-29)
X [auth a]SCOP2B SuperfamilySm-like ribonucleoproteins8077613 3000419 SCOP2B (2022-06-29)
Z [auth c]SCOP2B SuperfamilySm-like ribonucleoproteins8043703 3000419 SCOP2B (2022-06-29)
GA [auth j]SCOP2B SuperfamilySm-like ribonucleoproteins8043703 3000419 SCOP2B (2022-06-29)
AA [auth d]SCOP2B SuperfamilySm-like ribonucleoproteins8098668 3000419 SCOP2B (2022-06-29)
HA [auth k]SCOP2B SuperfamilySm-like ribonucleoproteins8098668 3000419 SCOP2B (2022-06-29)
IA [auth l]SCOP2B SuperfamilySm-like ribonucleoproteins8098694 3000419 SCOP2B (2022-06-29)
BA [auth e]SCOP2B SuperfamilySm-like ribonucleoproteins8098694 3000419 SCOP2B (2022-06-29)
DA [auth g]SCOP2B SuperfamilySm-like ribonucleoproteins8063490 3000419 SCOP2B (2022-06-29)
MA [auth p]SCOP2B SuperfamilyRNA-binding domain RBD8073745 3000110 SCOP2B (2022-06-29)
OA [auth r]SCOP2B SuperfamilyRING/U-box like8037831 3000160 SCOP2B (2022-06-29)
PA [auth s]SCOP2B SuperfamilyRING/U-box like8037831 3000160 SCOP2B (2022-06-29)
NA [auth q]SCOP2B SuperfamilyRING/U-box like8037831 3000160 SCOP2B (2022-06-29)
QA [auth t]SCOP2B SuperfamilyRING/U-box like8037831 3000160 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
APF10596,PF10597e5ylzA4 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,PF08083e5ylzA1 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)
APF10598e5ylzA5 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)
APF10596e5ylzA2 A: a/b three-layered sandwichesX: Restriction endonuclease-likeH: Restriction endonuclease-like (From Topology)T: Restriction endonuclease-likeF: PF10596ECOD (1.6)
APF12134e5ylzA3 A: mixed a+b and a/bX: Ribonuclease H-likeH: Ribonuclease H-like (From Topology)T: Ribonuclease H-likeF: PF12134ECOD (1.6)
LPF01125e5ylzL1 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)
M [auth T]PF00400e5ylzT1 A: beta duplicates or obligate multimersX: beta-propeller-likeH: beta-propellerT: 7-bladedF: PF00400ECOD (1.6)
N [auth M]F_UNCLASSIFIEDe5ylzM2 A: a+b two layersX: Alpha-beta plaitsH: RNA-binding domain, RBD (From Topology)T: RNA-binding domain, RBDF: F_UNCLASSIFIEDECOD (1.6)
N [auth M]PF21369e5ylzM1 A: few secondary structure elementsX: RING/U-box-likeH: RING/U-box-likeT: FYVE/PHD zinc fingerF: PF21369ECOD (1.6)
P [auth O]PF00400e5ylzO1 A: beta duplicates or obligate multimersX: beta-propeller-likeH: beta-propellerT: 7-bladedF: PF00400ECOD (1.6)
S [auth R]F_UNCLASSIFIEDe5ylzR1 A: alpha duplicates or obligate multimersX: cwf21 domain (From Topology)H: cwf21 domain (From Topology)T: cwf21 domainF: F_UNCLASSIFIEDECOD (1.6)
T [auth S]PF02847e5ylzS1 A: alpha superhelicesX: Repetitive alpha hairpinsH: ARM repeat (From Topology)T: ARM repeatF: PF02847ECOD (1.6)
UPF02840e5ylzU1 A: alpha bundlesX: 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 Prp18F: PF02840ECOD (1.6)
VPF11708e5ylzV1 A: extended segmentsX: Prp8-binding region of SLU7 (From Topology)H: Prp8-binding region of SLU7 (From Topology)T: Prp8-binding region of SLU7F: PF11708ECOD (1.6)
WPF07717e5ylzW3 A: beta barrelsX: OB-foldH: Nucleic acid-binding proteins (From Topology)T: Nucleic acid-binding proteinsF: PF07717ECOD (1.6)
WPF04408,PF21010e5ylzW1 A: alpha arraysX: Sec63 N-terminal subdomain-like (From Topology)H: Sec63 N-terminal subdomain-like (From Topology)T: Sec63 N-terminal subdomain-likeF: PF04408,PF21010ECOD (1.6)
WPF00270e5ylzW2 A: a/b three-layered sandwichesX: P-loop domains-likeH: P-loop domains-relatedT: P-loop containing nucleoside triphosphate hydrolasesF: PF00270ECOD (1.6)
WPF00271e5ylzW4 A: a/b three-layered sandwichesX: P-loop domains-likeH: P-loop domains-relatedT: P-loop containing nucleoside triphosphate hydrolasesF: PF00271ECOD (1.6)
EA [auth h]PF01423e5ylzh1 A: beta barrelsX: SH3H: SH3T: SH3F: PF01423ECOD (1.6)
X [auth a]PF01423e5ylza1 A: beta barrelsX: SH3H: SH3T: SH3F: PF01423ECOD (1.6)
FA [auth i]PF01423e5ylzi1 A: beta barrelsX: SH3H: SH3T: SH3F: PF01423ECOD (1.6)
Y [auth b]PF01423e5ylzb1 A: beta barrelsX: SH3H: SH3T: SH3F: PF01423ECOD (1.6)
Z [auth c]PF01423e5ylzc1 A: beta barrelsX: SH3H: SH3T: SH3F: PF01423ECOD (1.6)
GA [auth j]PF01423e5ylzj1 A: beta barrelsX: SH3H: SH3T: SH3F: PF01423ECOD (1.6)
AA [auth d]PF01423e5ylzd1 A: beta barrelsX: SH3H: SH3T: SH3F: PF01423ECOD (1.6)
HA [auth k]PF01423e5ylzk1 A: beta barrelsX: SH3H: SH3T: SH3F: PF01423ECOD (1.6)
IA [auth l]PF01423e5ylzl1 A: beta barrelsX: SH3H: SH3T: SH3F: PF01423ECOD (1.6)
BA [auth e]PF01423e5ylze1 A: beta barrelsX: SH3H: SH3T: SH3F: PF01423ECOD (1.6)
CA [auth f]PF01423e5ylzf1 A: beta barrelsX: SH3H: SH3T: SH3F: PF01423ECOD (1.6)
JA [auth m]PF01423e5ylzm1 A: beta barrelsX: SH3H: SH3T: SH3F: PF01423ECOD (1.6)
KA [auth n]PF01423e5ylzn1 A: beta barrelsX: SH3H: SH3T: SH3F: PF01423ECOD (1.6)
DA [auth g]PF01423e5ylzg1 A: beta barrelsX: SH3H: SH3T: SH3F: PF01423ECOD (1.6)
LA [auth o]PF14580e5ylzo1 A: beta duplicates or obligate multimersX: Single-stranded right-handed beta-helixH: Leucine-rich repeats (From Topology)T: Leucine-rich repeatsF: PF14580ECOD (1.6)
MA [auth p]PF13893e5ylzp1 A: a+b two layersX: Alpha-beta plaitsH: RNA-binding domain, RBD (From Topology)T: RNA-binding domain, RBDF: PF13893ECOD (1.6)
HF_UNCLASSIFIEDe5ylzH1 A: alpha superhelicesX: Repetitive alpha hairpinsH: ARM repeat (From Topology)T: ARM repeatF: F_UNCLASSIFIEDECOD (1.6)
IF_UNCLASSIFIEDe5ylzI1 A: alpha superhelicesX: Repetitive alpha hairpinsH: ARM repeat (From Topology)T: ARM repeatF: F_UNCLASSIFIEDECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
U1.20.940.10 Mainly Alpha Up-down Bundle RNA Binding Protein, Prp18 Chain ACATH (utative)
FA [auth i]2.30.30.100 Mainly Beta Roll SH3 type barrels. CATH (4.3.0)
Y [auth b]2.30.30.100 Mainly Beta Roll SH3 type barrels. CATH (4.3.0)
Z [auth c]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)
AA [auth d]2.30.30.100 Mainly Beta Roll SH3 type barrels. CATH (4.3.0)
HA [auth k]2.30.30.100 Mainly Beta Roll SH3 type barrels. CATH (4.3.0)
IA [auth l]2.30.30.100 Mainly Beta Roll SH3 type barrels. CATH (4.3.0)
BA [auth e]2.30.30.100 Mainly Beta Roll SH3 type barrels. CATH (4.3.0)
KA [auth n]2.30.30.100 Mainly Beta Roll SH3 type barrels. CATH (4.3.0)
DA [auth g]2.30.30.100 Mainly Beta Roll SH3 type barrels. CATH (4.3.0)
MA [auth p]3.30.70.330 Alpha Beta 2-Layer Sandwich Alpha-Beta Plaits RRM (RNA recognition motif) domainCATH (4.3.0)
QA [auth t]3.30.40.10 Alpha Beta 2-Layer Sandwich Herpes Virus-1 Zinc/RING finger domain, C3HC4 (zinc finger)CATH (utative)

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
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
PF11831pre-mRNA splicing factor component (Myb_Cef)pre-mRNA splicing factor component- Family
PF08231SYF2 splicing factor (SYF2)SYF2 splicing factorProteins in this family are involved in cell cycle progression and pre-mRNA splicing [1] [2].Domain
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
M [auth T]PF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat
N [auth M]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
O [auth N]PF16131Torus domain (Torus)Torus domainThis domain is found in pre-mRNA-splicing factor CWC2. It includes a CCCH-type zinc finger [1].Domain
O [auth N]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
P [auth O]PF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat
R [auth Q]PF02731SKIP/SNW domain (SKIP_SNW)SKIP/SNW domain- Family
T [auth S]PF02847MA3 domain (MA3)MA3 domain- Repeat
PF02840Prp18 domain (Prp18)Prp18 domain- Family
PF11708Pre-mRNA splicing Prp18-interacting factor (Slu7)Pre-mRNA splicing Prp18-interacting factorThe spliceosome, an assembly of snRNAs (U1, U2, U4/U6, and U5) and proteins, catalyses the excision of introns from pre-mRNAs in two successive trans-esterification reactions. Step 2 depends upon integral spliceosome constituents such as U5 snRNA and ...The spliceosome, an assembly of snRNAs (U1, U2, U4/U6, and U5) and proteins, catalyses the excision of introns from pre-mRNAs in two successive trans-esterification reactions. Step 2 depends upon integral spliceosome constituents such as U5 snRNA and Prp8 and non-spliceosomal proteins Prp16, Slu7, Prp18, and Prp22. ATP hydrolysis by the DEAH-box enzyme Prp16 promotes a conformational change in the spliceosome that leads to protection of the 3'ss from targeted RNase H cleavage. This change, which probably reflects binding of the 3'ss PyAG in the catalytic centre of the spliceosome, requires the ordered recruitment of Slu7, Prp18, and Prp22 to the spliceosome. There is a close functional relationship between Prp8, Prp18, and Slu7, and Prp18 interacts with Slu7, so that together they recruit Prp22 to the spliceosome. Most members of the family carry a zinc-finger of the CCHC-type upstream of this domain.
Domain
PF04408Helicase associated domain (HA2), winged-helix (HA2_N)Helicase associated domain (HA2), winged-helixThe helicase associated domain (HA2) has an all alpha-helical fold and consists of a N-terminal winged-helix (WH) domain and a C-terminal degenerate helical-bundle domain, referred to as the ratchet-like domain [1,2,3]. These domains collaborate wit ...The helicase associated domain (HA2) has an all alpha-helical fold and consists of a N-terminal winged-helix (WH) domain and a C-terminal degenerate helical-bundle domain, referred to as the ratchet-like domain [1,2,3]. These domains collaborate with RecA domains at the N-terminal in completing an RNA binding channel to allow the helicases to keep a stable grip on the RNA [3] and assure its correct function. This entry represents the WH domain, which connects the N- (RecA domains) and C-terminal domains (ratchet-like and OB-fold) of helicases.
Domain
PF07717Oligonucleotide/oligosaccharide-binding (OB)-fold (OB_NTP_bind)Oligonucleotide/oligosaccharide-binding (OB)-foldThis family is found towards the C-terminus of the DEAD-box helicases (Pfam:PF00270). In these helicases it is apparently always found in association with Pfam:PF04408. There do seem to be a couple of instances where it occurs by itself - e.g. Swiss: ...This family is found towards the C-terminus of the DEAD-box helicases (Pfam:PF00270). In these helicases it is apparently always found in association with Pfam:PF04408. There do seem to be a couple of instances where it occurs by itself - e.g. Swiss:Q84VZ2. The structure PDB:3i4u adopts an OB-fold. helicases (Pfam:PF00270). In these helicases it is apparently always found in association with Pfam:PF04408. This C-terminal domain of the yeast helicase contains an oligonucleotide/oligosaccharide-binding (OB)-fold which seems to be placed at the entrance of the putative nucleic acid cavity. It also constitutes the binding site for the G-patch-containing domain of Pfa1p. When found on DEAH/RHA helicases, this domain is central to the regulation of the helicase activity through its binding of both RNA and G-patch domain proteins [1].
Domain
PF00270DEAD/DEAH box helicase (DEAD)DEAD/DEAH box helicaseMembers of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome ...Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.
Domain
PF00271Helicase conserved C-terminal domain (Helicase_C)Helicase conserved C-terminal domainThe Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.Domain
PF21010Helicase associated domain (HA2), ratchet-like (HA2_C)Helicase associated domain (HA2), ratchet-likeThe helicase associated domain (HA2) has an all alpha-helical fold and consists of a N-terminal winged-helix (WH) domain (Pfam:PF04408) and a C-terminal degenerate helical-bundle domain, referred to as the ratchet-like domain [1,2,3]. These domains c ...The helicase associated domain (HA2) has an all alpha-helical fold and consists of a N-terminal winged-helix (WH) domain (Pfam:PF04408) and a C-terminal degenerate helical-bundle domain, referred to as the ratchet-like domain [1,2,3]. These domains collaborate with the RecA domains at the N-terminal in completing an RNA binding channel to allow the helicases to keep a stable grip on the RNA [3]. This entry represents the ratchet-like domain, which may be important for RNA translocation [1,2].
Domain
EA [auth h],
X [auth a]		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 i],
Y [auth b]		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],
Z [auth c]		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 d],
HA [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
BA [auth e],
IA [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
CA [auth f],
JA [auth m]		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
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
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
PF16004116 kDa U5 small nuclear ribonucleoprotein component N-terminus (EFTUD2)116 kDa U5 small nuclear ribonucleoprotein component N-terminus- Family
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
DA [auth g],
KA [auth n]		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
LA [auth o]PF14580Leucine-rich repeat (LRR_9)Leucine-rich repeat- Repeat
MA [auth p]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
PF02184HAT (Half-A-TPR) repeat (HAT)HAT (Half-A-TPR) repeat- Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
Pre-mRNA-splicing factor 8
Pre-mRNA-splicing factor CEF1
Pre-mRNA-splicing factor SYF2-
Pre-mRNA-splicing factor BUD31-
M [auth T]Pre-mRNA-processing factor 17
N [auth M]Pre-mRNA-splicing factor SLT11
O [auth N]Pre-mRNA-splicing factor CWC2
P [auth O]Pre-mRNA-splicing factor PRP46-
Q [auth P]Pre-mRNA-splicing factor CWC15
R [auth Q]Pre-mRNA-processing protein 45-
S [auth R]Pre-mRNA-splicing factor CWC21-
U5 snRNA---
T [auth S]Pre-mRNA-splicing factor CWC22
Pre-mRNA-splicing factor 18-
Pre-mRNA-splicing factor SLU7
Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP22
EA [auth h],
X [auth a]		Small nuclear ribonucleoprotein-associated protein B
FA [auth i],
Y [auth b]		Small nuclear ribonucleoprotein E
GA [auth j],
Z [auth c]		Small nuclear ribonucleoprotein F
AA [auth d],
HA [auth k]		Small nuclear ribonucleoprotein G
BA [auth e],
IA [auth l]		Small nuclear ribonucleoprotein Sm D3
CA [auth f],
JA [auth m]		Small nuclear ribonucleoprotein Sm D1
Pre-mRNA-splicing factor SNU114
DA [auth g],
KA [auth n]		Small nuclear ribonucleoprotein Sm D2
LA [auth o]U2 small nuclear ribonucleoprotein A'
MA [auth p]U2 small nuclear ribonucleoprotein B''
NA [auth q],
OA [auth r],
PA [auth s],
QA [auth t]		Pre-mRNA-processing factor 19
U6 snRNA---
mRNA/intron lariat---
U2 snRNA---
Pre-mRNA-splicing factor SNT309-
Pre-mRNA-splicing factor SYF1-
Pre-mRNA-splicing factor CLF1

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
IPR047240Pre-mRNA splicing factor component CDC5L/Cef1, second SANT/myb-like domainDomain
IPR017930Myb domainDomain
IPR009057Homeobox-like domain superfamilyHomologous Superfamily
IPR047242Pre-mRNA splicing factor component CDC5L/Cef1Family
IPR001005SANT/Myb domainDomain
IPR021786Pre-mRNA splicing factor component Cdc5p/Cef1, C-terminalDomain
IPR013260mRNA splicing factor SYF2Family
IPR001748Pre-mRNA-splicing factor BUD31Family
IPR018230BUD31/G10-related, conserved siteConserved Site
M [auth T]IPR032847Pre-mRNA-processing factor 17Family
M [auth T]IPR036322WD40-repeat-containing domain superfamilyHomologous Superfamily
M [auth T]IPR001680WD40 repeatRepeat
M [auth T]IPR020472G-protein beta WD-40 repeatRepeat
M [auth T]IPR015943WD40/YVTN repeat-like-containing domain superfamilyHomologous Superfamily
N [auth M]IPR039171Pre-mRNA-splicing factor Cwc2/Slt11Family
N [auth M]IPR034356Slt11, RNA recognition motifDomain
N [auth M]IPR048995STL11/RBM22-like, N-terminal domainDomain
O [auth N]IPR039171Pre-mRNA-splicing factor Cwc2/Slt11Family
O [auth N]IPR034181Pre-mRNA-splicing factor Cwc2, RNA recognition motifDomain
O [auth N]IPR000504RNA recognition motif domainDomain
O [auth N]IPR032297Torus domainDomain
O [auth N]IPR000571Zinc finger, CCCH-typeDomain
O [auth N]IPR012677Nucleotide-binding alpha-beta plait domain superfamilyHomologous Superfamily
O [auth N]IPR035979RNA-binding domain superfamilyHomologous Superfamily
P [auth O]IPR045241WD repeat Prp46/PLRG1-likeFamily
P [auth O]IPR001680WD40 repeatRepeat
P [auth O]IPR019775WD40 repeat, conserved siteConserved Site
P [auth O]IPR020472G-protein beta WD-40 repeatRepeat
P [auth O]IPR036322WD40-repeat-containing domain superfamilyHomologous Superfamily
P [auth O]IPR015943WD40/YVTN repeat-like-containing domain superfamilyHomologous Superfamily
Q [auth P]IPR006973Pre-mRNA-splicing factor Cwf15/Cwc15Family
R [auth Q]IPR017862SKI-interacting protein, SKIPFamily
R [auth Q]IPR004015SKI-interacting protein SKIP, SNW domainDomain
S [auth R]IPR013170mRNA splicing factor Cwf21 domainDomain
T [auth S]IPR003891Initiation factor eIF-4 gamma, MA3Domain
T [auth S]IPR003890MIF4G-like, type 3Domain
T [auth S]IPR016024Armadillo-type foldHomologous Superfamily
IPR039979Pre-mRNA-splicing factor 18Family
IPR004098Prp18Domain
IPR001878Zinc finger, CCHC-typeDomain
IPR036875Zinc finger, CCHC-type superfamilyHomologous Superfamily
IPR021715Pre-mRNA-splicing factor SLU7 domainDomain
IPR039974Pre-mRNA-splicing factor SLU7Family
IPR049588DHX8, GH2-like domainDomain
IPR003029S1 domainDomain
IPR011709DEAD-box helicase, OB foldDomain
IPR001650Helicase, C-terminal domain-likeDomain
IPR014001Helicase superfamily 1/2, ATP-binding domainDomain
IPR048333Helicase associated domain (HA2), winged-helix domainDomain
IPR049621DHX8 helicase, S1 domainDomain
IPR044762DHX8/ Prp22, DEXH-box helicase domainDomain
IPR002464DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved siteConserved Site
IPR012340Nucleic acid-binding, OB-foldHomologous Superfamily
IPR007502Helicase-associated domainDomain
IPR011545DEAD/DEAH box helicase domainDomain
IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily
EA [auth h],
X [auth a]		IPR001163Sm domain, eukaryotic/archaea-typeDomain
EA [auth h],
X [auth a]		IPR047575Sm domainDomain
EA [auth h],
X [auth a]		IPR010920LSM domain superfamilyHomologous Superfamily
FA [auth i],
Y [auth b]		IPR027078Small nuclear ribonucleoprotein EFamily
FA [auth i],
Y [auth b]		IPR001163Sm domain, eukaryotic/archaea-typeDomain
FA [auth i],
Y [auth b]		IPR047575Sm domainDomain
FA [auth i],
Y [auth b]		IPR010920LSM domain superfamilyHomologous Superfamily
GA [auth j],
Z [auth c]		IPR016487Sm-like protein Lsm6/SmFFamily
GA [auth j],
Z [auth c]		IPR034100Small nuclear ribonucleoprotein FFamily
GA [auth j],
Z [auth c]		IPR001163Sm domain, eukaryotic/archaea-typeDomain
GA [auth j],
Z [auth c]		IPR047575Sm domainDomain
GA [auth j],
Z [auth c]		IPR010920LSM domain superfamilyHomologous Superfamily
AA [auth d],
HA [auth k]		IPR044641Sm-like protein Lsm7/SmGFamily
AA [auth d],
HA [auth k]		IPR034098Small nuclear ribonucleoprotein GFamily
AA [auth d],
HA [auth k]		IPR001163Sm domain, eukaryotic/archaea-typeDomain
AA [auth d],
HA [auth k]		IPR047575Sm domainDomain
AA [auth d],
HA [auth k]		IPR010920LSM domain superfamilyHomologous Superfamily
BA [auth e],
IA [auth l]		IPR027141Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3Family
BA [auth e],
IA [auth l]		IPR034099Small nuclear ribonucleoprotein Sm D3Family
BA [auth e],
IA [auth l]		IPR001163Sm domain, eukaryotic/archaea-typeDomain
BA [auth e],
IA [auth l]		IPR047575Sm domainDomain
BA [auth e],
IA [auth l]		IPR010920LSM domain superfamilyHomologous Superfamily
CA [auth f],
JA [auth m]		IPR027141Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3Family
CA [auth f],
JA [auth m]		IPR001163Sm domain, eukaryotic/archaea-typeDomain
CA [auth f],
JA [auth m]		IPR047575Sm domainDomain
CA [auth f],
JA [auth m]		IPR010920LSM domain superfamilyHomologous Superfamily
IPR005517Translation elongation factor EFG/EF2, domain IVDomain
IPR000795Translational (tr)-type GTP-binding domainDomain
IPR035647EF-G domain III/V-likeHomologous Superfamily
IPR035655116kDa U5 small nuclear ribonucleoprotein component, C-terminalDomain
IPR009000Translation protein, beta-barrel domain superfamilyHomologous Superfamily
IPR020568Ribosomal protein uS5 domain 2-type superfamilyHomologous Superfamily
IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily
IPR014721Small ribosomal subunit protein uS5 domain 2-type fold, subgroupHomologous Superfamily
IPR031950116kDa U5 small nuclear ribonucleoprotein component, N-terminalDomain
IPR000640Elongation factor EFG, domain V-likeDomain
IPR044121Snu114, GTP-binding domainDomain
DA [auth g],
KA [auth n]		IPR001163Sm domain, eukaryotic/archaea-typeDomain
DA [auth g],
KA [auth n]		IPR047575Sm domainDomain
DA [auth g],
KA [auth n]		IPR027248Small nuclear ribonucleoprotein Sm D2Family
DA [auth g],
KA [auth n]		IPR010920LSM domain superfamilyHomologous Superfamily
LA [auth o]IPR032675Leucine-rich repeat domain superfamilyHomologous Superfamily
LA [auth o]IPR001611Leucine-rich repeatRepeat
LA [auth o]IPR003603U2A'/phosphoprotein 32 family A, C-terminalDomain
MA [auth p]IPR012677Nucleotide-binding alpha-beta plait domain superfamilyHomologous Superfamily
MA [auth p]IPR000504RNA recognition motif domainDomain
MA [auth p]IPR035979RNA-binding domain superfamilyHomologous Superfamily
NA [auth q],
OA [auth r],
PA [auth s],
QA [auth t]		IPR003613U-box domainDomain
NA [auth q],
OA [auth r],
PA [auth s],
QA [auth t]		IPR013915Pre-mRNA-splicing factor 19Domain
NA [auth q],
OA [auth r],
PA [auth s],
QA [auth t]		IPR013083Zinc finger, RING/FYVE/PHD-typeHomologous Superfamily
NA [auth q],
OA [auth r],
PA [auth s],
QA [auth t]		IPR011047Quinoprotein alcohol dehydrogenase-like superfamilyHomologous Superfamily
NA [auth q],
OA [auth r],
PA [auth s],
QA [auth t]		IPR015943WD40/YVTN repeat-like-containing domain superfamilyHomologous Superfamily
NA [auth q],
OA [auth r],
PA [auth s],
QA [auth t]		IPR038959Pre-mRNA-processing factor 19Family
IPR011990Tetratricopeptide-like helical domain superfamilyHomologous Superfamily
IPR003107HAT (Half-A-TPR) repeatRepeat
IPR045075Pre-mRNA-splicing factor Syf1-likeFamily
IPR011990Tetratricopeptide-like helical domain superfamilyHomologous Superfamily
IPR003107HAT (Half-A-TPR) repeatRepeat
IPR045075Pre-mRNA-splicing factor Syf1-likeFamily