6FF4

human Bact spliceosome core structure


ChainDomainClassArchitectureTopologyHomology
2.40.100.10 Mainly Beta Beta Barrel Cyclophilin Cyclophilin-like
1.20.1390.10 Mainly Alpha Up-down Bundle PWI domain PWI domain
2.40.100.10 Mainly Beta Beta Barrel Cyclophilin Cyclophilin-like

Protein Family Annotation Pfam Database Homepage

ChainsAccessionIdentifierDescriptionCommentsSource
PF00076RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) (RRM_1)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. 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
PF09736Pre-mRNA-splicing factor of RES complex (Bud13)Pre-mRNA-splicing factor of RES complex- Family
PF12874Zinc-finger of C2H2 type (zf-met)Zinc-finger of C2H2 typeThis is a zinc-finger domain with the CxxCx(12)Hx(6)H motif, found in multiple copies in a wide range of proteins from plants to metazoans. Some member proteins, particularly those from plants, are annotated as being RNA-binding.Domain
PF04037Domain of unknown function (DUF382) (DUF382)Domain of unknown function (DUF382)- Family
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
PF12134PRP8 domain IV core (PRP8_domainIV)PRP8 domain IV coreThis domain is found in eukaryotes, and is about 20 amino acids in length. It is found associated with Pfam:PF10597, Pfam:PF10596, Pfam:PF10598, Pfam:PF08083, Pfam:PF08082, Pfam:PF01398, Pfam:PF08084. There is a conserved LILR sequence motif. The dom ...This domain is found in eukaryotes, and is about 20 amino acids in length. It is found associated with Pfam:PF10597, Pfam:PF10596, Pfam:PF10598, Pfam:PF08083, Pfam:PF08082, Pfam:PF01398, Pfam:PF08084. There is a conserved LILR sequence motif. The domain is a selenomethionine domain in a subunit of the spliceosome. The function of PRP8 domain IV is believed to be interaction with the splicosomal core.
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
PF01398JAB1/Mov34/MPN/PAD-1 ubiquitin protease (JAB)JAB1/Mov34/MPN/PAD-1 ubiquitin protease- Family
PF08084PROCT (NUC072) domain (PROCT)PROCT (NUC072) domainThe PROCT domain is the C-terminal domain in pre-mRNA splicing factors of PRO8 family [1].Domain
PF02731SKIP/SNW domain (SKIP_SNW)SKIP/SNW domain- Family
PF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat
PF13921Myb-like DNA-binding domain (Myb_DNA-bind_6)Myb-like DNA-binding domainThis family contains the DNA binding domains from Myb proteins, as well as the SANT domain family [1].Domain
PF02184HAT (Half-A-TPR) repeat (HAT)HAT (Half-A-TPR) repeat- Repeat
PF00076RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) (RRM_1)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. 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
PF01125G10 protein (G10)G10 protein- Domain
PF04889Cwf15/Cwc15 cell cycle control protein (Cwf_Cwc_15)Cwf15/Cwc15 cell cycle control protein- Family
PF00160Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD (Pro_isomerase)Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLDThe peptidyl-prolyl cis-trans isomerases, also known as cyclophilins, share this domain of about 109 amino acids. Cyclophilins have been found in all organisms studied so far and catalyse peptidyl-prolyl isomerisation during which the peptide bond pr ...The peptidyl-prolyl cis-trans isomerases, also known as cyclophilins, share this domain of about 109 amino acids. Cyclophilins have been found in all organisms studied so far and catalyse peptidyl-prolyl isomerisation during which the peptide bond preceding proline (the peptidyl-prolyl bond) is stabilised in the cis conformation. Mammalian cyclophilin A (CypA) is a major cellular target for the immunosuppressive drug cyclosporin A (CsA). Other roles for cyclophilins may include chaperone and cell signalling function [1].
Domain
PF01480PWI domain (PWI)PWI domain- Family
PF00160Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD (Pro_isomerase)Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLDThe peptidyl-prolyl cis-trans isomerases, also known as cyclophilins, share this domain of about 109 amino acids. Cyclophilins have been found in all organisms studied so far and catalyse peptidyl-prolyl isomerisation during which the peptide bond pr ...The peptidyl-prolyl cis-trans isomerases, also known as cyclophilins, share this domain of about 109 amino acids. Cyclophilins have been found in all organisms studied so far and catalyse peptidyl-prolyl isomerisation during which the peptide bond preceding proline (the peptidyl-prolyl bond) is stabilised in the cis conformation. Mammalian cyclophilin A (CypA) is a major cellular target for the immunosuppressive drug cyclosporin A (CsA). Other roles for cyclophilins may include chaperone and cell signalling function [1].
Domain
PF00642Zinc finger C-x8-C-x5-C-x3-H type (and similar) (zf-CCCH)Zinc finger C-x8-C-x5-C-x3-H type (and similar)- Family
PF13920Zinc finger, C3HC4 type (RING finger) (zf-C3HC4_3)Zinc finger, C3HC4 type (RING finger)- Domain
PF08920Splicing factor 3B subunit 1 (SF3b1)Splicing factor 3B subunit 1This family consists of several eukaryotic splicing factor 3B subunit 1 proteins, which associate with p14 through a C-terminus beta-strand that interacts with beta-3 of the p14 RNA recognition motif (RRM) beta-sheet, which is in turn connected to an ...This family consists of several eukaryotic splicing factor 3B subunit 1 proteins, which associate with p14 through a C-terminus beta-strand that interacts with beta-3 of the p14 RNA recognition motif (RRM) beta-sheet, which is in turn connected to an alpha-helix by a loop that makes extensive contacts with both the shorter C-terminal helix and RRM of p14. This subunit is required for 'A' splicing complex assembly (formed by the stable binding of U2 snRNP to the branchpoint sequence in pre-mRNA) and 'E' splicing complex assembly [1].
Domain
PF10433Mono-functional DNA-alkylating methyl methanesulfonate N-term (MMS1_N)Mono-functional DNA-alkylating methyl methanesulfonate N-termMMS1 is a protein that protects against replication-dependent DNA damage in Saccharomyces cerevisiae [1]. MMS1 belongs to the DDB1 family of cullin 4 adaptors and the two proteins are homologous. MMS1 bridges the interaction of MMS22 and Crt10 with C ...MMS1 is a protein that protects against replication-dependent DNA damage in Saccharomyces cerevisiae [1]. MMS1 belongs to the DDB1 family of cullin 4 adaptors and the two proteins are homologous. MMS1 bridges the interaction of MMS22 and Crt10 with Cul8/Rtt101 [2]. Cul8/Rtt101 is a cullin protein involved in the regulation of DNA replication subsequent to DNA damage. The N-terminal region of MMS1 and the C-terminal of MMS22 are required for the the MMS1-MMS22 interaction [3]. The human HIV-1 virion-associated protein Vpr assembles with DDB1 through interaction with DCAF1 (chromatin assembly factor) to form an E3 ubiquitin ligase that targets cellular substrates for proteasome-mediated degradation and subsequent G2 arrest [4].
Domain
PF03178CPSF A subunit region (CPSF_A)CPSF A subunit region- Repeat
PF07189Splicing factor 3B subunit 10 (SF3b10) (SF3b10)Splicing factor 3B subunit 10 (SF3b10)- Family
PF03660PHF5-like protein (PHF5)PHF5-like protein- Family
PF00076RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) (RRM_1)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. 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
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
PF14492Elongation Factor G, domain III (EFG_III)Elongation Factor G, domain IIIThis domain is found in Elongation Factor G. It shares a similar structure with domain V (Pfam:PF00679). Structural studies in drosophila indicate this is domain 3 [1].Domain
PF16004116 kDa U5 small nuclear ribonucleoprotein component N-terminus (EFTUD2)116 kDa U5 small nuclear ribonucleoprotein component N-terminus- Family
PF03144Elongation factor Tu domain 2 (GTP_EFTU_D2)Elongation factor Tu domain 2Elongation factor Tu consists of three structural domains, this is the second domain. This domain adopts a beta barrel structure. This the second domain is involved in binding to charged tRNA [1]. This domain is also found in other proteins such as e ...Elongation factor Tu consists of three structural domains, this is the second domain. This domain adopts a beta barrel structure. This the second domain is involved in binding to charged tRNA [1]. This domain is also found in other proteins such as elongation factor G and translation initiation factor IF-2. This domain is structurally related to Pfam:PF03143, and in fact has weak sequence matches to this domain.
Domain
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

Gene Product Annotation Gene Product Annotation

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
RNA-binding motif protein, X-linked 2
    U2 snRNAnonenonenone
    BUD13 homolog
      U5 snRNAnonenonenone
      U6 snRNAnonenonenone
      Splicing factor 3A subunit 2
        Splicing factor 3B subunit 2
        Pre-mRNA-processing-splicing factor 8
        SNW domain-containing protein 1
        Pleiotropic regulator 1
            Pre-mRNA-processing factor 17
              Cell division cycle 5-like protein
              Crooked neck-like protein 1
                Pre-mRNA-splicing factor RBM22
                  Protein BUD31 homolog
                    Spliceosome-associated protein CWC15 homolog
                      Serine/arginine repetitive matrix protein 2
                        Peptidyl-prolyl cis-trans isomerase-like 1
                          Serine/arginine repetitive matrix protein 1
                            pre mRNAnonenonenone
                            Peptidyl-prolyl cis-trans isomerase CWC27 homolog
                                RING finger protein 113A
                                  Splicing factor 3B subunit 1
                                  Splicing factor 3B subunit 3
                                    Splicing factor 3B subunit 5
                                      PHD finger-like domain-containing protein 5A
                                      Splicing factor 3B subunit 6
                                        116 kDa U5 small nuclear ribonucleoprotein component