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Conserved domains on  [gi|1983831687]
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Chain n, Small nuclear ribonucleoprotein Sm D1

Protein Classification

small nuclear ribonucleoprotein Sm D1( domain architecture ID 10109585)

small nuclear ribonucleoprotein D1 is part of the eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) which is assemble into a hetero-heptameric ring around the Sm site of the 2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and U5 snRNAs (Sm snRNAs) forming the core of the snRNP particle

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Sm_D1 cd01724
Sm protein D1; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a ...
 2-93 4.40e-60

Sm protein D1; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a hetero-heptameric ring around the Sm site of the 2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and U5 snRNAs (Sm snRNAs) forming the core of the snRNP particle. The snRNP particle, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D1 heterodimerizes with subunit D2 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing DB, D3, E, F, and G subunits.


:

Pssm-ID: 212471  Cd Length: 92  Bit Score: 178.96  E-value: 4.40e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983831687   2 KLVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNIRYFILPDSLPLDTLLV 81
Cdd:cd01724     1 KLVRFLMKLSNETVTIELKNGTVVHGTITGVDVSMNTHLKNVKLTLKGKNPVSLDTLSIRGNNIRYIILPDSLNLDTLLV 80

                          90
                  ....*....|..
gi 1983831687  82 DVEPKVKSKKRE 93
Cdd:cd01724    81 DDTPKAKAKKRA 92
 
Name Accession Description Interval E-value
Sm_D1 cd01724
Sm protein D1; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a ...
 2-93 4.40e-60

Sm protein D1; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a hetero-heptameric ring around the Sm site of the 2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and U5 snRNAs (Sm snRNAs) forming the core of the snRNP particle. The snRNP particle, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D1 heterodimerizes with subunit D2 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing DB, D3, E, F, and G subunits.


Pssm-ID: 212471  Cd Length: 92  Bit Score: 178.96  E-value: 4.40e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983831687   2 KLVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNIRYFILPDSLPLDTLLV 81
Cdd:cd01724     1 KLVRFLMKLSNETVTIELKNGTVVHGTITGVDVSMNTHLKNVKLTLKGKNPVSLDTLSIRGNNIRYIILPDSLNLDTLLV 80

                          90
                  ....*....|..
gi 1983831687  82 DVEPKVKSKKRE 93
Cdd:cd01724    81 DDTPKAKAKKRA 92
Sm smart00651
snRNP Sm proteins; small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA ...
 5-70 8.95e-17

snRNP Sm proteins; small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing


Pssm-ID: 197820 [Multi-domain]  Cd Length: 67  Bit Score: 68.68  E-value: 8.95e-17
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1983831687    5 RFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKN-REPVQLETLSIRGNNIRYFIL 70
Cdd:smart00651   1 KFLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDgEKKRKLGLVFIRGNNIVYIIL 67
LSM pfam01423
LSM domain; The LSM domain contains Sm proteins as well as other related LSM (Like Sm) ...
 5-70 1.43e-16

LSM domain; The LSM domain contains Sm proteins as well as other related LSM (Like Sm) proteins. The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F and G) 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. 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.


Pssm-ID: 426258  Cd Length: 66  Bit Score: 68.30  E-value: 1.43e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1983831687   5 RFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNIRYFIL 70
Cdd:pfam01423   1 KFLKKLLGKRVLVELKNGRELRGTLKGFDQFMNLVLDDVEETIKDGEVRKLGLVLIRGNNIVLISP 66
LSM1 COG1958
Small nuclear ribonucleoprotein (snRNP) homolog [Transcription];
1-65 2.93e-08

Small nuclear ribonucleoprotein (snRNP) homolog [Transcription];


Pssm-ID: 441561  Cd Length: 71  Bit Score: 47.10  E-value: 2.93e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1983831687   1 MKLVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNI 65
Cdd:COG1958     3 ERPLKVLEKSLGKRVLVKLKDGREYRGKLKGYDQHMNLVLEDAEEIDDGEVVRKLGTVVIRGDNV 67
 
Name Accession Description Interval E-value
Sm_D1 cd01724
Sm protein D1; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a ...
 2-93 4.40e-60

Sm protein D1; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a hetero-heptameric ring around the Sm site of the 2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and U5 snRNAs (Sm snRNAs) forming the core of the snRNP particle. The snRNP particle, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D1 heterodimerizes with subunit D2 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing DB, D3, E, F, and G subunits.


Pssm-ID: 212471  Cd Length: 92  Bit Score: 178.96  E-value: 4.40e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983831687   2 KLVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNIRYFILPDSLPLDTLLV 81
Cdd:cd01724     1 KLVRFLMKLSNETVTIELKNGTVVHGTITGVDVSMNTHLKNVKLTLKGKNPVSLDTLSIRGNNIRYIILPDSLNLDTLLV 80

                          90
                  ....*....|..
gi 1983831687  82 DVEPKVKSKKRE 93
Cdd:cd01724    81 DDTPKAKAKKRA 92
Sm smart00651
snRNP Sm proteins; small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA ...
 5-70 8.95e-17

snRNP Sm proteins; small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing


Pssm-ID: 197820 [Multi-domain]  Cd Length: 67  Bit Score: 68.68  E-value: 8.95e-17
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1983831687    5 RFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKN-REPVQLETLSIRGNNIRYFIL 70
Cdd:smart00651   1 KFLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDgEKKRKLGLVFIRGNNIVYIIL 67
LSM pfam01423
LSM domain; The LSM domain contains Sm proteins as well as other related LSM (Like Sm) ...
 5-70 1.43e-16

LSM domain; The LSM domain contains Sm proteins as well as other related LSM (Like Sm) proteins. The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F and G) 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. 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.


Pssm-ID: 426258  Cd Length: 66  Bit Score: 68.30  E-value: 1.43e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1983831687   5 RFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNIRYFIL 70
Cdd:pfam01423   1 KFLKKLLGKRVLVELKNGRELRGTLKGFDQFMNLVLDDVEETIKDGEVRKLGLVLIRGNNIVLISP 66
Sm_D3 cd01721
Sm protein D3; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a ...
 9-72 2.82e-15

Sm protein D3; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a hetero-heptameric ring around the Sm site of the 2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and U5 snRNAs (Sm snRNAs) forming the core of the snRNP particle. The snRNP particle, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D3 heterodimerizes with subunit B and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits.


Pssm-ID: 212468  Cd Length: 70  Bit Score: 64.85  E-value: 2.82e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1983831687   9 KLSHE----TVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNIRYFILPD 72
Cdd:cd01721     3 KLLHEaeghIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTARDGKVSKLEQVYIRGSQIRFIILPD 70
Sm_like cd00600
Sm and related proteins; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to ...
 7-69 3.56e-13

Sm and related proteins; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.


Pssm-ID: 212462 [Multi-domain]  Cd Length: 63  Bit Score: 59.57  E-value: 3.56e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1983831687   7 LMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNIRYFI 69
Cdd:cd00600     1 LKDFIGKTVSVELKDGRVLTGTLVAFDKYMNLVLDDVVETGRDGKVRVLGLVLIRGSNIVSIR 63
LSm4 cd01723
Like-Sm protein 4; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a ...
 15-74 1.42e-09

Like-Sm protein 4; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus uridylation tag of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. LSm2-8 form the core of the snRNP particle that, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. LSm1-7 is involved in recognition of the 3' uridylation tag and recruitment of the decapping machinery. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet.


Pssm-ID: 212470 [Multi-domain]  Cd Length: 76  Bit Score: 50.65  E-value: 1.42e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1983831687  15 VTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREP-VQLETLSIRGNNIRYFILPDSL 74
Cdd:cd01723    14 VLVELKNGETYNGHLVNCDNWMNIHLKNVICTSKDGDRfWKMPECYIRGNTIKYLRLPDEV 74
LSm10 cd01733
Like-Sm protein 10; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form ...
 3-67 6.74e-09

Like-Sm protein 10; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm10 is an SmD1-like protein which is thought to bind U7 snRNA along with LSm11 and five other Sm subunits to form a 7-membered ring structure. LSm10 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing.


Pssm-ID: 212480  Cd Length: 78  Bit Score: 48.69  E-value: 6.74e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1983831687   3 LVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNIRY 67
Cdd:cd01733    10 LVCLLQALQGRVTTVELRNETSVRGIIDNVDGFMNITLSDATFTDRRGKQHHFDEFFVQGRNIRY 74
LSM1 COG1958
Small nuclear ribonucleoprotein (snRNP) homolog [Transcription];
1-65 2.93e-08

Small nuclear ribonucleoprotein (snRNP) homolog [Transcription];


Pssm-ID: 441561  Cd Length: 71  Bit Score: 47.10  E-value: 2.93e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1983831687   1 MKLVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNI 65
Cdd:COG1958     3 ERPLKVLEKSLGKRVLVKLKDGREYRGKLKGYDQHMNLVLEDAEEIDDGEVVRKLGTVVIRGDNV 67
LSm2 cd01725
Like-Sm protein 2; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a ...
 15-94 1.12e-06

Like-Sm protein 2; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus uridylation tag of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. LSm2-8 form the core of the snRNP particle that, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. LSm1-7 is involved in recognition of the 3' uridylation tag and recruitment of the decapping machinery. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet.


Pssm-ID: 212472  Cd Length: 89  Bit Score: 43.35  E-value: 1.12e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1983831687  15 VTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREP--VQLETLSIRGNNIRYFILPDSlpldtlLVDVEPKVKSKKR 92
Cdd:cd01725    14 VTVELKNDLSITGTLHSVDQYLNIKLTNISVNDPEKYPhlLSVKNCFIRGSVVRYVQLPAD------EVDTELLQDATRR 87


                  ..
gi 1983831687  93 EA 94
Cdd:cd01725    88 EA 89
LSm6 cd01726
Like-Sm protein 6; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a ...
 5-67 2.98e-04

Like-Sm protein 6; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus uridylation tag of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. LSm2-8 form the core of the snRNP particle that, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. LSm1-7 is involved in recognition of the 3' uridylation tag and recruitment of the decapping machinery. LSm657 is believed to be an assembly intermediate for both the LSm1-7 and LSm2-8 rings. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet.


Pssm-ID: 212473  Cd Length: 68  Bit Score: 36.35  E-value: 2.98e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1983831687   5 RFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNIRY 67
Cdd:cd01726     4 KFLKKIIGKPVVVKLKNGVEYRGVLACLDGYMNLVLEDTEEYVDGQLVAKYGDAFIRGNNVLY 66
archaeal_Sm1 cd01731
archaeal Sm protein 1; The archaeal Sm1 proteins: The Sm proteins are conserved in all three ...
 14-65 2.21e-03

archaeal Sm protein 1; The archaeal Sm1 proteins: The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences. They function to mediate RNA-RNA interactions and RNA biogenesis. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. Eukaryotic Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6). Since archaebacteria do not have any splicing apparatus, their Sm proteins may play a more general role. Archaeal LSm proteins are likely to represent the ancestral Sm domain.


Pssm-ID: 212478  Cd Length: 69  Bit Score: 34.09  E-value: 2.21e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1983831687  14 TVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNI 65
Cdd:cd01731    13 NVLVKLKGGKEVRGVLKGFDQHLNLVLENAEEIIEGESVRKLGTVLVRGDNV 64
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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