NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|82795247|ref|NP_010666|]
View 

U4/U6-U5 snRNP complex subunit LSM6 [Saccharomyces cerevisiae S288C]

Protein Classification

LSm family protein( domain architecture ID 249)

LSm family protein such as eukaryotic LSm (Sm-like proteins) and bacterial LSm-related Hfq proteins, that have an Sm fold consisting of a five-stranded beta-sheet and an alpha-helix at the N-terminus, and are involved in processes associated with RNA processing and gene expression regulation

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
Sm_like super family cl00259
Sm and related proteins; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to ...
 14-82 1.26e-18

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.


The actual alignment was detected with superfamily member cd01726:

Pssm-ID: 469694  Cd Length: 68  Bit Score: 72.17  E-value: 1.26e-18
                       10        20        30        40        50        60
               ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 82795247 14 EFLSDIIGKTVNVKLASGLLYSGRLESIDGFMNVALSSATEHYESnnnkLLNKFNSDVFLRGTQVMYIS 82
Cdd:cd01726  4 KFLKKIIGKPVVVKLKNGVEYRGVLACLDGYMNLVLEDTEEYVDG----QLVAKYGDAFIRGNNVLYIS 68
 
Name Accession Description Interval E-value
LSm6 cd01726
Like-Sm protein 6; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a ...
 14-82 1.26e-18

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: 72.17  E-value: 1.26e-18
                       10        20        30        40        50        60
               ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 82795247 14 EFLSDIIGKTVNVKLASGLLYSGRLESIDGFMNVALSSATEHYESnnnkLLNKFNSDVFLRGTQVMYIS 82
Cdd:cd01726  4 KFLKKIIGKPVVVKLKNGVEYRGVLACLDGYMNLVLEDTEEYVDG----QLVAKYGDAFIRGNNVLYIS 68
LSM pfam01423
LSM domain; The LSM domain contains Sm proteins as well as other related LSM (Like Sm) ...
 14-83 5.11e-14

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: 60.21  E-value: 5.11e-14
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 82795247   14 EFLSDIIGKTVNVKLASGLLYSGRLESIDGFMNVALSSATEHYESnnnkLLNKFNSDVFLRGTQVMYISE 83
Cdd:pfam01423  1 KFLKKLLGKRVLVELKNGRELRGTLKGFDQFMNLVLDDVEETIKD----GEVRKLGLVLIRGNNIVLISP 66
Sm smart00651
snRNP Sm proteins; small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA ...
 15-83 4.34e-13

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


Pssm-ID: 197820 [Multi-domain]  Cd Length: 67  Bit Score: 57.89  E-value: 4.34e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 82795247    15 FLSDIIGKTVNVKLASGLLYSGRLESIDGFMNVALSSATEHYESnnnKLLNKFNSDVFLRGTQVMYISE 83
Cdd:smart00651  2 FLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKD---GEKKRKLGLVFIRGNNIVYIIL 67
LSM1 COG1958
Small nuclear ribonucleoprotein (snRNP) homolog [Transcription];
16-82 1.09e-09

Small nuclear ribonucleoprotein (snRNP) homolog [Transcription];


Pssm-ID: 441561  Cd Length: 71  Bit Score: 49.41  E-value: 1.09e-09
                       10        20        30        40        50        60
               ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 82795247 16 LSDIIGKTVNVKLASGLLYSGRLESIDGFMNVALSSATEhyesNNNKLLNKFNSDVFLRGTQVMYIS 82
Cdd:COG1958  9 LEKSLGKRVLVKLKDGREYRGKLKGYDQHMNLVLEDAEE----IDDGEVVRKLGTVVIRGDNVVFIS 71
PRK00737 PRK00737
small nuclear ribonucleoprotein; Provisional
 18-82 3.29e-04

small nuclear ribonucleoprotein; Provisional


Pssm-ID: 179104  Cd Length: 72  Bit Score: 35.36  E-value: 3.29e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 82795247  18 DIIGKTVN----VKLASGLLYSGRLESIDGFMNVALSSATEHYESNNNKLLNKfnsdVFLRGTQVMYIS 82
Cdd:PRK00737  7 DVLNNALNspvlVRLKGGREFRGELQGYDIHMNLVLDNAEEIQDGEVVRKLGK----VVIRGDNVVYVS 71
 
Name Accession Description Interval E-value
LSm6 cd01726
Like-Sm protein 6; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a ...
 14-82 1.26e-18

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: 72.17  E-value: 1.26e-18
                       10        20        30        40        50        60
               ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 82795247 14 EFLSDIIGKTVNVKLASGLLYSGRLESIDGFMNVALSSATEHYESnnnkLLNKFNSDVFLRGTQVMYIS 82
Cdd:cd01726  4 KFLKKIIGKPVVVKLKNGVEYRGVLACLDGYMNLVLEDTEEYVDG----QLVAKYGDAFIRGNNVLYIS 68
LSM pfam01423
LSM domain; The LSM domain contains Sm proteins as well as other related LSM (Like Sm) ...
 14-83 5.11e-14

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: 60.21  E-value: 5.11e-14
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 82795247   14 EFLSDIIGKTVNVKLASGLLYSGRLESIDGFMNVALSSATEHYESnnnkLLNKFNSDVFLRGTQVMYISE 83
Cdd:pfam01423  1 KFLKKLLGKRVLVELKNGRELRGTLKGFDQFMNLVLDDVEETIKD----GEVRKLGLVLIRGNNIVLISP 66
Sm smart00651
snRNP Sm proteins; small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA ...
 15-83 4.34e-13

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


Pssm-ID: 197820 [Multi-domain]  Cd Length: 67  Bit Score: 57.89  E-value: 4.34e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 82795247    15 FLSDIIGKTVNVKLASGLLYSGRLESIDGFMNVALSSATEHYESnnnKLLNKFNSDVFLRGTQVMYISE 83
Cdd:smart00651  2 FLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKD---GEKKRKLGLVFIRGNNIVYIIL 67
Sm_F cd01722
Sm protein F; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a ...
 15-83 2.00e-12

Sm protein F; 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 F is capable of forming both homo- and hetero-heptamer ring structures. To form the hetero-heptamer, Sm subunit F initially binds subunits E and G to form a trimer which then assembles onto snRNA along with the D3/B and D1/D2 heterodimers.


Pssm-ID: 212469  Cd Length: 69  Bit Score: 56.45  E-value: 2.00e-12
                       10        20        30        40        50        60
               ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 82795247 15 FLSDIIGKTVNVKLASGLLYSGRLESIDGFMNVALSSATEHyesnNNKLLNKFNSDVFLRGTQVMYISE 83
Cdd:cd01722  5 FLNGLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEY----IDGKFTGNLGEVLIRCNNVLYIRE 69
LSM1 COG1958
Small nuclear ribonucleoprotein (snRNP) homolog [Transcription];
16-82 1.09e-09

Small nuclear ribonucleoprotein (snRNP) homolog [Transcription];


Pssm-ID: 441561  Cd Length: 71  Bit Score: 49.41  E-value: 1.09e-09
                       10        20        30        40        50        60
               ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 82795247 16 LSDIIGKTVNVKLASGLLYSGRLESIDGFMNVALSSATEhyesNNNKLLNKFNSDVFLRGTQVMYIS 82
Cdd:COG1958  9 LEKSLGKRVLVKLKDGREYRGKLKGYDQHMNLVLEDAEE----IDDGEVVRKLGTVVIRGDNVVFIS 71
Sm_like cd00600
Sm and related proteins; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to ...
 16-82 1.29e-06

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: 41.47  E-value: 1.29e-06
                       10        20        30        40        50        60
               ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 82795247 16 LSDIIGKTVNVKLASGLLYSGRLESIDGFMNVALSSATEHYESnnnkLLNKFNSDVFLRGTQVMYIS 82
Cdd:cd00600  1 LKDFIGKTVSVELKDGRVLTGTLVAFDKYMNLVLDDVVETGRD----GKVRVLGLVLIRGSNIVSIR 63
archaeal_Sm1 cd01731
archaeal Sm protein 1; The archaeal Sm1 proteins: The Sm proteins are conserved in all three ...
 16-82 1.05e-05

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: 39.48  E-value: 1.05e-05
                       10        20        30        40        50        60
               ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 82795247 16 LSDIIGKTVNVKLASGLLYSGRLESIDGFMNVALSSATEHYESNNNKLLNKfnsdVFLRGTQVMYIS 82
Cdd:cd01731  6 LNESLNKNVLVKLKGGKEVRGVLKGFDQHLNLVLENAEEIIEGESVRKLGT----VLVRGDNVVFIS 68
PRK00737 PRK00737
small nuclear ribonucleoprotein; Provisional
 18-82 3.29e-04

small nuclear ribonucleoprotein; Provisional


Pssm-ID: 179104  Cd Length: 72  Bit Score: 35.36  E-value: 3.29e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 82795247  18 DIIGKTVN----VKLASGLLYSGRLESIDGFMNVALSSATEHYESNNNKLLNKfnsdVFLRGTQVMYIS 82
Cdd:PRK00737  7 DVLNNALNspvlVRLKGGREFRGELQGYDIHMNLVLDNAEEIQDGEVVRKLGK----VVIRGDNVVYVS 71
Sm_D3 cd01721
Sm protein D3; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a ...
 15-81 5.72e-04

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: 34.80  E-value: 5.72e-04
                       10        20        30        40        50        60        70
               ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 82795247 15 FLSDIIGKTVNVKLASGLLYSGRLESIDGFMNVALSSAT--------EHYESnnnkllnkfnsdVFLRGTQVMYI 81
Cdd:cd01721  4 LLHEAEGHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTvtardgkvSKLEQ------------VYIRGSQIRFI 66
LSMD1 cd06168
LSM domain containing 1; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to ...
 13-55 1.99e-03

LSM domain containing 1; 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. LSMD1 proteins have a single Sm-like domain structure. Sm-like proteins exist in archaea as well as prokaryotes, forming heptameric and hexameric ring structures similar to those found in eukaryotes.


Pssm-ID: 212486  Cd Length: 73  Bit Score: 33.68  E-value: 1.99e-03
                       10        20        30        40
               ....*....|....*....|....*....|....*....|...
gi 82795247 13 TEFLSDIIGKTVNVKLASGLLYSGRLESIDGFMNVALSSATEH 55
Cdd:cd06168  1 RLKLRKLLGRTLRVTLTDGRVLVGTFVCTDKDGNIILSNAEEY 43
LSm10 cd01733
Like-Sm protein 10; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form ...
 15-81 3.04e-03

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: 33.28  E-value: 3.04e-03
                       10        20        30        40        50        60
               ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 82795247 15 FLSDIIGKTVNVKLASGLLYSGRLESIDGFMNVALSSATEHYESnnnkLLNKFNSDVFLRGTQVMYI 81
Cdd:cd01733 13 LLQALQGRVTTVELRNETSVRGIIDNVDGFMNITLSDATFTDRR----GKQHHFDEFFVQGRNIRYV 75
LSm4 cd01723
Like-Sm protein 4; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a ...
 21-54 4.52e-03

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: 32.55  E-value: 4.52e-03
                       10        20        30
               ....*....|....*....|....*....|....
gi 82795247 21 GKTVNVKLASGLLYSGRLESIDGFMNVALSSATE 54
Cdd:cd01723 11 GHPVLVELKNGETYNGHLVNCDNWMNIHLKNVIC 44
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH