1H64,1I5L,1I81,1I8F,1M8V,1TH7


Conserved Protein Domain Family
archaeal_Sm1

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cd01731: archaeal_Sm1 
Click on image for an interactive view with Cn3D
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.
Statistics
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PSSM-Id: 212478
Aligned: 29 rows
Threshold Bit Score: 82.623
Created: 10-May-2012
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
Conserved site includes 32 residues -Click on image for an interactive view with Cn3D
Feature 1:heptamer interface [polypeptide binding site]
Evidence:
  • Structure:1M8V; Pyrococcus abyssi Sm core heptamers, contacts at 4A

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1       ##  #  #      # ###  #      #### ### #                # ##############
1H64_1        4 RPLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIqdge-vvkRYGKIVIRGDNVLAISP 72  Pyrococcus abyssi
1I81_A       15 RPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELedge-vtrRLGTVLIRGDNIVYISP 83  Methanothermobacter therma...
1M8V_A        6 RPLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIqdge-vvkRYGKIVIRGDNVLAISP 74  Pyrococcus abyssi
Q8TL47        4 RPLDILNNALDTPVIVRLKGAREFRGELKGYDIHMNLVLDNAEELrdge-vvsKFSSVVIRGDNVVYVSP 72  Methanosarcina acetivorans...
EET90024      5 RPFDLLNRVISQQVLIRLKNNLNIRGKVTSFDAHMNIVLDNAEELdangelkaKLGTILLRGGNIIFVSP 74  uncultured euryarchaeote A...
EEZ93248      8 RPLDLLNSAKGKMVLVELKNGHAITGKLVAFDVHINVTLENAEEKkdad-tlrKLGNVFIRGDTIILISP 76  Candidatus Parvarchaeum ac...
EGQ39804      7 RPLDVLGDARGTNVMIELKDETVVSGTLRAFDSHLNMWLDDASKTged--greDFGKILIRGDNVVHVSP 74  Candidatus Nanosalinarum s...
YP_001581683  7 EISTLMTNSKDKVVLLRLRNNKTVQGTLKDFDIHMNLTLENAEDVsee--kpnPIGKVLLRGDNILAISL 74  Nitrosopumilus maritimus SCM1
YP_001435565  3 DTAHKVMAEAIGKIVLVKLRDGKVRGRLKTFDMHLNIVLEDAEEVred--qtrPLGTILIRGDGVVFVSP 70  Ignicoccus hospitalis KIN4/I
EGQ42881     11 VLDDAKEGNVLIKLKKFGDEETTVSGELQAFDKHLNVWLQNATVKgee--sttEHGRLFVRGDNVLFVSP 78  Candidatus Nanosalina sp. ...

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