1B34,2Y9A


Conserved Protein Domain Family
Sm_D1

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cd01724: Sm_D1 
Click on image for an interactive view with Cn3D
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.
Statistics
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PSSM-Id: 212471
Aligned: 42 rows
Threshold Bit Score: 122.719
Created: 10-May-2012
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
Conserved site includes 34 residues -Click on image for an interactive view with Cn3D
Feature 1:heptamer interface [polypeptide binding site]
Evidence:
  • Structure:2Y9A; Human spliceosomal U4 snRNP core domain hetero-heptamer, contacts at 4A

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1         #  ##          ####        ## ####  #                                          
1B34_A         2 KLVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKn---------------------------REPVQ 54  human
2Y9A_B         2 KLVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKn---------------------------REPVQ 54  human
Q02260         2 KLVNFLKKLRNEQVTIELKNGTTVWGTLQSVSPQMNAILTDVKLTLPqprlnklnsngiamaslyltggqqptasDNIAS 81  Saccharomyces c...
CAG83694       2 KLVRFLMKLTSESVQIELKNGTVLLGTVMSVSNNMNTTLKNVKMTMKn---------------------------RPPTS 54  Yarrowia lipoly...
EAL37203       2 KLIRFLMKLINNSVVIELKNGTIIQGTIVSVDMSMNTYLKNVKMSVKh---------------------------RNPVS 54  Cryptosporidium...
XP_001913982   2 KLVRFLMRLTNEVVTIELKSGAVLTGTIVGVDNYMNVHLKVVKMTQKg---------------------------KNPIN 54  Entamoeba histo...
XP_001324496   2 KLVHFLRKLVRETVTVELKDNTVIKGTVVGVDSAMNTHLRLVHIKAPg---------------------------QEEKR 54  Trichomonas vag...
XP_001565015  12 TLITFLQHLRGTLVEIELKNASIVSGEIAYVDANMNTYMSHVKITSKg---------------------------KNPVE 64  Leishmania braz...
XP_002784335   2 KLVRFLQKLNSETVTVELKNGTVVHGTVTGVDVSMNTHMKNVKVTVRg---------------------------RNPVG 54  Perkinsus marin...
XP_002291269   2 KLVKFLQKLNREQVTIELKNGTVISGTVVGVDATMNAHLKKAKLTAKg---------------------------KNPVS 54  Thalassiosira p...
Feature 1        # ###############  #    #                    ##     
1B34_A        55 LETLSIRGNNIRYFILPDSLPLDTLLvd-------------vePKVKSKKRE 93  human
2Y9A_B        55 LETLSIRGNNIRYFILPDSLPLDTLLvd-------------vePKVKSKKRE 93  human
Q02260        82 LQYINIRGNTIRQIILPDSLNLDSLLvdqkqlnslrrsgqianDPSKKRRRD 133 Saccharomyces cerevisiae S288c
CAG83694      55 LDYINIRGNTIRFFILPDSLPLDTLLid-------------dtPKAKRRKVE 93  Yarrowia lipolytica
EAL37203      55 LSQITVRGNTIRYFILPDSLPLDALLid-------------dtPKQNPPRVN 93  Cryptosporidium hominis
XP_001913982  55 LDQSTVRGNTIRNIILPESLNLDTYLvdd-----------tprLKVKAAVKS 95  Entamoeba histolytica HM-1:IMSS
XP_001324496  55 LENLTIRGASIRYVILPDVLNLDTLLvd--------------dSPTKTRMRH 92  Trichomonas vaginalis G3
XP_001565015  65 VEEYMVRGSTIRYIILPESLNTYDVLk---------------qASAKKNGAA 101 Leishmania braziliensis MHOM/BR/75/M2904
XP_002784335  55 MDHLTIRGSTIRYFILPDHIPLDTLLid-------------dgPKNKAARER 93  Perkinsus marinus ATCC 50983
XP_002291269  55 YATLSVRGSTVRSWILPDGLNLDALLve-------------daPKNVQKSAP 93  Thalassiosira pseudonana CCMP1335

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