1SZA,4JXT,2LO6,3D9P


Conserved Protein Domain Family
CID
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cd03562: CID 
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CID (CTD-Interacting Domain) family
The CTD-Interacting Domain (CID) is present in several eukaryotic RNA-processing factors including yeast proteins, Pcf11 and Nrd1, and vertebrate proteins, CTD-associated factors 8 (SCAF8) and Regulation of nuclear pre-mRNA domain-containing proteins (such as RPRD1 and RPRD2). Pcf11 is a conserved and essential subunit of the yeast cleavage factor IA, which is required for polyadenylation-dependent 3'-RNA processing and transcription termination. Nrd1 is implicated in polyadenylation-independent 3'-RNA processing. CID binds tightly to the carboxy-terminal domain (CTD) of RNA polymerase (Pol) II (RNAP II). During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.
Links
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Statistics
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PSSM-Id: 340766
Aligned: 4 rows
Threshold Bit Score: 162.301
Created: 3-Mar-2006
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
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CTD binding
Conserved site includes 12 residues -Click on image for an interactive view with Cn3D
Feature 1:CTD binding site [polypeptide binding site]
Evidence:
  • Comment:based on the interaction site between CTD (C-terminal domain of RNAP II) peptides and CIDs (CTD-Interacting Domain) of human RPRD1A , yeast Pcf11, human SCAF8, and yeast Nrd1
  • Structure:4JXT: Human RPRD1A CID in complex with a phosphorylated peptide from RPB1-CTD; contacts at 4A
  • Structure:1SZA_B; Saccharomyces cerevisiae Pcf11 CID binds the CTD peptide; contacts at 4A
  • Structure:3D9P_B: Human SCAF8 CID binds an RNAP II CTD peptide; contacts at 4A
  • Structure:2LO6: Saccharomyces cerevisiae Nrd1 CID binds Ser5 phosphorylated RNAP II CTD peptide; contacts at 4A
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Sequence Alignment
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Format: Row Display: Color Bits: Type Selection: 
Feature 1                #     ##  #                                     #  ##  ##            
1SZA_B     10 KDFNSILEELTFn----SRPIITTLTKLAEENiSCAQYFVDAIESRIEKCmpKQKLYAFYALDSICKNVGs--------- 76  baker's yeast
4JXT_A      8 AALEKKLSELSN-----SQQSVQTLSLWLIHHrKHSRPIVTVWERELRKAkpNRKLTFLYLANDVIQNSKrk-------- 74  human
2LO6_A      8 QNFVATLESFKDlksgiSGSRIKKLTTYALDHiDIESKIISLIIDYSRLCpdSHKLGSLYIIDSIGRAYLdetrsnsnss 87  Saccharomyces cere...
3D9P_B      5 KTFNSELYSLNDykppiSKAKMTQITKAAIKAiKFYKHVVQSVEKFIQKCkpEYKVPGLYVIDSIVRQSRhqfg------ 78  human

Feature 1                                           ##  #                       
1SZA_B     77 --------PYTIYFSRNLFNLYKRTyllvDNTTRTKLINMFKLWLNPndtglplFEGSALEKIEQF 134 baker's yeast
4JXT_A     75 ------gpEFTKDFAPVIVEAFKHVssetDESCKKHLGRVLSIWEERs-----vYENDVLEQLKQA 129 human
2LO6_A     88 snkpgtcaHAINTLGEVIQELLSDAiaksNQDHKEKIRMLLDIWDRSg-----lFQKSYLNAIRSK 148 Saccharomyces cerevisiae S288c
3D9P_B     79 ----qekdVFAPRFSNNIISTFQNLyr-cPGDDKSKIVTVLNLWQKNn-----vFKSEIIQPLLDM 134 human

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