3D9P,3D9O


Conserved Protein Domain Family
CID_SCAF8_like
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cd16983: CID_SCAF8_like 
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CID (CTD-Interacting Domain) of SR-related and CTD-associated factor 8 and similar proteins
This subfamily includes SR-related and CTD-associated factors 8 (SCAF8) and 4 (SCAF4), and similar proteins. SCAF4 is also called Splicing factor arginine serine rich 15 (SFRS15). Members may play roles in mRNA processing. Both SCAF4 and SCAF8 contains a CTD-interacting domain (CID) at the amino terminus and a Ser/Arg-rich domain followed by an RNA recognition motif. 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: 340780
Aligned: 28 rows
Threshold Bit Score: 161.626
Created: 27-May-2015
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
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CTD binding
Conserved site includes 10 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 CID (CTD-Interacting Domain) of human SCAF8
  • Structure:3D9P_B: Human SCAF8 CID binds an RNAP II CTD peptide; contacts at 4A
  • Structure:3D9O_B: Human SCAF8 CID binds an 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                       ####  #                                     #  ##  #           
3D9P_B       5 KTFNSELYSLNDyk--pPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCkpEYKVPGLYVIDSIVRQSRHqfgq--- 79   human
CDH50375     8 SLFDKELKSILDak--lPVSASKINALQSLAISHPKHHNYIVQCVVRFIETAppDYRLAGLYVVDAISRTVQKqmrktad 85   Lichtheimia cory...
EGF83650    10 LAFDKELYALSEsk--lPVSASRITTLTKLAIVHIKLYKHIVHSIEKFVQKCqpDYKLAGLYVIDSILRASLKptakek- 86   Batrachochytrium...
KFH65041    10 AEFDKELYNLFDs---rAVSASKIDKLTKLAFKAAKYYKNIVYCLEKFITRCvpEYKLTGLYVLDSICRTSQSvktksss 86   Mortierella vert...
KJE97907    38 EELDAELDEMEAqaksaAVSSKRIHAVSKIAVRNYKHYKHIVHCIERFIHRAraEHKLAGVYIIDAIVRGSQHklg---- 113  Capsaspora owcza...
CEF64416    12 ESFSIQLNALTSsk--pSFGKQRIEEIAKLGLAAVSNYKHVVMHLEKFIWKTtsKYKLIGIYILDALLCASKHkyk---- 85   Strongyloides ratti
EEY64231    23 EKLKKALEGLATa---kGVSQSRISAVAKLAAHYSKFYKHVVHDIEVFLWKAevEHRLAGLYAVDAIIRQSHTkng---- 95   Phytophthora inf...
ETV94617     8 EELKGALASLASa---kGVSANRIKAACTTCMKWSKEYKRVVHAVEMAMWKSdvEHRLAYMYLIDALIRASQTkygd--- 81   Aphanomyces inva...
CDH50225     7 SLFDGDLQALLDvr--pPVPISRINALRDLALAHREHLNYITQRILRFLETSppDYRVAGLYLIDAIIRKPKDqqae--- 81   Lichtheimia cory...
CBN77033    10 ASMHKALKVLATss--rPISASRVKTAAARALDNVKEYKRVVHAIERYIRKAqpQHRIGGCFVIDSVCRQAQSkwg---- 83   Ectocarpus silic...

Feature 1                                                   #                   
3D9P_B      80 -------ekdVFAPRFSNNIISTFQNLyr--cPGDDKSKIVTVLNLWQKNnvFKSEIIQPLLDMA 135  human
CDH50375    86 egnqhsveteVYLRRFAMVLKDGALQGcfvpcSSKDKEKVKKTLDIWELNgvFTKETVDYIRQSF 150  Lichtheimia corymbifera JMRC:FS...
EGF83650    87 -----apttsVYVRRFEEKLENIFTNLvq--aNLKDRTRMKRVVALWVKSniLSSEQLEVIDKAY 144  Batrachochytrium dendrobatidis ...
KFH65041    87 s--sgsfsgaEYVARFEKNIEALFTEFtk-vqEDKEKEKVKRVVDLWERSstFAPSITESIRKKY 148  Mortierella verticillata NRRL 6337
KJE97907   114 -------akdNYADRFGRNLGATIEYCfn-kcSAVDQDRVRRIVSLWLQNhiFPFDIVAPIESKI 170  Capsaspora owczarzaki ATCC 30864
CEF64416    86 -------gkdKFRVRFAVNLFKTIKNVl---nNVSDKKKVIRVVKLWEAKkiFEKSVLTPIYKYC 140  Strongyloides ratti
EEY64231    96 -------skdAYVKRFLIRMSDTIAAVkk--vPEQFQPKVKHVIEEWQKRaiYTPRQIEDLGGRE 151  Phytophthora infestans T30-4
ETV94617    82 -------ekdHFAKRFGQHLHHTLAACrk--aPDDHKANVKRVVAEWQKRgvYTTQEIEQAGGAD 137  Aphanomyces invadans
CDH50225    82 ------cavnDYRLRFQAVLRDHALQGlfslcSEEDKARVIRVFTYWGEKhiFPKHFAEQLKIDA 140  Lichtheimia corymbifera JMRC:FS...
CBN77033    84 -------hkdVFTPRFAQRMSETVENLrn--vPDGDKPPVFRVIREWHEKgmFKGLEAFASTGAA 139  Ectocarpus siliculosus

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