3D9P,2DIW,3D9O


Conserved Protein Domain Family
CID_SCAF8
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cd17004: CID_SCAF8 
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CID (CTD-Interacting Domain) of SR-related and CTD-associated factor 8
SR-related and CTD-associated factor 8 (SCAF8) is also called CDC5L complex-associated protein 7 (CCAP7) or RNA-binding motif protein 16 (RBM16). It may play a role in mRNA processing. 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: 340801
Aligned: 8 rows
Threshold Bit Score: 261.89
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 KTFNSELYSLNDykpPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCkpEYKVPGLYVIDSIVRQSRHqfgqeKDVF 84   human
2DIW_A         14 KTFNSELYSLNDykpPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCkpEYKVPGLYVIDSIVRQSRHqfgqeKDVF 93   human
3D9O_B          5 KTFNSELYSLXDxkpPISKAKXTQITKAAIKAIKFYKHVVQSVEKFIQKCkpEYKVPGLYVIDSIVRQSRHqfgqeKDVF 84   human
AAH89292        5 KTFNTELYSLNDykpPISKAKMTQITKAAIKAIKFYKHVVQSVEKFVQKCkpEYKVSGLYVIDSIVRQSRHqfgqdKDLF 84   African clawe...
KFQ02065        3 PLFFWQLYSLNDykpPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCkpEYKVPGLYVIDSIVRQSRHqfgqeKDVF 82   Leptosomus di...
KKF33591        5 KAFNNELYSLNEykpPISKAKMTQITKSGIKAIKFYKHVVQSVEKFIQKCkpEYKVPGLYVIDSIVRQSRHqfgteKDVF 84   large yellow ...
Q9UPN6          5 KTFNSELYSLNDykpPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCkpEYKVPGLYVIDSIVRQSRHqfgqeKDVF 84   human
XP_007903677    5 KAFNNELYSLNEykpPISRAKMNQVTKAAIKAIKFYKHVVQSVEKFVQKCkpEYKVPGLYVIDSIVRQSRHqfgpeKDVF 84   elephant shark

Feature 1                                        #                   
3D9P_B         85 APRFSNNIISTFQNLyrcPGDDKSKIVTVLNLWQKNnvFKSEIIQPLLDMA 135  human
2DIW_A         94 APRFSNNIISTFQNLyrcPGDDKSKIVRVLNLWQKNnvFKSEIIQPLLDMA 144  human
3D9O_B         85 APRFSNNIISTFQNLyrcPGDDKSKIVRVLNLWQKNnvFKSEIIQPLLDXA 135  human
AAH89292       85 APRFSNNIINTFQNLyrcPADEKSKIVRVLNLWQKNnvFKSEIIQPLLDMA 135  African clawed frog
KFQ02065       83 APRFSNNIISTFQNLyrcPGDDKSKIVRVLNLWQKNnvFKSEIIQPLLDMA 133  Leptosomus discolor
KKF33591       85 APRFSKNIIATFQHLyrcPSDDKSKIVRVLNLWQKNavFKSDIIQPLLDMA 135  large yellow croaker
Q9UPN6         85 APRFSNNIISTFQNLyrcPGDDKSKIVRVLNLWQKNnvFKSEIIQPLLDMA 135  human
XP_007903677   85 APRFCKNINSTFQNLykcPADDKSKVVRVLNLWQKNsvFKSEVIQPLLDMA 135  elephant shark

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