Conserved Protein Domain Family

cd00024: CD_CSD 
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CHROMO (CHRromatin Organization Modifier) domains and chromo shadow domains
Members of this group are chromodomains or chromo shadow domains; these are SH3-fold-beta-barrel domains of the chromo-like superfamily. Chromodomains lack the first strand of the SH3-fold-beta-barrel, this first strand is altered by insertion in the chromo shadow domains. The chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. Chromodomain-containing proteins include: i) those having an N-terminal chromodomain followed by a related chromo shadow domain, such as Drosophila and human heterochromatin protein Su(var)205 (HP1), and mammalian modifier 1 and 2; ii) those having a single chromodomain, such as Drosophila protein Polycomb (Pc), mammalian modifier 3, human Mi-2 autoantigen, and several yeast and Caenorhabditis elegans proteins of unknown function; iii) those having paired tandem chromodomains, such as mammalian DNA-binding/helicase proteins CHD-1 to CHD-4 and yeast protein CHD1; (iv) and elongation factor eEF3, a member of the ATP-binding cassette (ABC) family of proteins, that serves an essential function in the translation cycle of fungi. eEF3 is a soluble factor lacking a transmembrane domain and having two ABC domains arranged in tandem, with a unique chromodomain inserted within the ABC2 domain.
PSSM-Id: 349274
View PSSM: cd00024
Aligned: 521 rows
Threshold Bit Score: 31.2933
Threshold Setting Gi: 902861038
Created: 1-Nov-2000
Updated: 11-Jul-2018
Aligned Rows:
Conserved site includes 20 residues -Click on image for an interactive view with Cn3D
Feature 1:putative peptide binding site [polypeptide binding site]
  • Comment:based on chromodomains and chromo shadow domains with structure
  • Structure:5E4W; Arabidopsis thaliana Cpsrp43 chromodomains 2 and 3 bind with a linear motif in the Alb3 C-terminal tail, contacts 4A
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  • Structure:2RSN; Schizosaccharomyces pombe Chp1 chromodomain binds H3k9me3 peptide, contacts at 4A
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  • Structure:4U68; Drosophila melanogaster Rhino chromodomain binds the H3k9me (trimethylated lysine 9 of histone H3) peptide, contacts at 4A
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  • Structure:5EQ0; human CBX8 chromodomain binds UNC3866, which closely mimics a methylated H3 tail, contacts at 4A
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  • Structure:3DM1; human CBX3 chromodomain binds methylated peptide from histone G9a, contacts at 4A
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  • Structure:5T1I; human CBX3 chromo shadow domain binds a histone H3 peptide, contacts at 4A
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Sequence Alignment
Format: Row Display: Color Bits: Type Selection:
                           10        20        30        40        50        60        70
Feature 1          #####                 # ####                # #### ##            #  ##  
3F2U_A           3 YVVEKVLDRRVvk---gKVEYLLKWKGFsd-------------eDNTWEPEENLdc-------pdLIAEFLQ 51
5E4W_D           6 AEVDEIVEKRGkg---kDVEYLVRWKDGg---------------DCEWVKGVHVae--------dVAKDYED 51
4NW2_A         140 QIVERIIAHSNqksaagYPDYYCKWQGLpy-------------sECSWEDGALIskk-----fqaCIDEYFS 193
2IWH_B         800 RRIAGIHSRRKfk---nTYEYECSFLLGenigmkserwvpmmsvDNAWIPRGELves-----hskMVAEVDM 863
1E0B_A          11 DLVSSIDTIERkd--dgTLEIYLTWKNG----------------AISHHPSTITnkkc----pqkMLQFYES 60
gi 308259619   137 KSVVHILGMTKap---gTMHFLCKMNDG----------------SVTLVPDHIVherf----pnqSIKFYES 185
5T1I_A          13 LDPERIIGATDss---gELMFLMKWKDSd---------------EADLVLAKEAnmkc----pqiVIAFYEE 62
gi 1238986928   28 YAIESIVDHQGgk---kTLRFLIKWQGYss-------------aENSWVPAASMkkdmtlasfkeLVTEYES 83
gi 574106770   127 YEVEAIVDARYvaa-kkDYEVLLKWRGLnd-------------vENSWEPAATIked------vsMAKAYFT 178
gi 646303941   768 YDVEAIVGFRHqf--ngGPEWLCKWVGYddd----------aaeWRPWSSLSNCk---------kMVLAYNK 818

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