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Conserved domains on  [gi|17556803|ref|NP_498108|]
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Histone H2A/H2B/H3 domain-containing protein [Caenorhabditis elegans]

Protein Classification

histone H3/H4 domain-containing protein( domain architecture ID 581047)

histone H3/H4 domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HFD_SF super family cl45933
histone fold domain (HFD) superfamily; The histone fold domain (HFD) is a structurally ...
 120-204 4.35e-08

histone fold domain (HFD) superfamily; The histone fold domain (HFD) is a structurally conserved interaction motif involved in heterodimerization of the core histones and their assembly into the nucleosome octamer. Histone fold heterodimers play crucial roles in gene regulation. The minimal HFD consists of three alpha helices connected by two short, unstructured loops. The HFD is found in core histones, TATA box-binding protein-associated factors (TAFs), and many other transcription factors. HFD plays a role in the nucleosomal core particle by conserving histone interactions; these contain more than one HFD. The structure of the nucleosome core particle has two modes that have the largest interaction surfaces, and these are the H3-H4 and H2A-H2B heterodimer interactions. Several TAFs interact via histone-fold (HF) motifs. Five HF-containing TAF pairs have been described in transcription factor II D (TFIID): TAF6-TAF9, TAF4-TAF12, TAF11-TAF13, TAF8-TAF10 and TAF3-TAF10.


The actual alignment was detected with superfamily member smart00428:

Pssm-ID: 480273 [Multi-domain]  Cd Length: 105  Bit Score: 49.37  E-value: 4.35e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556803    120 KRYmsKKEKDLNDEKKNFKDLVLTIGQNQiqDPDEDFQITKEAIDLLQSESDKILLEMFTSSNAIATAGERDILTPTDIQ 199
Cdd:smart00428  20 RKY--QKSTDLLIRKAPFQRLVREIAQKF--TTGVDLRFQSSAIMALQEAAEAYLVGLFEDTNLLAIHAKRVTIMPKDIQ 95


                   ....*
gi 17556803    200 TARHI 204
Cdd:smart00428  96 LARRI 100
 
Name Accession Description Interval E-value
H3 smart00428
Histone H3;
120-204 4.35e-08

Histone H3;


Pssm-ID: 128705 [Multi-domain]  Cd Length: 105  Bit Score: 49.37  E-value: 4.35e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556803    120 KRYmsKKEKDLNDEKKNFKDLVLTIGQNQiqDPDEDFQITKEAIDLLQSESDKILLEMFTSSNAIATAGERDILTPTDIQ 199
Cdd:smart00428  20 RKY--QKSTDLLIRKAPFQRLVREIAQKF--TTGVDLRFQSSAIMALQEAAEAYLVGLFEDTNLLAIHAKRVTIMPKDIQ 95


                   ....*
gi 17556803    200 TARHI 204
Cdd:smart00428  96 LARRI 100
HFD_H3 cd22911
histone-fold domain found in histone H3 and similar proteins; Histone H3 is a core component ...
 134-205 1.25e-04

histone-fold domain found in histone H3 and similar proteins; Histone H3 is a core component of the nucleosome, which wraps and compacts DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication, and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called the histone code, and nucleosome remodeling. The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4 assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of DNA.


Pssm-ID: 467036  Cd Length: 95  Bit Score: 39.83  E-value: 1.25e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 17556803 134 KKNFKDLVLTIGQNQiqdPDEDFQITKEAIDLLQSESDKILLEMFTSSNAIATAGERDILTPTDIQTARHIQ 205
Cdd:cd22911  26 KLPFQRLVREIAQDF---KTKDLRFQSSALLALQEAAEAYLVGLFEDSNLCAIHAKRVTLMPKDMQLARRIR 94
Histone pfam00125
Core histone H2A/H2B/H3/H4;
114-205 3.40e-04

Core histone H2A/H2B/H3/H4;


Pssm-ID: 459682 [Multi-domain]  Cd Length: 126  Bit Score: 38.95  E-value: 3.40e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556803   114 SKASPRKRYMSKKEKDLNDEKKNFKDLVLTIGQNQI--------QDPDEDFQITKEAIDLLQSESDKILLEMFTSSNAIA 185
Cdd:pfam00125  27 SSSKKKTRRYRPGTVALKEIRKYQSSTDLLIYKLPFarvvrevvQSTKTDLRISADAVVALQEAVEDFLVELFEEANLLA 106

                          90       100
                  ....*....|....*....|
gi 17556803   186 TAGERDILTPTDIQTARHIQ 205
Cdd:pfam00125 107 IHAKRVTLTPKDIQLARRLR 126
 
Name Accession Description Interval E-value
H3 smart00428
Histone H3;
120-204 4.35e-08

Histone H3;


Pssm-ID: 128705 [Multi-domain]  Cd Length: 105  Bit Score: 49.37  E-value: 4.35e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556803    120 KRYmsKKEKDLNDEKKNFKDLVLTIGQNQiqDPDEDFQITKEAIDLLQSESDKILLEMFTSSNAIATAGERDILTPTDIQ 199
Cdd:smart00428  20 RKY--QKSTDLLIRKAPFQRLVREIAQKF--TTGVDLRFQSSAIMALQEAAEAYLVGLFEDTNLLAIHAKRVTIMPKDIQ 95


                   ....*
gi 17556803    200 TARHI 204
Cdd:smart00428  96 LARRI 100
HFD_H3 cd22911
histone-fold domain found in histone H3 and similar proteins; Histone H3 is a core component ...
 134-205 1.25e-04

histone-fold domain found in histone H3 and similar proteins; Histone H3 is a core component of the nucleosome, which wraps and compacts DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication, and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called the histone code, and nucleosome remodeling. The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4 assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of DNA.


Pssm-ID: 467036  Cd Length: 95  Bit Score: 39.83  E-value: 1.25e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 17556803 134 KKNFKDLVLTIGQNQiqdPDEDFQITKEAIDLLQSESDKILLEMFTSSNAIATAGERDILTPTDIQTARHIQ 205
Cdd:cd22911  26 KLPFQRLVREIAQDF---KTKDLRFQSSALLALQEAAEAYLVGLFEDSNLCAIHAKRVTLMPKDMQLARRIR 94
Histone pfam00125
Core histone H2A/H2B/H3/H4;
114-205 3.40e-04

Core histone H2A/H2B/H3/H4;


Pssm-ID: 459682 [Multi-domain]  Cd Length: 126  Bit Score: 38.95  E-value: 3.40e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556803   114 SKASPRKRYMSKKEKDLNDEKKNFKDLVLTIGQNQI--------QDPDEDFQITKEAIDLLQSESDKILLEMFTSSNAIA 185
Cdd:pfam00125  27 SSSKKKTRRYRPGTVALKEIRKYQSSTDLLIYKLPFarvvrevvQSTKTDLRISADAVVALQEAVEDFLVELFEEANLLA 106

                          90       100
                  ....*....|....*....|
gi 17556803   186 TAGERDILTPTDIQTARHIQ 205
Cdd:pfam00125 107 IHAKRVTLTPKDIQLARRLR 126
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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