NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|315113506|pdb|3O34|B]
View 

Chain B, Histone H3.1

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

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 ...
 1-20 1.00e-02

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 PTZ00018:

Pssm-ID: 480273 [Multi-domain]  Cd Length: 136  Bit Score: 29.87  E-value: 1.00e-02
                         10        20
                 ....*....|....*....|
3O34_B         1 GKAPRKQLAT*AARKSAPAT 20
Cdd:PTZ00018  14 GKAPRKQLASKAARKSAPVT 33
 
Name Accession Description Interval E-value
PTZ00018 PTZ00018
histone H3; Provisional
 1-20 1.00e-02

histone H3; Provisional


Pssm-ID: 185400 [Multi-domain]  Cd Length: 136  Bit Score: 29.87  E-value: 1.00e-02
                         10        20
                 ....*....|....*....|
3O34_B         1 GKAPRKQLAT*AARKSAPAT 20
Cdd:PTZ00018  14 GKAPRKQLASKAARKSAPVT 33
 
Name Accession Description Interval E-value
PTZ00018 PTZ00018
histone H3; Provisional
 1-20 1.00e-02

histone H3; Provisional


Pssm-ID: 185400 [Multi-domain]  Cd Length: 136  Bit Score: 29.87  E-value: 1.00e-02
                         10        20
                 ....*....|....*....|
3O34_B         1 GKAPRKQLAT*AARKSAPAT 20
Cdd:PTZ00018  14 GKAPRKQLASKAARKSAPVT 33
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH