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Conserved domains on  [gi|392894580|ref|NP_497812|]
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Histone H3.3-like type 1 [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 ...
 1-133 3.33e-73

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: 214.38  E-value: 3.33e-73
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894580   1 MARTKHTARKSFGGKAPRKSLATKAARKVFPVDGQVKK--RYRPSSNALKEIRKYQKSTELLVRKLPFQRLVREVAQEIM 78
Cdd:PTZ00018   1 MARTKQTARKSTGGKAPRKQLASKAARKSAPVTGGIKKphRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFK 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 392894580  79 PNVRFQSAAIQALHEAAEAYLIGLFEDTNLCAIHAKRVTIMPKDMQLARRIRGER 133
Cdd:PTZ00018  81 TDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGER 135
 
Name Accession Description Interval E-value
PTZ00018 PTZ00018
histone H3; Provisional
 1-133 3.33e-73

histone H3; Provisional


Pssm-ID: 185400 [Multi-domain]  Cd Length: 136  Bit Score: 214.38  E-value: 3.33e-73
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894580   1 MARTKHTARKSFGGKAPRKSLATKAARKVFPVDGQVKK--RYRPSSNALKEIRKYQKSTELLVRKLPFQRLVREVAQEIM 78
Cdd:PTZ00018   1 MARTKQTARKSTGGKAPRKQLASKAARKSAPVTGGIKKphRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFK 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 392894580  79 PNVRFQSAAIQALHEAAEAYLIGLFEDTNLCAIHAKRVTIMPKDMQLARRIRGER 133
Cdd:PTZ00018  81 TDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGER 135
HFD_H3 cd22911
histone-fold domain found in histone H3 and similar proteins; Histone H3 is a core component ...
 38-131 2.05e-56

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: 170.41  E-value: 2.05e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894580  38 KRYRPSSNALKEIRKYQKSTELLVRKLPFQRLVREVAQEIMPNV-RFQSAAIQALHEAAEAYLIGLFEDTNLCAIHAKRV 116
Cdd:cd22911    1 RRYRPGTVALREIRRYQKSTELLIPKLPFQRLVREIAQDFKTKDlRFQSSALLALQEAAEAYLVGLFEDSNLCAIHAKRV 80

                         90
                 ....*....|....*
gi 392894580 117 TIMPKDMQLARRIRG 131
Cdd:cd22911   81 TLMPKDMQLARRIRG 95
H3 smart00428
Histone H3;
35-134 1.33e-53

Histone H3;


Pssm-ID: 128705 [Multi-domain]  Cd Length: 105  Bit Score: 163.77  E-value: 1.33e-53
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894580    35 QVKKRYRPSSNALKEIRKYQKSTELLVRKLPFQRLVREVAQEIMPNV--RFQSAAIQALHEAAEAYLIGLFEDTNLCAIH 112
Cdd:smart00428   4 TKHRRYRPGQVALREIRKYQKSTDLLIRKAPFQRLVREIAQKFTTGVdlRFQSSAIMALQEAAEAYLVGLFEDTNLLAIH 83

                           90       100
                   ....*....|....*....|..
gi 392894580   113 AKRVTIMPKDMQLARRIRGERG 134
Cdd:smart00428  84 AKRVTIMPKDIQLARRIRGERL 105
Histone pfam00125
Core histone H2A/H2B/H3/H4;
1-130 9.28e-45

Core histone H2A/H2B/H3/H4;


Pssm-ID: 459682 [Multi-domain]  Cd Length: 126  Bit Score: 142.19  E-value: 9.28e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894580    1 MARTKHTARKSFGGKAPRKSLATKAARKVfpvdGQVKKRYRPSSNALKEIRKYQKSTELLVRKLPFQRLVREVAQEIMPN 80
Cdd:pfam00125   1 MARNKNKANPRRGGTAPEKKISQKSSSSS----KKKTRRYRPGTVALKEIRKYQSSTDLLIYKLPFARVVREVVQSTKTD 76

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 392894580   81 VRFQSAAIQALHEAAEAYLIGLFEDTNLCAIHAKRVTIMPKDMQLARRIR 130
Cdd:pfam00125  77 LRISADAVVALQEAVEDFLVELFEEANLLAIHAKRVTLTPKDIQLARRLR 126
 
Name Accession Description Interval E-value
PTZ00018 PTZ00018
histone H3; Provisional
 1-133 3.33e-73

histone H3; Provisional


Pssm-ID: 185400 [Multi-domain]  Cd Length: 136  Bit Score: 214.38  E-value: 3.33e-73
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894580   1 MARTKHTARKSFGGKAPRKSLATKAARKVFPVDGQVKK--RYRPSSNALKEIRKYQKSTELLVRKLPFQRLVREVAQEIM 78
Cdd:PTZ00018   1 MARTKQTARKSTGGKAPRKQLASKAARKSAPVTGGIKKphRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFK 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 392894580  79 PNVRFQSAAIQALHEAAEAYLIGLFEDTNLCAIHAKRVTIMPKDMQLARRIRGER 133
Cdd:PTZ00018  81 TDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGER 135
PLN00121 PLN00121
histone H3; Provisional
 1-133 1.33e-65

histone H3; Provisional


Pssm-ID: 177733 [Multi-domain]  Cd Length: 136  Bit Score: 195.27  E-value: 1.33e-65
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894580   1 MARTKHTARKSFGGKAPRKSLATKAARKVFPVDGQVKK--RYRPSSNALKEIRKYQKSTELLVRKLPFQRLVREVAQEIM 78
Cdd:PLN00121   1 MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKphRYRPGTVALREIRKYQKSTELLIRKLPFQRLVREIAQDFK 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 392894580  79 PNVRFQSAAIQALHEAAEAYLIGLFEDTNLCAIHAKRVTIMPKDMQLARRIRGER 133
Cdd:PLN00121  81 TDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGER 135
HFD_H3 cd22911
histone-fold domain found in histone H3 and similar proteins; Histone H3 is a core component ...
 38-131 2.05e-56

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: 170.41  E-value: 2.05e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894580  38 KRYRPSSNALKEIRKYQKSTELLVRKLPFQRLVREVAQEIMPNV-RFQSAAIQALHEAAEAYLIGLFEDTNLCAIHAKRV 116
Cdd:cd22911    1 RRYRPGTVALREIRRYQKSTELLIPKLPFQRLVREIAQDFKTKDlRFQSSALLALQEAAEAYLVGLFEDSNLCAIHAKRV 80

                         90
                 ....*....|....*
gi 392894580 117 TIMPKDMQLARRIRG 131
Cdd:cd22911   81 TLMPKDMQLARRIRG 95
H3 smart00428
Histone H3;
35-134 1.33e-53

Histone H3;


Pssm-ID: 128705 [Multi-domain]  Cd Length: 105  Bit Score: 163.77  E-value: 1.33e-53
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894580    35 QVKKRYRPSSNALKEIRKYQKSTELLVRKLPFQRLVREVAQEIMPNV--RFQSAAIQALHEAAEAYLIGLFEDTNLCAIH 112
Cdd:smart00428   4 TKHRRYRPGQVALREIRKYQKSTDLLIRKAPFQRLVREIAQKFTTGVdlRFQSSAIMALQEAAEAYLVGLFEDTNLLAIH 83

                           90       100
                   ....*....|....*....|..
gi 392894580   113 AKRVTIMPKDMQLARRIRGERG 134
Cdd:smart00428  84 AKRVTIMPKDIQLARRIRGERL 105
Histone pfam00125
Core histone H2A/H2B/H3/H4;
1-130 9.28e-45

Core histone H2A/H2B/H3/H4;


Pssm-ID: 459682 [Multi-domain]  Cd Length: 126  Bit Score: 142.19  E-value: 9.28e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894580    1 MARTKHTARKSFGGKAPRKSLATKAARKVfpvdGQVKKRYRPSSNALKEIRKYQKSTELLVRKLPFQRLVREVAQEIMPN 80
Cdd:pfam00125   1 MARNKNKANPRRGGTAPEKKISQKSSSSS----KKKTRRYRPGTVALKEIRKYQSSTDLLIYKLPFARVVREVVQSTKTD 76

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 392894580   81 VRFQSAAIQALHEAAEAYLIGLFEDTNLCAIHAKRVTIMPKDMQLARRIR 130
Cdd:pfam00125  77 LRISADAVVALQEAVEDFLVELFEEANLLAIHAKRVTLTPKDIQLARRLR 126
PLN00161 PLN00161
histone H3; Provisional
 1-131 1.31e-43

histone H3; Provisional


Pssm-ID: 215082 [Multi-domain]  Cd Length: 135  Bit Score: 139.75  E-value: 1.31e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894580   1 MARTKHtARKSFGGKAPRKSLATKAARKvfpvDGQVKKRYRPSSNALKEIRKYQKSTELLVRKLPFQRLVREVAQEIMPN 80
Cdd:PLN00161   1 MARRLQ-GKRFRKGKKPQKEASGVTRQE----LDKKPHRYRPGTVALREIRKYQKSTELLIRKLPFARLVREISNEMLRE 75

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 392894580  81 -VRFQSAAIQALHEAAEAYLIGLFEDTNLCAIHAKRVTIMPKDMQLARRIRG 131
Cdd:PLN00161  76 pFRWTAEALLALQEATEDFLVHLFEDCNLCAIHAKRVTIMPKDMQLARRIRG 127
PLN00160 PLN00160
histone H3; Provisional
 41-132 4.00e-38

histone H3; Provisional


Pssm-ID: 165727  Cd Length: 97  Bit Score: 124.39  E-value: 4.00e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894580  41 RPSSNALKEIRKYQKSTELLVRKLPFQRLVREVAQEIMPNV-RFQSAAIQALHEAAEAYLIGLFEDTNLCAIHAKRVTIM 119
Cdd:PLN00160   2 RPGEKALKEIKMYQKSTDLLIRRLPFARLVREIQMEMSREAyRWQGSAILALQEAAEAHLVGLFEDSNLCAIHGKRVTIM 81

                         90
                 ....*....|...
gi 392894580 120 PKDMQLARRIRGE 132
Cdd:PLN00160  82 PKDMQLARRIRGQ 94
HFD_SF cd00076
histone fold domain (HFD) superfamily; The histone fold domain (HFD) is a structurally ...
 66-126 8.01e-04

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.


Pssm-ID: 467021  Cd Length: 63  Bit Score: 35.66  E-value: 8.01e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 392894580  66 FQRLVREVAQEIMPNvRFQSAAIQALHEAAEAYLIGLFEDTNLCAIHAKRVTIMPKDMQLA 126
Cdd:cd00076    2 LRSAVARILKSAGFD-SVSKSALELLSDLLERYLEELARAAKAYAELAGRTTPNAEDVELA 61
HFD_CENP-S cd22919
histone-fold domain found in centromere protein S (CENP-S) and similar proteins; CENP-S, also ...
 68-128 9.26e-04

histone-fold domain found in centromere protein S (CENP-S) and similar proteins; CENP-S, also called MHF1, apoptosis-inducing TAF9-like domain-containing protein 1 (APITD1), FANCM-associated histone fold protein 1, FANCM-interacting histone fold protein 1, or Fanconi anemia-associated polypeptide of 16 kDa (FAAP16), is a DNA-binding component of the Fanconi anemia (FA) core complex. It is required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage. CENP-S, together with CENP-X, forms the MHF heterodimer, which can further assemble to form tetrameric structures. CENP-S acts as a crucial cofactor for FANCM, in both binding and ATP-dependent remodeling of DNA. It can stabilize FANCM. CENP-S also forms a discrete complex with FANCM and CENP-X, called FANCM-MHF. This interaction leads to synergistic activation of double-stranded DNA binding and strongly stimulates FANCM-mediated DNA remodeling. In complex with CENP-T, CENP-W and CENP-X (CENP-T-W-S-X heterotetramer), CENP-S is involved in the formation of a functional kinetochore outer plate, which is essential for kinetochore-microtubule attachment and faithful mitotic progression. As a component of MHF and CENP-T-W-S-X complexes, CENP-S binds DNA and bends it to form a nucleosome-like structure. Its DNA-binding function is fulfilled in the presence of CENP-X. It does not bind DNA on its own.


Pssm-ID: 467044  Cd Length: 77  Bit Score: 35.62  E-value: 9.26e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 392894580  68 RLVREVAQEimPNVRFQSAAIQALHEAAEAYLIGLFEDTNLCAIHAKRVTIMPKDMQL-ARR 128
Cdd:cd22919   11 KICEEEAEE--KGVTVSPQFVAALAELVYKQLESLARDLEAFARHAKRKTITVDDVKLlARR 70
 
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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