SCOPe 2.03: Family a.4.1.1: Homeodomain

Lineage for Family a.4.1.1: Homeodomain

1. Root: SCOPe 2.03

2. Class a: All alpha proteins [46456] (284 folds)

3. Fold a.4: DNA/RNA-binding 3-helical bundle [46688] (14 superfamilies)
   core: 3-helices; bundle, closed or partly opened, right-handed twist; up-and down

4. Superfamily a.4.1: Homeodomain-like [46689] (20 families)
   consists only of helices

5. Family a.4.1.1: Homeodomain [46690] (41 proteins)
   Pfam PF00046

Proteins:

1. Antennapedia Homeodomain [46716] (1 species)

   • Species Fruit fly (Drosophila melanogaster) [TaxId:7227] [46717] (5 PDB entries)

2. DNA-binding protein SATB2 [116776] (1 species)

   • Species Human (Homo sapiens) [TaxId:9606] [116777] (1 PDB entry)
     Uniprot Q9UPW6 615-672 # the structure of the 1st CUT domain (350-437) is also known: 1WIZ

3. Engrailed Homeodomain [46691] (1 species)

   • Species Fruit fly (Drosophila melanogaster) [TaxId:7227] [46692] (12 PDB entries)

4. Even-skipped homeodomain [63465] (1 species)

   • Species Fruit fly (Drosophila melanogaster) [TaxId:7227] [63466] (1 PDB entry)

5. Extradenticle (exd) homeodomain [46720] (1 species)

   • Species Fruit fly (Drosophila melanogaster) [TaxId:7227] [46721] (1 PDB entry)

6. Fushi Tarazu protein [46722] (1 species)

   • Species Fruit fly (Drosophila melanogaster) [TaxId:7227] [46723] (1 PDB entry)

7. Hepatocyte nuclear factor 1a (LFB1/HNF1) [46697] (2 species)
   atypical Homeodomain with a large insertion into HTH motif

   1. Species Human (Homo sapiens) [TaxId:9606] [81680] (1 PDB entry)

   2. Species Rat (Rattus rattus) [TaxId:10117] [46698] (2 PDB entries)

8. Hepatocyte nuclear factor 6 [116780] (1 species)

   • Species Mouse (Mus musculus) [TaxId:10090] [116781] (1 PDB entry)
     Uniprot O08755 291-437

9. Homeo-prospero domain of Prospero protein [81681] (1 species)
   single domain composed of a homeodomain-homology N-terminal region (1245-1295) and the prospero-specific C-terminal region (1296-1396) that forms a 4-helical bundle

   • Species Fruit fly (Drosophila melanogaster) [TaxId:7227] [81682] (2 PDB entries)

10. Homeobox protein hox-a9 [100994] (1 species)

    • Species Mouse (Mus musculus) [TaxId:10090] [100995] (1 PDB entry)

11. Homeobox protein hox-b1 [46709] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [46710] (1 PDB entry)

12. Homeobox protein hox-b13 [140161] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [140162] (1 PDB entry)
      Uniprot Q92826 216-273

13. Homeobox protein pknox1 [140153] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [140154] (1 PDB entry)
      Uniprot P55347 257-318

14. Homeobox protein prh [140149] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [140150] (1 PDB entry)
      Uniprot Q03014 138-194

15. Homeobox-containing protein 1, HMBOX1 (Flj21616) [140159] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [140160] (1 PDB entry)
      Uniprot Q6NT76 268-350

16. Homeobox-leucine zipper protein Homez [116778] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [116779] (1 PDB entry)
      Uniprot Q8IX15 337-399
      Structural genomics target

17. Homeodomain-only protein, Hop [109647] (1 species)

    • Species Mouse (Mus musculus) [TaxId:10090] [109648] (2 PDB entries)
      Uniprot Q8R1H0

18. Homeotic bicoid protein [140155] (1 species)

    • Species Fruit fly (Drosophila melanogaster) [TaxId:7227] [140156] (1 PDB entry)
      Uniprot P09081 97-163

19. Hypothetical protein 4930532d21rik [140157] (1 species)

    • Species Mouse (Mus musculus) [TaxId:10090] [140158] (1 PDB entry)
      Uniprot Q8C0V1 712-760

20. Insulin gene enhancer protein isl-1 [46714] (1 species)

    • Species Norway rat (Rattus norvegicus) [TaxId:10116] [46715] (1 PDB entry)

21. LAG1 longevity assurance homolog 5, LASS5 [140141] (1 species)

    • Species Mouse (Mus musculus) [TaxId:10090] [140142] (1 PDB entry)
      Uniprot Q9D6K9 77-135

22. Lag1 longevity assurance homolog 6, LASS6 [140147] (1 species)

    • Species Mouse (Mus musculus) [TaxId:10090] [140148] (1 PDB entry)
      Uniprot Q8C172 76-127

23. mat alpha2 Homeodomain [46695] (1 species)

    • Species Baker's yeast (Saccharomyces cerevisiae) [TaxId:4932] [46696] (6 PDB entries)

24. Mating type protein A1 Homeodomain [46693] (1 species)

    • Species Baker's yeast (Saccharomyces cerevisiae) [TaxId:4932] [46694] (6 PDB entries)

25. Msx-1 homeodomain [63463] (1 species)

    • Species Mouse (Mus musculus) [TaxId:10090] [63464] (1 PDB entry)

26. Oct-1 POU Homeodomain [46699] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [46700] (7 PDB entries)

27. Oct-2 POU Homeodomain [46705] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [46706] (1 PDB entry)

28. Oct-3 POU Homeodomain [46707] (1 species)

    • Species Mouse (Mus musculus) [TaxId:10090] [46708] (1 PDB entry)

29. Paired box protein pax6 [140143] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [140144] (1 PDB entry)
      Uniprot P26367 211-278

30. Paired protein [46726] (1 species)

    • Species Fruit fly (Drosophila melanogaster) [TaxId:7227] [46727] (1 PDB entry)

31. pbx1 [46711] (2 species)

    1. Species Human (Homo sapiens) [TaxId:9606] [46712] (2 PDB entries)

    2. Species Mouse (Mus musculus) [TaxId:10090] [46713] (2 PDB entries)

32. Pit-1 POU homeodomain [46701] (1 species)

    • Species Norway rat (Rattus norvegicus) [TaxId:10116] [46702] (1 PDB entry)

33. Pituitary homeobox 2 [140151] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [140152] (1 PDB entry)
      Uniprot Q99697 85-144

34. Thyroid transcription factor 1 homeodomain [46703] (1 species)

    • Species Norway rat (Rattus norvegicus) [TaxId:10116] [46704] (1 PDB entry)

35. Transcriptional adaptor 2-like, TADA2L, isoform b [140145] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [140146] (1 PDB entry)
      Uniprot Q9BVJ0 72-118

36. Ultrabithorax (ubx) homeodomain [46718] (1 species)

    • Species Fruit fly (Drosophila melanogaster) [TaxId:7227] [46719] (1 PDB entry)

37. VND/NK-2 protein [46724] (1 species)

    • Species Fruit fly (Drosophila melanogaster) [TaxId:7227] [46725] (4 PDB entries)

38. ZF-HD homeobox protein At4g24660 [116774] (1 species)

    • Species Thale cress (Arabidopsis thaliana) [TaxId:3702] [116775] (1 PDB entry)
      Uniprot Q9SB61 148-215

39. ZF-HD homeobox protein At5g65410 [116772] (1 species)

    • Species Thale cress (Arabidopsis thaliana) [TaxId:3702] [116773] (1 PDB entry)
      Uniprot Q9FKP8 182-248

40. Zinc fingers and homeoboxes protein 1, ZHX1 [158242] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [158243] (1 PDB entry)
      Uniprot Q9UKY1 565-640

41. automated matches [190360] (2 species)
    not a true protein

    1. Species Fruit fly (Drosophila melanogaster) [TaxId:7227] [187191] (5 PDB entries)

    2. Species Human (Homo sapiens) [TaxId:9606] [188758] (3 PDB entries)

More info for Family a.4.1.1: Homeodomain

Timeline for Family a.4.1.1: Homeodomain:

• Family a.4.1.1: Homeodomain first appeared (with stable ids) in SCOP 1.55
  
• Family a.4.1.1: Homeodomain appears in SCOPe 2.02
  
• Family a.4.1.1: Homeodomain appears in SCOPe 2.04
  
• Family a.4.1.1: Homeodomain appears in the current release, SCOPe 2.08