Structural Classification of Proteins

Fold: Four-helical up-and-down bundle

: core: 4 helices; bundle, closed or partly opened, left-handed twist; up-and-down

Lineage:

Root: scop
Class: All alpha proteins [46456]
Fold: Four-helical up-and-down bundle [47161]
core: 4 helices; bundle, closed or partly opened, left-handed twist; up-and-down

Superfamilies:

Apolipoprotein [47162] (1)
uperfamily
1. Apolipoprotein [47163] (3)
  Can exist in a coiled-coil oligomeric form, see PDB entry 1AV1
  family may also include the five-helical bundle protein Apolipophorin-III
  1. Apolipoprotein E [88703]
    1. Human (Homo sapiens), E3 [TaxId: 9606] [47165] (7)
    2. Human (Homo sapiens), E2 [TaxId: 9606] [47167] (2)
    3. Human (Homo sapiens), E4 [TaxId: 9606] [47169] (3)
Aspartate receptor, ligand-binding domain [47170] (1)
uperfamily
1. Aspartate receptor, ligand-binding domain [47171] (2)
  1. Aspartate receptor, ligand-binding domain [47172]
    1. Escherichia coli [TaxId: 562] [47173] (1)
    2. Salmonella typhimurium [TaxId: 90371] [47174] (7)
Cytochromes [47175] (2)
Heme-containing proteins
uperfamily
1. Cytochrome b562 [47176] (1)
  1. Cytochrome b562 [47177]
    1. Escherichia coli [TaxId: 562] [47178] (6)
2. Cytochrome c'-like [47179] (9)
  1. Cytochrome c' [47180]
    1. Rhodospirillum molischianum [TaxId: 1083] [47181] (1)
    2. Chromatium vinosum [TaxId: 1049] [47182] (1)
    3. Alcaligenes denitrificans [TaxId: 32002] [47183] (1)
    4. Alcaligenes sp. [TaxId: 512] [47184] (5)
    5. Rhodocyclus gelatinosus [TaxId: 28068] [47185] (5)
    6. Rhodobacter capsulatus [TaxId: 1061] [47186] (4)
    7. Rhodobacter sphaeroides [TaxId: 1063] [81734] (1)
    8. Rhodopseudomonas palustris [TaxId: 1076] [47187] (2)
  2. Cytochrome c-556 [101109]
    1. Rhodopseudomonas palustris [TaxId: 1076] [101110] (1)
Hemerythrin-like [47188] (1)
uperfamily
1. Hemerythrin-like [47189] (3)
  Iron-binding proteins
  1. Hemerythrin [47190]
    1. Sipunculid worm (Themiste dyscritum) [TaxId: 6436] [47191] (4)
    2. Phascolopsis gouldii [TaxId: 6442] [47192] (4)
  2. Myohemerythin [47193]
    1. Sipunculan worm (Themiste zostericola) [TaxId: 6437] [47194] (3)
TMV-like viral coat proteins [47195] (1)
uperfamily
1. TMV-like viral coat proteins [47196] (3)
  1. Tobacco mosaic virus coat protein [47197]
    1. Tobacco mosaic virus, vulgare strain [TaxId: 12242] [47198] (4)
  2. Cucumber green mottle mosaic virus [47199]
    1. Cucumber green mottle mosaic virus, strain watermelon [TaxId: 12235] [47200] (1)
  3. Ribgrass mosaic virus [47201]
    1. Ribgrass mosaic virus [TaxId: 51680] [47202] (1)
FKBP12-rapamycin-binding domain of FKBP-rapamycin-associated protein (FRAP) [47212] (1)
uperfamily
1. FKBP12-rapamycin-binding domain of FKBP-rapamycin-associated protein (FRAP) [47213] (1)
  1. FKBP12-rapamycin-binding domain of FKBP-rapamycin-associated protein (FRAP) [47214]
    1. Human (Homo sapiens) [TaxId: 9606] [47215] (7)
Proteasome activator [47216] (1)
uperfamily
1. Proteasome activator [47217] (2)
  1. Proteasome activator reg(alpha) [47218]
    The structure of the proteasome complex with this protein from (Trypanosoma brucei) is available (1fnt); however, PDB entry 1FNT designates protein chains by both upper case and lower case letters creating problems with its processing and presentation; the proteasome activator pa26 chains are designated by lower case letters (c;d;e;f;g;h;i;j;k;l;m;n;o;p)
    1. Human (Homo sapiens) [TaxId: 9606] [47219] (1)
  2. Proteasome activator protein PA26 [158392]
    1. Trypanosoma brucei [TaxId: 5691] [158393] (21)
      SQ Q9U8G2 4-231
alpha-catenin/vinculin-like [47220] (2)
uperfamily
1. alpha-catenin/vinculin [47221] (4)
  possible duplication: contains several domains of this fold
  The listed PDB entries contain different large fragments but not the whole proteins
  1. alpha-catenin [47222]
    1. Mouse (Mus musculus) [TaxId: 10090] [47223] (2)
    2. Human (Homo sapiens) [TaxId: 9606] [63511] (2)
  2. Vinculin [47224]
    1. Chicken (Gallus gallus) [TaxId: 9031] [47225] (3)
      SQ P12003
    2. Human (Homo sapiens) [TaxId: 9606] [101111] (4)
      SQ P18206 1-257
2. VBS domain [140408] (1)
  Pfam 08913; Vinculin Binding Site
  1. Talin 1 [140409]
    1. Mouse (Mus musculus) [TaxId: 10090] [140410] (1)
      SQ P26039 1838-1973
FAT domain of focal adhesion kinase [68993] (1)
uperfamily
1. FAT domain of focal adhesion kinase [68994] (3)
  1. FAT domain of focal adhesion kinase [68995]
    1. Human (Homo sapiens) [TaxId: 9606] [68996] (9)
    2. Mouse (Mus musculus) [TaxId: 10090] [68997] (1)
    3. Chicken (Gallus gallus) [TaxId: 9031] [81735] (3)
      SQ Q00944 RE 920-1053
Oxygen-evolving enhancer protein 3, [101112] (1)
uperfamily
1. Oxygen-evolving enhancer protein 3, [101113] (1)
  1. Oxygen-evolving enhancer protein 3, [101114]
    PsbQ protein of photosystem II
    1. Spinach (Spinacia oleracea) [TaxId: 3562] [101115] (1)
Histidine-containing phosphotransfer domain, HPT domain [47226] (6)
contains additional, fifth helix at the N-terminus
uperfamily
1. Aerobic respiration control sensor protein, ArcB [47227] (1)
  1. Aerobic respiration control sensor protein, ArcB [47228]
    1. Escherichia coli [TaxId: 562] [47229] (4)
2. Phosphorelay protein-like [47230] (3)
  1. Phosphorelay protein ypd1 [47231]
    1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [47232] (6)
  2. Histidine-containing phosphotransfer protein HP2 [140411]
    1. Maize (Zea mays) [TaxId: 4577] [140412] (4)
      SQ Q9SLX1 9-139
  3. Histidine-containing phosphotransfer protein HP1 [140413]
    1. Rice (Oryza sativa) [TaxId: 4530] [140414] (4)
      SQ Q6VAK4 2-143
3. Chemotaxis protein CheA P1 domain [63512] (2)
  1. Chemotaxis protein CheA P1 domain [63513]
    1. Salmonella typhimurium [TaxId: 90371] [63514] (1)
    2. Thermotoga maritima [TaxId: 2336] [109765] (1)
      SQ Q56310 4-104
4. Sensor-like histidine kinase YojN, C-terminal domain [116868] (1)
  1. Sensor-like histidine kinase YojN, C-terminal domain [116869]
    1. Escherichia coli [TaxId: 562] [116870] (1)
      SQ P39838 775-890
5. Phosphorelay protein luxU [116871] (1)
  1. Phosphorelay protein luxU [116872]
    1. Vibrio harveyi [TaxId: 669] [116873] (1)
      SQ Q9ZBB6
6. SphA-like [158394] (1)
  1. Histidine phosphotransferase ShpA [158395]
    1. Caulobacter crescentus [TaxId: 155892] [158396] (2)
      SQ A0EJF9 8-111
Bacterial GAP domain [47233] (1)
contains extra helices in the loops at one end of the bundle
uperfamily
1. Bacterial GAP domain [47234] (3)
  1. ExoS toxin [47235]
    1. Pseudomonas aeruginosa [TaxId: 287] [47236] (2)
  2. SptP tyrosine phosphatase [47237]
    1. Salmonella typhimurium [TaxId: 90371] [47238] (2)
  3. YopE [68998]
    1. Yersinia pestis [TaxId: 632] [68999] (1)
Outer surface protein C (OspC) [63515] (1)
uperfamily
1. Outer surface protein C (OspC) [63516] (1)
  1. Outer surface protein C (OspC) [63517]
    1. Lyme disease spirochete (Borrelia burgdorferi), different strains [TaxId: 139] [63518] (3)
Flagellar export chaperone FliS [101116] (1)
can form closed, open and helix-swapped bundles
uperfamily
1. Flagellar export chaperone FliS [101117] (2)
  1. Flagellar export chaperone FliS [101118]
    1. Aquifex aeolicus [TaxId: 63363] [101119] (2)
    2. Bacillus subtilis [TaxId: 1423] [101120] (1)
Domain of the SRP/SRP receptor G-proteins [47364] (1)
uperfamily
1. Domain of the SRP/SRP receptor G-proteins [47365] (7)
  1. Signal sequence recognition protein Ffh [47366]
    1. Thermus aquaticus [TaxId: 271] [47367] (25)
    2. Archaeon Acidianus ambivalens [TaxId: 2283] [63538] (2)
    3. Archaeon Sulfolobus solfataricus [TaxId: 2287] [101121] (2)
  2. Signal recognition particle receptor, FtsY [47368]
    1. Escherichia coli [TaxId: 562] [47369] (2)
    2. Thermus aquaticus [TaxId: 271] [101122] (8)
    3. Thermotoga maritima [TaxId: 2336] [109766] (1)
      SQ Q9WZ40
  3. Signal recognition particle 54 kDa protein, SRP54 [116874]
    1. Mouse (Mus musculus) [TaxId: 10090] [116875] (1)
      SQ P14576 4-85
FAD-dependent thiol oxidase [69000] (1)
uperfamily
1. FAD-dependent thiol oxidase [69001] (2)
  1. Thiol oxidase Erv2p [69002]
    1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [69003] (2)
  2. Augmenter of liver regeneration [89018]
    a mammalian FAD-dependent sulfhydryl oxidase
    1. Rat (Rattus norvegicus) [TaxId: 10116] [89019] (1)
Group V grass pollen allergen [81736] (1)
uperfamily
1. Group V grass pollen allergen [81737] (2)
  1. Pollen allergen Phl P 6 [81738]
    1. Timothy grass (Phleum pratense) [TaxId: 15957] [81739] (1)
  2. Functional domain of pollen allergen Phl P 5b [89020]
    1. Timothy grass (Phleum pratense) [TaxId: 15957] [89021] (1)
Nucleotidyltransferase substrate binding subunit/domain [81593] (4)
uperfamily
1. Family 1 bi-partite nucleotidyltransferase subunit [81740] (2)
  1. Hypothetical protein HI0074 [81741]
    function unknown; form complex with putative catalytic subunit HI0073 (see 1no5)
    1. Haemophilus influenzae [TaxId: 727] [81742] (1)
  2. Probable nucleotidyltransferase subunit TTHA0048 [116876]
    1. Thermus thermophilus [TaxId: 274] [116877] (5)
      SQ Q5SM95
      Structural genomics target
2. HEPN domain [89022] (2)
  1. Hypothetical protein TM0613 [89023]
    Family 5 probable bi-partite nucleotidyltransferase subunit; predicted partner is putative catalytic subunit TM0614
    1. Thermotoga maritima [TaxId: 2336] [89024] (1)
  2. Hypothetical protein TT1696 [101123]
    1. Thermus thermophilus [TaxId: 274] [101124] (1)
3. Kanamycin nucleotidyltransferase (KNTase), C-terminal domain [81592] (1)
  N-terminal catalytic domain is followed by an all-alpha domain
  1. Kanamycin nucleotidyltransferase (KNTase), C-terminal domain [81591]
    1. Staphylococcus aureus [TaxId: 1280] [81590] (2)
4. Glutamine synthase adenylyltransferase GlnE, domain 2 [109767] (1)
  1. Glutamine synthase adenylyltransferase GlnE, domain 2 [109768]
    1. Escherichia coli [TaxId: 562] [109769] (1)
      SQ P30870 1-437
RecG, N-terminal domain [69008] (1)
uperfamily
1. RecG, N-terminal domain [69009] (1)
  1. RecG, N-terminal domain [69010]
    1. Thermotoga maritima [TaxId: 2336] [69011] (1)
Colicin D immunity protein [101125] (1)
uperfamily
1. Colicin D immunity protein [101126] (1)
  1. Colicin D immunity protein [101127]
    tRNA-mimic
    1. Escherichia coli [TaxId: 562] [101128] (3)
Nickel-containing superoxide dismutase, NiSOD [109770] (1)
uperfamily
1. Nickel-containing superoxide dismutase, NiSOD [109771] (2)
  1. Nickel-containing superoxide dismutase, NiSOD [109772]
    1. Streptomyces seoulensis [TaxId: 73044] [109773] (5)
      SQ P80734
    2. Streptomyces coelicolor [TaxId: 1902] [109774] (3)
      SQ P80735
Mannose-6-phosphate receptor binding protein 1 (Tip47), C-terminal domain [109775] (1)
contains extra alpha+beta subdomain formed by the N- and C-termini.
uperfamily
1. Mannose-6-phosphate receptor binding protein 1 (Tip47), C-terminal domain [109776] (1)
  1. Mannose-6-phosphate receptor binding protein 1 (Tip47), C-terminal domain [109777]
    1. Mouse (Mus musculus) [TaxId: 10090] [109778] (1)
      SQ Q9DBG5 206-431
Domain from hypothetical 2610208m17rik protein [109779] (1)
uperfamily
1. Domain from hypothetical 2610208m17rik protein [109780] (1)
  1. Domain from hypothetical 2610208m17rik protein [109781]
    1. Mouse (Mus musculus) [TaxId: 10090] [109782] (1)
      SQ Q8C4Q6 1-115
TrmE connector domain [116878] (1)
uperfamily
1. TrmE connector domain [116879] (1)
  1. TrmE connector domain [116880]
    1. Thermotoga maritima [TaxId: 2336] [116881] (2)
      SQ Q9WYA4
YppE-like [140415] (1)
flattened bundle at one end with helices 2 and coming in contact and separating helices 1 and 3
uperfamily
1. YppE-like [140416] (3)
  Pfam 08807; DUF1798
  1. Hypothetical protein Lin2004 [140417]
    1. Listeria innocua [TaxId: 1642] [140418] (1)
      SQ Q92AB8 1-120
  2. Hypothetical protein MW1337 [140419]
    SA1281 ortholog
    1. Staphylococcus aureus [TaxId: 1280] [140420] (1)
      SQ Q8NWP7 1-110
  3. Hypothetical protein YppE [140421]
    1. Bacillus subtilis [TaxId: 1423] [140422] (3)
      SQ P50833 1-123
MW0975(SA0943)-like [140423] (1)
open bundle; there is a long groove between helices 1 and 4
uperfamily
1. MW0975(SA0943)-like [140424] (1)
  1. Hypothetical protein MW0975 (SA0943) [140425]
    1. Staphylococcus aureus [TaxId: 1280] [140426] (1)
      SQ Q8NX77 21-205
VPS28 C-terminal domain-like [140427] (1)
uperfamily
1. VPS28 C-terminal domain-like [140428] (1)
  C-terminal part of Pfam 03997
  1. Vacuolar protein sorting-associated protein 28, VPS28 [140429]
    1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [140430] (10)
      SQ Q02767 148-241
TM1646-like [158397] (1)
1. TM1646-like [158398] (1)
  Pfam 03885; DUF327
  1. Hypothetical protein TM1646 [158399]
    1. Thermotoga maritima [TaxId: 2336] [158400] (1)
      SQ Q9X1X9 34-152