PDBsum entry 1an4

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protein dna_rna Protein-protein interface(s) links
Transcription/DNA PDB id
Protein chains
65 a.a. *
* Residue conservation analysis
PDB id:
Name: Transcription/DNA
Title: Structure and function of the b/hlh/z domain of usf
Structure: DNA (5'- d( Cp Ap Cp Cp Cp Gp Gp Tp Cp Ap Cp Gp Tp Gp Gp Cp C p Tp Ap Cp A)-3'). Chain: c. Engineered: yes. DNA (5'- d( Gp Tp Gp Tp Ap Gp Gp Cp Cp Ap Cp Gp Tp Gp Ap Cp C p Gp Gp Gp T)-3'). Chain: d.
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: bacteria. Expression_system_taxid: 2
Biol. unit: Tetramer (from PQS)
2.90Å     R-factor:   0.236    
Authors: A.R.Ferre-D'Amare,P.Pognonec,R.G.Roeder,S.K.Burley
Key ref: A.R.Ferré-D'Amaré et al. (1994). Structure and function of the b/HLH/Z domain of USF. EMBO J, 13, 180-189. PubMed id: 8306960
15-Mar-97     Release date:   17-Sep-97    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P22415  (USF1_HUMAN) -  Upstream stimulatory factor 1
310 a.a.
65 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     protein dimerization activity     1 term  


EMBO J 13:180-189 (1994)
PubMed id: 8306960  
Structure and function of the b/HLH/Z domain of USF.
A.R.Ferré-D'Amaré, P.Pognonec, R.G.Roeder, S.K.Burley.
The basic/helix-loop-helix/leucine zipper (b/HLH/Z) transcription factor upstream stimulatory factor (USF) and its isolated DNA binding domain undergo a random coil to alpha-helix folding transition on recognizing their cognate DNA. The USF b/HLH cocrystal structure resembles the structure of the b/HLH/Z domain of the homologous protein Max and reveals (i) that the truncated, b/HLH DNA binding domain homodimerizes, forming a parallel, left-handed four-helix bundle, and (ii) that the basic region becomes alpha-helical on binding to the major groove of the DNA sequence CACGTG. Hydrodynamic measurements show that the b/HLH/Z DNA binding domain of USF exists as a bivalent homotetramer. This tetramer forms at the USF physiological intranuclear concentration, and depends on the integrity of the leucine zipper motif. The ability to bind simultaneously to two independent sites suggests a role in DNA looping for the b/HLH/Z and Myc-related families of eukaryotic transcription factors.

Literature references that cite this PDB file's key reference

  PubMed id Reference
22955618 S.Neph, J.Vierstra, A.B.Stergachis, A.P.Reynolds, E.Haugen, B.Vernot, R.E.Thurman, S.John, R.Sandstrom, A.K.Johnson, M.T.Maurano, R.Humbert, E.Rynes, H.Wang, S.Vong, K.Lee, D.Bates, M.Diegel, V.Roach, D.Dunn, J.Neri, A.Schafer, R.S.Hansen, T.Kutyavin, E.Giste, M.Weaver, T.Canfield, P.Sabo, M.Zhang, G.Balasundaram, R.Byron, M.J.MacCoss, J.M.Akey, M.A.Bender, M.Groudine, R.Kaul, and J.A.Stamatoyannopoulos (2012).
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Regulation of the transcription factor Ets-1 by DNA-mediated homo-dimerization.
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PDB code: 2nny
17827227 E.P.Lamber, M.Wilmanns, and D.I.Svergun (2008).
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Regulatory Module Network of bHLH Transcription Factors in Mouse Brain.
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Intrinsic disorder in transcription factors.
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16966334 Y.Kodama, and H.Sano (2006).
Evolution of a basic helix-loop-helix protein from a transcriptional repressor to a plastid-resident regulatory factor: involvement in hypersensitive cell death in tobacco plants.
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Upstream stimulatory factor (USF) as a transcriptional suppressor of human telomerase reverse transcriptase (hTERT) in oral cancer cells.
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16055724 M.Ku, S.Y.Sokol, J.Wu, M.I.Tussie-Luna, A.L.Roy, and A.Hata (2005).
Positive and negative regulation of the transforming growth factor beta/activin target gene goosecoid by the TFII-I family of transcription factors.
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16162174 S.Corre, and M.D.Galibert (2005).
Upstream stimulating factors: highly versatile stress-responsive transcription factors.
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The structure of importin-beta bound to SREBP-2: nuclear import of a transcription factor.
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PDB code: 1ukl
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12086602 M.I.Rosenberg, and S.M.Parkhurst (2002).
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Mechanism for the action of bone morphogenetic proteins and regulation of their activity.
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Sex-specific gene regulation. The Doublesex DM motif is a bipartite DNA-binding domain.
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11170202 G.B.Chavali, C.Vijayalakshmi, and D.M.Salunke (2001).
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11467950 M.C.Chung, H.K.Kim, and S.Kawamoto (2001).
TFEC can function as a transcriptional activator of the nonmuscle myosin II heavy chain-A gene in transfected cells.
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11669632 M.L.Chiu, P.H.Viollier, T.Katoh, J.J.Ramsden, and C.J.Thompson (2001).
Ligand-induced changes in the Streptomyces lividans TipAL protein imply an alternative mechanism of transcriptional activation for MerR-like proteins.
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11031250 C.Grandori, S.M.Cowley, L.P.James, and R.N.Eisenman (2000).
The Myc/Max/Mad network and the transcriptional control of cell behavior.
  Annu Rev Cell Dev Biol, 16, 653-699.  
11118624 G.A.Breen, and E.M.Jordan (2000).
Upstream stimulatory factor 2 stimulates transcription through an initiator element in the mouse cytochrome c oxidase subunit Vb promoter.
  Biochim Biophys Acta, 1517, 119-127.  
  10790403 J.H.Hallsson, J.Favor, C.Hodgkinson, T.Glaser, M.L.Lamoreux, R.Magnúsdóttir, G.J.Gunnarsson, H.O.Sweet, N.G.Copeland, N.A.Jenkins, and E.Steingrímsson (2000).
Genomic, transcriptional and mutational analysis of the mouse microphthalmia locus.
  Genetics, 155, 291-300.  
  11206057 J.W.Cave, W.Kremer, and D.E.Wemmer (2000).
Backbone dynamics of sequence specific recognition and binding by the yeast Pho4 bHLH domain probed by NMR.
  Protein Sci, 9, 2354-2365.  
10725404 K.R.Wollenberg, and W.R.Atchley (2000).
Separation of phylogenetic and functional associations in biological sequences by using the parametric bootstrap.
  Proc Natl Acad Sci U S A, 97, 3288-3291.  
  10898790 L.Zhu, J.Wilken, N.B.Phillips, U.Narendra, G.Chan, S.M.Stratton, S.B.Kent, and M.A.Weiss (2000).
Sexual dimorphism in diverse metazoans is regulated by a novel class of intertwined zinc fingers.
  Genes Dev, 14, 1750-1764.
PDB code: 1lpv
11070082 P.Hemmerich, T.Stoyan, G.Wieland, M.Koch, J.Lechner, and S.Diekmann (2000).
Interaction of yeast kinetochore proteins with centromere-protein/transcription factor Cbf1.
  Proc Natl Acad Sci U S A, 97, 12583-12588.  
10594029 T.Kophengnavong, J.E.Michnowicz, and T.K.Blackwell (2000).
Establishment of distinct MyoD, E2A, and twist DNA binding specificities by different basic region-DNA conformations.
  Mol Cell Biol, 20, 261-272.  
10962024 X.Li, M.Commane, H.Nie, X.Hua, M.Chatterjee-Kishore, D.Wald, M.Haag, and G.R.Stark (2000).
Act1, an NF-kappa B-activating protein.
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Characterization of the dimerization domain in BglG, an RNA-binding transcriptional antiterminator from Escherichia coli.
  J Bacteriol, 181, 1755-1766.  
10593926 A.N.Billin, A.L.Eilers, C.Queva, and D.E.Ayer (1999).
Mlx, a novel Max-like BHLHZip protein that interacts with the Max network of transcription factors.
  J Biol Chem, 274, 36344-36350.  
9880489 A.Ribeiro, D.Pastier, D.Kardassis, J.Chambaz, and P.Cardot (1999).
Cooperative binding of upstream stimulatory factor and hepatic nuclear factor 4 drives the transcription of the human apolipoprotein A-II gene.
  J Biol Chem, 274, 1216-1225.  
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c-Myc target genes involved in cell growth, apoptosis, and metabolism.
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10025401 E.E.Zheleznova, P.N.Markham, A.A.Neyfakh, and R.G.Brennan (1999).
Structural basis of multidrug recognition by BmrR, a transcription activator of a multidrug transporter.
  Cell, 96, 353-362.
PDB codes: 1bow 2bow
10434034 G.A.Breen, and E.M.Jordan (1999).
Transcriptional activation of the F(1)F(0) ATP synthase alpha-subunit initiator element by USF2 is mediated by p300.
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10454619 H.I.Swanson, and J.H.Yang (1999).
Specificity of DNA binding of the c-Myc/Max and ARNT/ARNT dimers at the CACGTG recognition site.
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Structural features of protein-nucleic acid recognition sites.
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Upstream stimulatory factor regulates major histocompatibility complex class I gene expression: the U2DeltaE4 splice variant abrogates E-box activity.
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9634703 A.Párraga, L.Bellsolell, A.R.Ferré-D'Amaré, and S.K.Burley (1998).
Co-crystal structure of sterol regulatory element binding protein 1a at 2.3 A resolution.
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PDB code: 1am9
9501313 E.Steingrímsson, J.Favor, A.F.Ferré-D'Amaré, N.G.Copeland, and N.A.Jenkins (1998).
Mitfmi-enu122 is a missense mutation in the HLH dimerization domain.
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9488706 H.Wendt, R.M.Thomas, and T.Ellenberger (1998).
DNA-mediated folding and assembly of MyoD-E47 heterodimers.
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Targeting the microphthalmia basic helix-loop-helix-leucine zipper transcription factor to a subset of E-box elements in vitro and in vivo.
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Role of the PAS domain in regulation of dimerization and DNA binding specificity of the dioxin receptor.
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Dimerization as a regulatory mechanism in signal transduction.
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Cooperative interaction of ets-1 with USF-1 required for HIV-1 enhancer activity in T cells.
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LSF and NTF-1 share a conserved DNA recognition motif yet require different oligomerization states to form a stable protein-DNA complex.
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c-Myc/Max heterodimers bind cooperatively to the E-box sequences located in the first intron of the rat ornithine decarboxylase (ODC) gene.
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Role of Oncogenic Transcription Factor c-Myc in Cell Cycle Regulation, Apoptosis and Metabolism.
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Structural basis of DNA bending and oriented heterodimer binding by the basic leucine zipper domains of Fos and Jun.
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A general method to design dominant negatives to B-HLHZip proteins that abolish DNA binding.
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The basic helix-loop-helix-zipper transcription factor USF1 regulates expression of the surfactant protein-A gene.
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A three-protein-DNA complex on a B cell-specific domain of the immunoglobulin mu heavy chain gene enhancer.
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Regulation of the nuclear gene that encodes the alpha-subunit of the mitochondrial F0F1-ATP synthase complex. Activation by upstream stimulatory factor 2.
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Rox, a novel bHLHZip protein expressed in quiescent cells that heterodimerizes with Max, binds a non-canonical E box and acts as a transcriptional repressor.
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Eukaryotic transcription factor-DNA complexes.
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Assembly of a bZIP-bHLH transcription activation complex: formation of the yeast Cbf1-Met4-Met28 complex is regulated through Met28 stimulation of Cbf1 DNA binding.
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Lac repressor-operator complex.
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Architectural transcription factors: proteins that remodel DNA.
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The crystal structure of an intact human Max-DNA complex: new insights into mechanisms of transcriptional control.
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PDB code: 1hlo
  9199298 P.L.Blaiseau, A.D.Isnard, Y.Surdin-Kerjan, and D.Thomas (1997).
Met31p and Met32p, two related zinc finger proteins, are involved in transcriptional regulation of yeast sulfur amino acid metabolism.
  Mol Cell Biol, 17, 3640-3648.  
8999857 R.A.Rippe, A.Umezawa, J.P.Kimball, M.Breindl, and D.A.Brenner (1997).
Binding of upstream stimulatory factor to an E-box in the 3'-flanking region stimulates alpha1(I) collagen gene transcription.
  J Biol Chem, 272, 1753-1760.  
9782776 R.E.Dickerson, and T.K.Chiu (1997).
Helix bending as a factor in protein/DNA recognition.
  Biopolymers, 44, 361-403.  
  9007990 R.Fairman, R.K.Beran-Steed, and T.M.Handel (1997).
Heteronuclear (1H, 13C, 15N) NMR assignments and secondary structure of the basic region-helix-loop-helix domain of E47.
  Protein Sci, 6, 175-184.  
9139720 R.T.Utley, J.Côté, T.Owen-Hughes, and J.L.Workman (1997).
SWI/SNF stimulates the formation of disparate activator-nucleosome complexes but is partially redundant with cooperative binding.
  J Biol Chem, 272, 12642-12649.  
9283077 T.K.Kerppola (1997).
Comparison of DNA bending by Fos-Jun and phased A tracts by multifactorial phasing analysis.
  Biochemistry, 36, 10872-10884.  
9303313 T.Shimizu, A.Toumoto, K.Ihara, M.Shimizu, Y.Kyogoku, N.Ogawa, Y.Oshima, and T.Hakoshima (1997).
Crystal structure of PHO4 bHLH domain-DNA complex: flanking base recognition.
  EMBO J, 16, 4689-4697.
PDB code: 1a0a
9053397 W.D.Kohn, C.T.Mant, and R.S.Hodges (1997).
Alpha-helical protein assembly motifs.
  J Biol Chem, 272, 2583-2586.  
  9343420 Y.Hamamori, H.Y.Wu, V.Sartorelli, and L.Kedes (1997).
The basic domain of myogenic basic helix-loop-helix (bHLH) proteins is the novel target for direct inhibition by another bHLH protein, Twist.
  Mol Cell Biol, 17, 6563-6573.  
9374477 Y.Takahashi, K.Nakayama, S.Itoh, Y.Fujii-Kuriyama, and T.Kamataki (1997).
Inhibition of the transcription of CYP1A1 gene by the upstream stimulatory factor 1 in rabbits. Competitive binding of USF1 with AhR.Arnt complex.
  J Biol Chem, 272, 30025-30031.  
8631989 B.N.Fukunaga, and O.Hankinson (1996).
Identification of a novel domain in the aryl hydrocarbon receptor required for DNA binding.
  J Biol Chem, 271, 3743-3749.  
8576131 B.Viollet, A.M.Lefrançois-Martinez, A.Henrion, A.Kahn, M.Raymondjean, and A.Martinez (1996).
Immunochemical characterization and transacting properties of upstream stimulatory factor isoforms.
  J Biol Chem, 271, 1405-1415.  
8898913 C.Aperlo, K.E.Boulukos, and P.Pognonec (1996).
The basic region/helix-loop-helix/leucine repeat transcription factor USF interferes with Ras transformation.
  Eur J Biochem, 241, 249-253.  
  8947051 E.Steingrímsson, A.Nii, D.E.Fisher, A.R.Ferré-D'Amaré, R.J.McCormick, L.B.Russell, S.K.Burley, J.M.Ward, N.A.Jenkins, and N.G.Copeland (1996).
The semidominant Mi(b) mutation identifies a role for the HLH domain in DNA binding in addition to its role in protein dimerization.
  EMBO J, 15, 6280-6289.  
8940186 H.I.Swanson, and J.Yang (1996).
Mapping the protein/DNA contact sites of the Ah receptor and Ah receptor nuclear translocator.
  J Biol Chem, 271, 31657-31665.  
  8665858 M.Vettese-Dadey, P.A.Grant, T.R.Hebbes, C.Crane- Robinson, C.D.Allis, and J.L.Workman (1996).
Acetylation of histone H4 plays a primary role in enhancing transcription factor binding to nucleosomal DNA in vitro.
  EMBO J, 15, 2508-2518.  
8962069 R.J.McCormick, T.Badalian, and D.E.Fisher (1996).
The leucine zipper may induce electrophoretic mobility anomalies without DNA bending.
  Proc Natl Acad Sci U S A, 93, 14434-14439.  
8621524 S.G.Bacsi, and O.Hankinson (1996).
Functional characterization of DNA-binding domains of the subunits of the heterodimeric aryl hydrocarbon receptor complex imputing novel and canonical basic helix-loop-helix protein-DNA interactions.
  J Biol Chem, 271, 8843-8850.  
8810904 T.den Blaauwen, P.Fekkes, Wit, W.Kuiper, and A.J.Driessen (1996).
Domain interactions of the peripheral preprotein Translocase subunit SecA.
  Biochemistry, 35, 11994-12004.  
  8657110 X.Luo, and M.Sawadogo (1996).
Functional domains of the transcription factor USF2: atypical nuclear localization signals and context-dependent transcriptional activation domains.
  Mol Cell Biol, 16, 1367-1375.  
7784186 C.A.Panagiotidis, S.Artandi, K.Calame, and S.J.Silverstein (1995).
Polyamines alter sequence-specific DNA-protein interactions.
  Nucleic Acids Res, 23, 1800-1809.  
  7823943 C.Antonsson, M.L.Whitelaw, J.McGuire, J.A.Gustafsson, and L.Poellinger (1995).
Distinct roles of the molecular chaperone hsp90 in modulating dioxin receptor function via the basic helix-loop-helix and PAS domains.
  Mol Cell Biol, 15, 756-765.  
7775458 C.Antonsson, V.Arulampalam, M.L.Whitelaw, S.Pettersson, and L.Poellinger (1995).
Constitutive function of the basic helix-loop-helix/PAS factor Arnt. Regulation of target promoters via the E box motif.
  J Biol Chem, 270, 13968-13972.  
  7862134 C.C.Adams, and J.L.Workman (1995).
Binding of disparate transcriptional activators to nucleosomal DNA is inherently cooperative.
  Mol Cell Biol, 15, 1405-1421.  
  7760817 C.Fernex, M.Capone, and P.Ferrier (1995).
The V(D)J recombinational and transcriptional activities of the immunoglobulin heavy-chain intronic enhancer can be mediated through distinct protein-binding sites in a transgenic substrate.
  Mol Cell Biol, 15, 3217-3226.  
  7707499 F.d'Adda di Fagagna, G.Marzio, M.I.Gutierrez, L.Y.Kang, A.Falaschi, and M.Giacca (1995).
Molecular and functional interactions of transcription factor USF with the long terminal repeat of human immunodeficiency virus type 1.
  J Virol, 69, 2765-2775.  
7592839 H.I.Swanson, W.K.Chan, and C.A.Bradfield (1995).
DNA binding specificities and pairing rules of the Ah receptor, ARNT, and SIM proteins.
  J Biol Chem, 270, 26292-26302.  
  7739539 J.B.Kim, G.D.Spotts, Y.D.Halvorsen, H.M.Shih, T.Ellenberger, H.C.Towle, and B.M.Spiegelman (1995).
Dual DNA binding specificity of ADD1/SREBP1 controlled by a single amino acid in the basic helix-loop-helix domain.
  Mol Cell Biol, 15, 2582-2588.  
7761476 K.E.McLane, D.R.Burton, and P.Ghazal (1995).
Transplantation of a 17-amino acid alpha-helical DNA-binding domain into an antibody molecule confers sequence-dependent DNA recognition.
  Proc Natl Acad Sci U S A, 92, 5214-5218.  
8578601 K.J.Moore (1995).
Insight into the microphthalmia gene.
  Trends Genet, 11, 442-448.  
7642609 M.Sha, A.R.Ferré-D'Amaré, S.K.Burley, and D.J.Goss (1995).
Anti-cooperative biphasic equilibrium binding of transcription factor upstream stimulatory factor to its cognate DNA monitored by protein fluorescence changes.
  J Biol Chem, 270, 19325-19329.  
  7737127 M.Shirakata, and B.M.Paterson (1995).
The E12 inhibitory domain prevents homodimer formation and facilitates selective heterodimerization with the MyoD family of gene regulatory factors.
  EMBO J, 14, 1766-1772.  
8749848 M.Suzuki, and M.Gerstein (1995).
Binding geometry of alpha-helices that recognize DNA.
  Proteins, 23, 525-535.  
7749979 P.Ernst, and S.T.Smale (1995).
Combinatorial regulation of transcription II: The immunoglobulin mu heavy chain gene.
  Immunity, 2, 427-438.  
7479029 S.E.Artandi, K.Merrell, N.Avitahl, K.K.Wong, and K.Calame (1995).
TFE3 contains two activation domains, one acidic and the other proline-rich, that synergistically activate transcription.
  Nucleic Acids Res, 23, 3865-3871.  
  7549873 S.L.Cohen, A.R.Ferré-D'Amaré, S.K.Burley, and B.T.Chait (1995).
Probing the solution structure of the DNA-binding protein Max by a combination of proteolysis and mass spectrometry.
  Protein Sci, 4, 1088-1099.  
7862526 S.Schwank, R.Ebbert, K.Rautenstrauss, E.Schweizer, and H.J.Schüller (1995).
Yeast transcriptional activator INO2 interacts as an Ino2p/Ino4p basic helix-loop-helix heteromeric complex with the inositol/choline-responsive element necessary for expression of phospholipid biosynthetic genes in Saccharomyces cerevisiae.
  Nucleic Acids Res, 23, 230-237.  
8524857 T.M.Laue, M.A.Starovasnik, H.Weintraub, X.H.Sun, L.Snider, and R.E.Klevit (1995).
MyoD forms micelles which can dissociate to form heterodimers with E47: implications of micellization on function.
  Proc Natl Acad Sci U S A, 92, 11824-11828.  
8052536 A.J.Bendall, and P.L.Molloy (1994).
Base preferences for DNA binding by the bHLH-Zip protein USF: effects of MgCl2 on specificity and comparison with binding of Myc family members.
  Nucleic Acids Res, 22, 2801-2810.  
8081751 A.R.Ferré-D'Amaré, and S.K.Burley (1994).
Use of dynamic light scattering to assess crystallizability of macromolecules and macromolecular assemblies.
  Structure, 2, 357-359.  
7664056 C.Wolberger (1994).
b/HLH without the zip.
  Nat Struct Biol, 1, 413-416.  
7874168 E.Steingrímsson, K.J.Moore, M.L.Lamoreux, A.R.Ferré-D'Amaré, S.K.Burley, D.C.Zimring, L.C.Skow, C.A.Hodgkinson, H.Arnheiter, and N.G.Copeland (1994).
Molecular basis of mouse microphthalmia (mi) mutations helps explain their developmental and phenotypic consequences.
  Nat Genet, 8, 256-263.  
  7957052 I.Wadman, J.Li, R.O.Bash, A.Forster, H.Osada, T.H.Rabbitts, and R.Baer (1994).
Specific in vivo association between the bHLH and LIM proteins implicated in human T cell leukemia.
  EMBO J, 13, 4831-4839.  
  7813441 L.J.Juan, R.T.Utley, C.C.Adams, M.Vettese-Dadey, and J.L.Workman (1994).
Differential repression of transcription factor binding by histone H1 is regulated by the core histone amino termini.
  EMBO J, 13, 6031-6040.  
7809040 M.Suzuki, and N.Yagi (1994).
DNA recognition code of transcription factors in the helix-turn-helix, probe helix, hormone receptor, and zinc finger families.
  Proc Natl Acad Sci U S A, 91, 12357-12361.  
  8035802 N.A.Kent, J.S.Tsang, D.J.Crowther, and J.Mellor (1994).
Chromatin structure modulation in Saccharomyces cerevisiae by centromere and promoter factor 1.
  Mol Cell Biol, 14, 5229-5241.  
  7969114 S.E.Artandi, C.Cooper, A.Shrivastava, and K.Calame (1994).
The basic helix-loop-helix-zipper domain of TFE3 mediates enhancer-promoter interaction.
  Mol Cell Biol, 14, 7704-7716.  
8075979 S.E.Phillips (1994).
Built by association: structure and function of helix-loop-helix DNA-binding proteins.
  Structure, 2, 1-4.  
7656043 S.K.Burley (1994).
Plus ça change, plus c'est la même chose.
  Nat Struct Biol, 1, 207-208.  
  7969122 Y.Peleg, and R.L.Metzenberg (1994).
Analysis of the DNA-binding and dimerization activities of Neurospora crassa transcription factor NUC-1.
  Mol Cell Biol, 14, 7816-7826.  
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