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PDBsum entry 1cf7
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protein dna_rna Protein-protein interface(s) links
Transcription/DNA PDB id
1cf7

 

 

 

 

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Contents
Protein chains
67 a.a. *
82 a.a. *
DNA/RNA
Waters ×75
* Residue conservation analysis
PDB id:
1cf7
Name: Transcription/DNA
Title: Structural basis of DNA recognition by the heterodimeric cell cycle transcription factor e2f-dp
Structure: DNA (5'-d( Ap Tp Tp Tp Tp Cp Gp Cp Gp Cp Gp Gp Tp Tp Tp T)- 3'). Chain: c. Fragment: adenovirus type 5 e2 promoter e2f-binding site. Engineered: yes. DNA (5'-d( Tp Ap Ap Ap Ap Cp Cp Gp Cp Gp Cp Gp Ap Ap Ap A)- 3'). Chain: d. Fragment: adenovirus type 5 e2 promoter e2f-binding site.
Source: Synthetic: yes. Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_cell_line: bl21(de3).
Biol. unit: Tetramer (from PQS)
Resolution:
2.60Å     R-factor:   0.223    
Authors: N.Zheng,E.Fraenkel,C.O.Pabo,N.P.Pavletich
Key ref: N.Zheng et al. (1999). Structural basis of DNA recognition by the heterodimeric cell cycle transcription factor E2F-DP. Genes Dev, 13, 666-674. PubMed id: 10090723
Date:
24-Mar-99     Release date:   02-Apr-99    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q16254  (E2F4_HUMAN) -  Transcription factor E2F4 from Homo sapiens
Seq:
Struc: 		413 a.a.
67 a.a.
Protein chain
Pfam   ArchSchema ?
Q14188  (TFDP2_HUMAN) -  Transcription factor Dp-2 from Homo sapiens
Seq:
Struc: 		446 a.a.
82 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

DNA/RNA chains
  T-T-T-T-C-G-C-G-C-G-G-T-T-T-T 15 bases
  A-A-A-A-C-C-G-C-G-C-G-A-A-A-A 15 bases

 

 
Genes Dev 13:666-674 (1999)
PubMed id: 10090723  
 
 
Structural basis of DNA recognition by the heterodimeric cell cycle transcription factor E2F-DP.
N.Zheng, E.Fraenkel, C.O.Pabo, N.P.Pavletich.
 
  ABSTRACT  
 
The E2F and DP protein families form heterodimeric transcription factors that play a central role in the expression of cell cycle-regulated genes. The crystal structure of an E2F4-DP2-DNA complex shows that the DNA-binding domains of the E2F and DP proteins both have a fold related to the winged-helix DNA-binding motif. Recognition of the central c/gGCGCg/c sequence of the consensus DNA-binding site is symmetric, and amino acids that contact these bases are conserved among all known E2F and DP proteins. The asymmetry in the extended binding site TTTc/gGCGCc/g is associated with an amino-terminal extension of E2F4, in which an arginine binds in the minor groove near the TTT stretch. This arginine is invariant among E2Fs but not present in DPs. E2F4 and DP2 interact through an extensive protein-protein interface, and structural features of this interface suggest it contributes to the preference for heterodimers over homodimers in DNA binding.
 

Literature references that cite this PDB file's key reference Google scholar

  PubMed id Reference
21310950 A.R.Cao, R.Rabinovich, M.Xu, X.Xu, V.X.Jin, and P.J.Farnham (2011).
Genome-wide analysis of transcription factor E2F1 mutant proteins reveals that N- and C-terminal protein interaction domains do not participate in targeting E2F1 to the human genome.
  J Biol Chem, 286, 11985-11996.  
21247883 B.K.Lee, A.A.Bhinge, and V.R.Iyer (2011).
Wide-ranging functions of E2F4 in transcriptional activation and repression revealed by genome-wide analysis.
  Nucleic Acids Res, 39, 3558-3573.  
21082705 J.Lin, T.Zhou, and J.Wang (2011).
Solution structure of the human HSPC280 protein.
  Protein Sci, 20, 216-223.
PDB code: 2l2o
20559320 L.Ingram, S.Munro, A.S.Coutts, and N.B.La Thangue (2011).
E2F-1 regulation by an unusual DNA damage-responsive DP partner subunit.
  Cell Death Differ, 18, 122-132.  
20410283 A.Workman, and C.Jones (2010).
Productive infection and bICP0 early promoter activity of bovine herpesvirus 1 are stimulated by E2F1.
  J Virol, 84, 6308-6317.  
21085677 D.Judah, W.Y.Chang, and L.Dagnino (2010).
EBP1 is a novel E2F target gene regulated by transforming growth factor-β.
  PLoS One, 5, e13941.  
19846609 J.Binkley, K.Karra, A.Kirby, M.Hosobuchi, E.A.Stone, and A.Sidow (2010).
ProPhylER: a curated online resource for protein function and structure based on evolutionary constraint analyses.
  Genome Res, 20, 142-154.  
19722278 B.I.Khayrutdinov, W.J.Bae, Y.M.Yun, J.H.Lee, T.Tsuyama, J.J.Kim, E.Hwang, K.S.Ryu, H.K.Cheong, C.Cheong, J.S.Ko, T.Enomoto, P.A.Karplus, P.Güntert, S.Tada, Y.H.Jeon, and Y.Cho (2009).
Structure of the Cdt1 C-terminal domain: conservation of the winged helix fold in replication licensing factors.
  Protein Sci, 18, 2252-2264.
PDB codes: 2klo 3a4c
19823669 H.Wang, L.B.Carey, Y.Cai, H.Wijnen, and B.Futcher (2009).
Recruitment of Cln3 cyclin to promoters controls cell cycle entry via histone deacetylase and other targets.
  PLoS Biol, 7, e1000189.  
19543322 J.A.Freedman, J.T.Chang, L.Jakoi, and J.R.Nevins (2009).
A combinatorial mechanism for determining the specificity of E2F activation and repression.
  Oncogene, 28, 2873-2881.  
19525434 J.A.Reynolds, and S.C.Hand (2009).
Embryonic diapause highlighted by differential expression of mRNAs for ecdysteroidogenesis, transcription and lipid sparing in the cricket Allonemobius socius.
  J Exp Biol, 212, 2075-2084.  
  19609728 L.Zhou, L.Luo, X.Qi, X.Li, and G.I.Gorodeski (2009).
Regulation of P2X(7) gene transcription.
  Purinergic Signal, 5, 409-426.  
19949542 M.Wu, X.Li, X.Li, and G.Li (2009).
Signaling Transduction Network Mediated by Tumor Suppressor/Susceptibility Genes in NPC.
  Curr Genomics, 10, 216-222.  
19150358 R.D.Shereda, N.J.Reiter, S.E.Butcher, and J.L.Keck (2009).
Identification of the SSB binding site on E. coli RecQ reveals a conserved surface for binding SSB's C terminus.
  J Mol Biol, 386, 612-625.  
19184528 R.Janowski, S.Panjikar, A.N.Eddine, S.H.Kaufmann, and M.S.Weiss (2009).
Structural analysis reveals DNA binding properties of Rv2827c, a hypothetical protein from Mycobacterium tuberculosis.
  J Struct Funct Genomics, 10, 137-150.
PDB code: 1zel
19032344 S.Kurosawa, R.Murakami, K.Onai, M.Morishita, D.Hasegawa, R.Iwase, T.Uzumaki, F.Hayashi, T.Kitajima-Ihara, S.Sakata, M.Murakami, T.Kouyama, and M.Ishiura (2009).
Functionally important structural elements of the cyanobacterial clock-related protein Pex.
  Genes Cells, 14, 1.
PDB codes: 2dql 2zfw
19662336 S.M.de Jager, S.Scofield, R.P.Huntley, A.S.Robinson, B.G.den Boer, and J.A.Murray (2009).
Dissecting regulatory pathways of G1/S control in Arabidopsis: common and distinct targets of CYCD3;1, E2Fa and E2Fc.
  Plant Mol Biol, 71, 345-365.  
  19218339 S.Romagnoli, E.Fasoli, V.Vaira, M.Falleni, C.Pellegrini, A.Catania, M.Roncalli, A.Marchetti, L.Santambrogio, G.Coggi, and S.Bosari (2009).
Identification of potential therapeutic targets in malignant mesothelioma using cell-cycle gene expression analysis.
  Am J Pathol, 174, 762-770.  
19201609 T.Lammens, J.Li, G.Leone, and L.De Veylder (2009).
Atypical E2Fs: new players in the E2F transcription factor family.
  Trends Cell Biol, 19, 111-118.  
18554521 L.Zhang, O.R.Sheppard, A.M.Shah, and A.C.Brewer (2008).
Positive regulation of the NADPH oxidase NOX4 promoter in vascular smooth muscle cells by E2F.
  Free Radic Biol Med, 45, 679-685.  
  17394670 I.S.Hagemann, K.D.Narzinski, and T.J.Baranski (2007).
E2F8 is a nonreceptor activator of heterotrimeric G proteins.
  J Mol Signal, 2, 3.  
17447837 J.Lee, Z.Li, R.Brower-Sinning, and B.John (2007).
Regulatory circuit of human microRNA biogenesis.
  PLoS Comput Biol, 3, e67.  
18029424 L.Carlier, J.Couprie, A.le Maire, L.Guilhaudis, I.Milazzo-Segalas, M.Courçon, M.Moutiez, M.Gondry, D.Davoust, B.Gilquin, and S.Zinn-Justin (2007).
Solution structure of the region 51-160 of human KIN17 reveals an atypical winged helix domain.
  Protein Sci, 16, 2750-2755.
PDB code: 2v1n
17908821 X.Xu, M.Bieda, V.X.Jin, A.Rabinovich, M.J.Oberley, R.Green, and P.J.Farnham (2007).
A comprehensive ChIP-chip analysis of E2F1, E2F4, and E2F6 in normal and tumor cells reveals interchangeable roles of E2F family members.
  Genome Res, 17, 1550-1561.  
16418725 A.Milton, K.Luoto, L.Ingram, S.Munro, N.Logan, A.L.Graham, T.R.Brummelkamp, E.M.Hijmans, R.Bernards, and N.B.La Thangue (2006).
A functionally distinct member of the DP family of E2F subunits.
  Oncogene, 25, 3212-3218.  
16792505 H.Liu, C.Peng, M.Zhou, J.Zhou, S.Shen, H.Zhou, W.Xiong, X.Luo, S.Peng, Z.Niu, J.Ouyang, X.Li, and G.Li (2006).
Cloning and characterization of the BRD7 gene promoter.
  DNA Cell Biol, 25, 346-358.  
16606705 M.Bieda, X.Xu, M.A.Singer, R.Green, and P.J.Farnham (2006).
Unbiased location analysis of E2F1-binding sites suggests a widespread role for E2F1 in the human genome.
  Genome Res, 16, 595-605.  
16387655 M.Teplova, Y.R.Yuan, A.T.Phan, L.Malinina, S.Ilin, A.Teplov, and D.J.Patel (2006).
Structural basis for recognition and sequestration of UUU(OH) 3' temini of nascent RNA polymerase III transcripts by La, a rheumatic disease autoantigen.
  Mol Cell, 21, 75-85.
PDB codes: 1yty 1zh5
16936737 W.Du, and J.Pogoriler (2006).
Retinoblastoma family genes.
  Oncogene, 25, 5190-5200.  
15966770 A.Oliva, A.Rosebrock, F.Ferrezuelo, S.Pyne, H.Chen, S.Skiena, B.Futcher, and J.Leatherwood (2005).
The cell cycle-regulated genes of Schizosaccharomyces pombe.
  PLoS Biol, 3, e225.  
16299514 C.Qian, Q.Zhang, S.Li, L.Zeng, M.J.Walsh, and M.M.Zhou (2005).
Structure and chromosomal DNA binding of the SWIRM domain.
  Nat Struct Mol Biol, 12, 1078-1085.
PDB codes: 2aqe 2aqf
15926895 D.Q.Pham, and C.A.Chavez (2005).
The ferritin light-chain homologue promoter in Aedes aegypti.
  Insect Mol Biol, 14, 263-270.  
16249342 E.P.Black, T.Hallstrom, H.K.Dressman, M.West, and J.R.Nevins (2005).
Distinctions in the specificity of E2F function revealed by gene expression signatures.
  Proc Natl Acad Sci U S A, 102, 15948-15953.  
16179649 J.Christensen, P.Cloos, U.Toftegaard, D.Klinkenberg, A.P.Bracken, E.Trinh, M.Heeran, L.Di Stefano, and K.Helin (2005).
Characterization of E2F8, a novel E2F-like cell-cycle regulated repressor of E2F-activated transcription.
  Nucleic Acids Res, 33, 5458-5470.  
16339893 J.S.Hu, H.Feng, W.Zeng, G.X.Lin, and X.G.Xi (2005).
Solution structure of a multifunctional DNA- and protein-binding motif of human Werner syndrome protein.
  Proc Natl Acad Sci U S A, 102, 18379-18384.
PDB code: 2axl
16158528 K.Tsuchiya, Y.Kim, F.G.Ondrey, and J.Lin (2005).
Characterization of a temperature-sensitive mouse middle ear epithelial cell line.
  Acta Otolaryngol, 125, 823-829.  
15808743 L.Aravind, V.Anantharaman, S.Balaji, M.M.Babu, and L.M.Iyer (2005).
The many faces of the helix-turn-helix domain: transcription regulation and beyond.
  FEMS Microbiol Rev, 29, 231-262.  
15897886 N.Logan, A.Graham, X.Zhao, R.Fisher, B.Maiti, G.Leone, and N.B.La Thangue (2005).
E2F-8: an E2F family member with a similar organization of DNA-binding domains to E2F-7.
  Oncogene, 24, 5000-5004.  
16137622 R.J.Klose, S.A.Sarraf, L.Schmiedeberg, S.M.McDermott, I.Stancheva, and A.P.Bird (2005).
DNA binding selectivity of MeCP2 due to a requirement for A/T sequences adjacent to methyl-CpG.
  Mol Cell, 19, 667-678.  
16360038 S.M.Rubin, A.L.Gall, N.Zheng, and N.P.Pavletich (2005).
Structure of the Rb C-terminal domain bound to E2F1-DP1: a mechanism for phosphorylation-induced E2F release.
  Cell, 123, 1093-1106.
PDB code: 2aze
15579210 A.K.Wernimont, and W.Weissenhorn (2004).
Crystal structure of subunit VPS25 of the endosomal trafficking complex ESCRT-II.
  BMC Struct Biol, 4, 10.
PDB code: 1xb4
14993291 J.P.Frederick, N.T.Liberati, D.S.Waddell, Y.Shi, and X.F.Wang (2004).
Transforming growth factor beta-mediated transcriptional repression of c-myc is dependent on direct binding of Smad3 to a novel repressive Smad binding element.
  Mol Cell Biol, 24, 2546-2559.  
15238633 M.Devany, N.P.Kotharu, and H.Matsuo (2004).
Solution NMR structure of the C-terminal domain of the human protein DEK.
  Protein Sci, 13, 2252-2259.
PDB code: 1q1v
15014447 P.H.Giangrande, W.Zhu, R.E.Rempel, N.Laakso, and J.R.Nevins (2004).
Combinatorial gene control involving E2F and E Box family members.
  EMBO J, 23, 1336-1347.  
15510213 W.Zhu, P.H.Giangrande, and J.R.Nevins (2004).
E2Fs link the control of G1/S and G2/M transcription.
  EMBO J, 23, 4615-4626.  
12609051 E.Ramirez-Parra, C.Fründt, and C.Gutierrez (2003).
A genome-wide identification of E2F-regulated genes in Arabidopsis.
  Plant J, 33, 801-811.  
14633988 L.Di Stefano, M.R.Jensen, and K.Helin (2003).
E2F7, a novel E2F featuring DP-independent repression of a subset of E2F-regulated genes.
  EMBO J, 22, 6289-6298.  
12748276 P.H.Giangrande, T.C.Hallstrom, C.Tunyaplin, K.Calame, and J.R.Nevins (2003).
Identification of E-box factor TFE3 as a functional partner for the E2F3 transcription factor.
  Mol Cell Biol, 23, 3707-3720.  
12586394 R.Giraldo (2003).
Common domains in the initiators of DNA replication in Bacteria, Archaea and Eukarya: combined structural, functional and phylogenetic perspectives.
  FEMS Microbiol Rev, 26, 533-554.  
12237874 A.D.Saiz, M.Olvera, S.Rezk, B.A.Florentine, A.McCourty, and R.K.Brynes (2002).
Immunohistochemical expression of cyclin D1, E2F-1, and Ki-67 in benign and malignant thyroid lesions.
  J Pathol, 198, 157-162.  
11921304 C.Lee, and Y.Cho (2002).
Interactions of SV40 large T antigen and other viral proteins with retinoblastoma tumour suppressor.
  Rev Med Virol, 12, 81-92.  
12040123 C.S.Sullivan, and J.M.Pipas (2002).
T antigens of simian virus 40: molecular chaperones for viral replication and tumorigenesis.
  Microbiol Mol Biol Rev, 66, 179-202.  
12411495 S.Schlisio, T.Halperin, M.Vidal, and J.R.Nevins (2002).
Interaction of YY1 with E2Fs, mediated by RYBP, provides a mechanism for specificity of E2F function.
  EMBO J, 21, 5775-5786.  
11463371 B.D.Page, S.Guedes, D.Waring, and J.R.Priess (2001).
The C. elegans E2F- and DP-related proteins are required for embryonic asymmetry and negatively regulate Ras/MAPK signaling.
  Mol Cell, 7, 451-460.  
11433027 D.Huang, M.Jokela, J.Tuusa, S.Skog, K.Poikonen, and J.E.Syväoja (2001).
E2F mediates induction of the Sp1-controlled promoter of the human DNA polymerase epsilon B-subunit gene POLE2.
  Nucleic Acids Res, 29, 2810-2821.  
11296236 D.M.van Aalten, C.C.DiRusso, and J.Knudsen (2001).
The structural basis of acyl coenzyme A-dependent regulation of the transcription factor FadR.
  EMBO J, 20, 2041-2050.
PDB codes: 1h9g 1h9t
11447104 P.Van Roey, C.A.Waddling, K.M.Fox, M.Belfort, and V.Derbyshire (2001).
Intertwined structure of the DNA-binding domain of intron endonuclease I-TevI with its substrate.
  EMBO J, 20, 3631-3637.
PDB code: 1i3j
11013219 D.M.van Aalten, C.C.DiRusso, J.Knudsen, and R.K.Wierenga (2000).
Crystal structure of FadR, a fatty acid-responsive transcription factor with a novel acyl coenzyme A-binding fold.
  EMBO J, 19, 5167-5177.
PDB code: 1e2x
10698945 F.Rastinejad, T.Wagner, Q.Zhao, and S.Khorasanizadeh (2000).
Structure of the RXR-RAR DNA-binding complex on the retinoic acid response element DR1.
  EMBO J, 19, 1045-1054.
PDB code: 1dsz
10679470 K.S.Gajiwala, and S.K.Burley (2000).
Winged helix proteins.
  Curr Opin Struct Biol, 10, 110-116.  
10675335 M.A.Martínez-Balbás, U.M.Bauer, S.J.Nielsen, A.Brehm, and T.Kouzarides (2000).
Regulation of E2F1 activity by acetylation.
  EMBO J, 19, 662-671.  
10716934 M.Okuda, Y.Watanabe, H.Okamura, F.Hanaoka, Y.Ohkuma, and Y.Nishimura (2000).
Structure of the central core domain of TFIIEbeta with a novel double-stranded DNA-binding surface.
  EMBO J, 19, 1346-1356.
PDB codes: 1d8j 1d8k
10535945 M.Schade, C.J.Turner, R.Kühne, P.Schmieder, K.Lowenhaupt, A.Herbert, A.Rich, and H.Oschkinat (1999).
The solution structure of the Zalpha domain of the human RNA editing enzyme ADAR1 reveals a prepositioned binding surface for Z-DNA.
  Proc Natl Acad Sci U S A, 96, 12465-12470.
PDB code: 1qgp
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.

 

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