spacer
spacer
Go to PDB code: 
protein dna_rna links
Transcription/DNA PDB id
1j4w
Jmol
Contents
Protein chain
145 a.a. *
DNA/RNA
* Residue conservation analysis
PDB id:
1j4w
Name: Transcription/DNA
Title: Complex of the kh3 and kh4 domains of fbp with a single_stranded 29mer DNA oligonucleotide from the fuse element of thE C-myc oncogene
Structure: Fuse binding protein. Chain: a. Fragment: residues 278-447, numberered 5-174. Kh3 and kh4 domains.. Synonym: fbp, far upstream binding element protein. Engineered: yes. Mutation: yes. DNA (5'- d( Gp Tp A Tp Ap Tp Tp Cp Cp Cp Tp Cp Gp Gp G Ap Tp Tp Tp T
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes
NMR struc: 1 models
Authors: G.M.Clore,D.T.Braddock
Key ref:
D.T.Braddock et al. (2002). Structure and dynamics of KH domains from FBP bound to single-stranded DNA. Nature, 415, 1051-1056. PubMed id: 11875576 DOI: 10.1038/4151051a
Date:
30-Nov-01     Release date:   06-Mar-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q96AE4  (FUBP1_HUMAN) -  Far upstream element-binding protein 1
Seq:
Struc:
 
Seq:
Struc:
644 a.a.
145 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     RNA binding     1 term  

 

 
DOI no: 10.1038/4151051a Nature 415:1051-1056 (2002)
PubMed id: 11875576  
 
 
Structure and dynamics of KH domains from FBP bound to single-stranded DNA.
D.T.Braddock, J.M.Louis, J.L.Baber, D.Levens, G.M.Clore.
 
  ABSTRACT  
 
Gene regulation can be tightly controlled by recognition of DNA deformations that are induced by stress generated during transcription. The KH domains of the FUSE-binding protein (FBP), a regulator of c-myc expression, bind in vivo and in vitro to the single-stranded far-upstream element (FUSE), 1,500 base pairs upstream from the c-myc promoter. FBP bound to FUSE acts through TFIIH at the promoter. Here we report the solution structure of a complex between the KH3 and KH4 domains of FBP and a 29-base single-stranded DNA from FUSE. The KH domains recognize two sites, 9-10 bases in length, separated by 5 bases, with KH4 bound to the 5' site and KH3 to the 3' site. The central portion of each site comprises a tetrad of sequence 5'd-ATTC for KH4 and 5'd-TTTT for KH3. Dynamics measurements show that the two KH domains bind as articulated modules to single-stranded DNA, providing a flexible framework with which to recognize transient, moving targets.
 
  Selected figure(s)  
 
Figure 1.
Figure 1: Structural analysis of the FBP3/4-ssDNA complex. a, Structure-based sequence alignment of the KH domains of FBP3/4, NOVA-2, hnRNP K and vigilin. Residues of the KH3 and KH4 domains of FBP3/4 that contact ssDNA are indicated in red; the equivalent residues in the other KH domains are coloured green. b, ssDNAs used in the current study. NMR analysis was carried out on FBP3/4 complexed to M29 and intermolecular NOE contacts were confirmed using complexes of the isolated KH4 and KH3 domains bound to M5' and M3'(UT), respectively. c, Backbone superposition of the KH domains of FBP3/4 (KH3 and KH4 in red and blue, respectively), NOVA-2 (ref. 9) (green) and hnRNP K10 (grey). The C root mean square (r.m.s.) differences range from 1.1 Å for FBP KH3 and KH4 versus NOVA-2 KH3^9 to 1.6 Å for FBP KH3 versus hnRNP K KH3 (ref. 10). d, e, Stereoviews showing best-fit superposition of the final 80 simulated annealing structures (protein backbone in red, DNA in blue) and a summary of the observed intermolecular contacts (with H-bonds and salt bridges represented by purple arrows; the dashed arrows indicate potential electrostatic interactions) for the KH4 and KH3 domains, respectively. The coordinate precision for the protein backbone plus DNA heavy atoms is 0.30 and 0.38 Å for the KH3 and KH4 halves of the complex, respectively. (The corresponding values for all heavy atoms are 0.64 and 0.70 Å, respectively.) The experimental NMR restraints for the KH3 and KH4 halves of the complex are as follows: 1,095/949 interproton distances (including 50/68 intermolecular contacts), 244/261 torsion angles, 33/36 3J[HN[ ]]couplings, 120/121 13C / shifts, and 61/61 1D[NH], 47/39 1D[NC'] and 46/40 2D[HNC'] dipolar couplings. There are no interproton distance or torsion angle violations >0.5 Å and >5°, respectively; the 1D[NH] dipolar coupling R-factor30 is <10%. The percentage residues in the most favourable region of the Ramachandran map is 96% for KH3 and 90% for KH4. A complete table of structural statistics is provided in the Supplementary Information.
Figure 3.
Figure 3: Interdomain motion in the FBP3/4 -M29 ssDNA complex, a, 15N-{1H} NOE values as a function of residue number. The low NOE values for the 30-residue linker indicate high flexibility for this segment of the polypeptide chain. b, Correlation of 1D[NH] dipolar couplings of structurally equivalent residues measured for the KH4 and KH3 domains in the FBP3/4 -M29 complex. The correlation coefficient is 0.83, as expected for very similar structures, but the magnitude of the alignment tensor15 for the N -H vectors in the KH3 domain (-7.2 Hz) is half that in the KH4 domain (-14.5 Hz), diagnostic of significant interdomain motion16. c, Depiction of interdomain motion in the FBP3/4 -M29 complex. The red and blue cones indicate the slow motion of the KH4 and KH3 halves of the complex, respectively. The KH4 and KH3 domains are shown as red and blue ribbons, respectively, and the ssDNA bound to them is shown in purple and green, respectively. The 5-base linker for the ssDNA and 30-residue linker for the protein are depicted by blue and red dashed lines, respectively. The semi-cone angle , derived from the internal slow order parameter S2[s] is about 30° for both domains. D[ ]nd D[ ]represent the parallel and perpendicular components of an axially symmetric diffusion tensor. The two domains are aligned relative to the long axis of the diffusion tensor. The overall length of the complex and the separation between the two domains is indicated and calculated as described in the text. Nucleotide numbering is in italics.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2002, 415, 1051-1056) copyright 2002.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21082706 I.Mermershtain, I.Finarov, L.Klipcan, N.Kessler, H.Rozenberg, and M.G.Safro (2011).
Idiosyncrasy and identity in the prokaryotic phe-system: crystal structure of E. coli phenylalanyl-tRNA synthetase complexed with phenylalanine and AMP.
  Protein Sci, 20, 160-167.
PDB code: 3pco
21358629 J.P.Mackay, J.Font, and D.J.Segal (2011).
The prospects for designer single-stranded RNA-binding proteins.
  Nat Struct Mol Biol, 18, 256-261.  
20711187 C.D.Cukier, D.Hollingworth, S.R.Martin, G.Kelly, I.Díaz-Moreno, and A.Ramos (2010).
Molecular basis of FIR-mediated c-myc transcriptional control.
  Nat Struct Mol Biol, 17, 1058-1064.  
20080952 J.A.Chao, Y.Patskovsky, V.Patel, M.Levy, S.C.Almo, and R.H.Singer (2010).
ZBP1 recognition of beta-actin zipcode induces RNA looping.
  Genes Dev, 24, 148-158.
PDB code: 3krm
19844700 P.Bernadó (2010).
Effect of interdomain dynamics on the structure determination of modular proteins by small-angle scattering.
  Eur Biophys J, 39, 769-780.  
20175752 V.Papadopoulou, A.Postigo, E.Sánchez-Tilló, A.C.Porter, and S.D.Wagner (2010).
ZEB1 and CtBP form a repressive complex at a distal promoter element of the BCL6 locus.
  Biochem J, 427, 541-550.  
19907434 T.A.Brooks, and L.H.Hurley (2009).
The role of supercoiling in transcriptional control of MYC and its importance in molecular therapeutics.
  Nat Rev Cancer, 9, 849-861.  
19274444 X.Xu, P.H.Keizers, W.Reinle, F.Hannemann, R.Bernhardt, and M.Ubbink (2009).
Intermolecular dynamics studied by paramagnetic tagging.
  J Biomol NMR, 43, 247-254.  
18059478 G.V.Crichlow, H.Zhou, H.H.Hsiao, K.B.Frederick, M.Debrosse, Y.Yang, E.J.Folta-Stogniew, H.J.Chung, C.Fan, E.M.De la Cruz, D.Levens, E.Lolis, and D.Braddock (2008).
Dimerization of FIR upon FUSE DNA binding suggests a mechanism of c-myc inhibition.
  EMBO J, 27, 277-289.
PDB code: 2qfj
18559344 I.Keren, L.Klipcan, A.Bezawork-Geleta, M.Kolton, F.Shaya, and O.Ostersetzer-Biran (2008).
Characterization of the Molecular Basis of Group II Intron RNA Recognition by CRS1-CRM Domains.
  J Biol Chem, 283, 23333-23342.  
18761455 K.Chen, and N.Tjandra (2008).
Extended model free approach to analyze correlation functions of multidomain proteins in the presence of motional coupling.
  J Am Chem Soc, 130, 12745-12751.  
19015535 L.R.Benjamin, H.J.Chung, S.Sanford, F.Kouzine, J.Liu, and D.Levens (2008).
Hierarchical mechanisms build the DNA-binding specificity of FUSE binding protein.
  Proc Natl Acad Sci U S A, 105, 18296-18301.  
18422648 R.Valverde, L.Edwards, and L.Regan (2008).
Structure and function of KH domains.
  FEBS J, 275, 2712-2726.  
18701464 Z.Du, S.Fenn, R.Tjhen, and T.L.James (2008).
Structure of a Construct of a Human Poly(C)-binding Protein Containing the First and Second KH Domains Reveals Insights into Its Regulatory Mechanisms.
  J Biol Chem, 283, 28757-28766.  
18400844 Z.Zhang, D.Harris, and V.N.Pandey (2008).
The FUSE binding protein is a cellular factor required for efficient replication of hepatitis C virus.
  J Virol, 82, 5761-5773.  
17473849 B.M.Lunde, C.Moore, and G.Varani (2007).
RNA-binding proteins: modular design for efficient function.
  Nat Rev Mol Cell Biol, 8, 479-490.  
17437720 M.F.García-Mayoral, D.Hollingworth, L.Masino, I.Díaz-Moreno, G.Kelly, R.Gherzi, C.F.Chou, C.Y.Chen, and A.Ramos (2007).
The structure of the C-terminal KH domains of KSRP reveals a noncanonical motif important for mRNA degradation.
  Structure, 15, 485-498.
PDB codes: 2hh2 2hh3
16914741 H.J.Chung, J.Liu, M.Dundr, Z.Nie, S.Sanford, and D.Levens (2006).
FBPs are calibrated molecular tools to adjust gene expression.
  Mol Cell Biol, 26, 6584-6597.  
16428607 N.H.Chmiel, D.C.Rio, and J.A.Doudna (2006).
Distinct contributions of KH domains to substrate binding affinity of Drosophila P-element somatic inhibitor protein.
  RNA, 12, 283-291.  
16982642 S.D.Auweter, F.C.Oberstrass, and F.H.Allain (2006).
Sequence-specific binding of single-stranded RNA: is there a code for recognition?
  Nucleic Acids Res, 34, 4943-4959.  
15987884 A.Eisenmann, S.Schwarz, S.Prasch, K.Schweimer, and P.Rösch (2005).
The E. coli NusA carboxy-terminal domains are structurally similar and show specific RNAP- and lambdaN interaction.
  Protein Sci, 14, 2018-2029.
PDB codes: 1wcl 1wcn
16193062 B.Beuth, S.Pennell, K.B.Arnvig, S.R.Martin, and I.A.Taylor (2005).
Structure of a Mycobacterium tuberculosis NusA-RNA complex.
  EMBO J, 24, 3576-3587.
PDB codes: 2asb 2atw
15805463 J.C.Darnell, C.E.Fraser, O.Mostovetsky, G.Stefani, T.A.Jones, S.R.Eddy, and R.B.Darnell (2005).
Kissing complex RNAs mediate interaction between the Fragile-X mental retardation protein KH2 domain and brain polyribosomes.
  Genes Dev, 19, 903-918.  
15777841 M.J.Wortman, E.M.Johnson, and A.D.Bergemann (2005).
Mechanism of DNA binding and localized strand separation by Pur alpha and comparison with Pur family member, Pur beta.
  Biochim Biophys Acta, 1743, 64-78.  
15756586 M.Sidiqi, J.A.Wilce, C.J.Porter, A.Barker, P.J.Leedman, and M.C.Wilce (2005).
Formation of an alphaCP1-KH3 complex with UC-rich RNA.
  Eur Biophys J, 34, 423-429.  
15731341 M.Sidiqi, J.A.Wilce, J.P.Vivian, C.J.Porter, A.Barker, P.J.Leedman, and M.C.Wilce (2005).
Structure and RNA binding of the third KH domain of poly(C)-binding protein 1.
  Nucleic Acids Res, 33, 1213-1221.
PDB code: 1wvn
16077728 R.Singh, and J.Valcárcel (2005).
Building specificity with nonspecific RNA-binding proteins.
  Nat Struct Mol Biol, 12, 645-653.  
16055531 S.M.Stagg, and S.C.Harvey (2005).
Exploring the flexibility of ribosome recycling factor using molecular dynamics.
  Biophys J, 89, 2659-2666.  
16186123 Z.Du, J.K.Lee, R.Tjhen, S.Li, H.Pan, R.M.Stroud, and T.L.James (2005).
Crystal structure of the first KH domain of human poly(C)-binding protein-2 in complex with a C-rich strand of human telomeric DNA at 1.7 A.
  J Biol Chem, 280, 38823-38830.
PDB code: 2axy
14559893 D.C.Williams, M.Cai, and G.M.Clore (2004).
Molecular basis for synergistic transcriptional activation by Oct1 and Sox2 revealed from the solution structure of the 42-kDa Oct1.Sox2.Hoxb1-DNA ternary transcription factor complex.
  J Biol Chem, 279, 1449-1457.
PDB code: 1o4x
15123728 J.C.Stern, B.J.Anderson, T.J.Owens, and J.F.Schildbach (2004).
Energetics of the sequence-specific binding of single-stranded DNA by the F factor relaxase domain.
  J Biol Chem, 279, 29155-29159.  
15159542 K.B.Arnvig, S.Pennell, B.Gopal, and M.J.Colston (2004).
A high-affinity interaction between NusA and the rrn nut site in Mycobacterium tuberculosis.
  Proc Natl Acad Sci U S A, 101, 8325-8330.  
15367696 K.Musunuru, and R.B.Darnell (2004).
Determination and augmentation of RNA sequence specificity of the Nova K-homology domains.
  Nucleic Acids Res, 32, 4852-4861.  
15041689 M.C.Murphy, I.Rasnik, W.Cheng, T.M.Lohman, and T.Ha (2004).
Probing single-stranded DNA conformational flexibility using fluorescence spectroscopy.
  Biophys J, 86, 2530-2537.  
15039586 P.H.Backe, R.B.Ravelli, E.Garman, and S.Cusack (2004).
Crystallization, microPIXE and preliminary crystallographic analysis of the complex between the third KH domain of hnRNP K and single-stranded DNA.
  Acta Crystallogr D Biol Crystallogr, 60, 784-787.  
14718656 T.Kasai, M.Inoue, S.Koshiba, T.Yabuki, M.Aoki, E.Nunokawa, E.Seki, T.Matsuda, N.Matsuda, Y.Tomo, M.Shirouzu, T.Terada, N.Obayashi, H.Hamana, N.Shinya, A.Tatsuguchi, S.Yasuda, M.Yoshida, H.Hirota, Y.Matsuo, K.Tani, H.Suzuki, T.Arakawa, P.Carninci, J.Kawai, Y.Hayashizaki, T.Kigawa, and S.Yokoyama (2004).
Solution structure of a BolA-like protein from Mus musculus.
  Protein Sci, 13, 545-548.
PDB code: 1v9j
15161980 T.Li, E.Evdokimov, R.F.Shen, C.C.Chao, E.Tekle, T.Wang, E.R.Stadtman, D.C.Yang, and P.B.Chock (2004).
Sumoylation of heterogeneous nuclear ribonucleoproteins, zinc finger proteins, and nuclear pore complex proteins: a proteomic analysis.
  Proc Natl Acad Sci U S A, 101, 8551-8556.  
15383143 Y.Huang, and D.Kowalski (2004).
PATTERNFINDER: combined analysis of DNA regulatory sequences and double-helix stability.
  BMC Bioinformatics, 5, 134.  
15331611 Z.Du, J.Yu, Y.Chen, R.Andino, and T.L.James (2004).
Specific recognition of the C-rich strand of human telomeric DNA and the RNA template of human telomerase by the first KH domain of human poly(C)-binding protein-2.
  J Biol Chem, 279, 48126-48134.  
12592003 A.Ramos, D.Hollingworth, and A.Pastore (2003).
The role of a clinically important mutation in the fold and RNA-binding properties of KH motifs.
  RNA, 9, 293-298.  
12686540 D.M.Jacobs, K.Saxena, M.Vogtherr, P.Bernado, M.Pons, and K.M.Fiebig (2003).
Peptide binding induces large scale changes in inter-domain mobility in human Pin1.
  J Biol Chem, 278, 26174-26182.  
14500828 K.M.Goolsby, and D.J.Shapiro (2003).
RNAi-mediated depletion of the 15 KH domain protein, vigilin, induces death of dividing and non-dividing human cells but does not initially inhibit protein synthesis.
  Nucleic Acids Res, 31, 5644-5653.  
12667456 N.G.Kolev, and P.W.Huber (2003).
VgRBP71 stimulates cleavage at a polyadenylation signal in Vg1 mRNA, resulting in the removal of a cis-acting element that represses translation.
  Mol Cell, 11, 745-755.  
12093748 D.T.Braddock, J.L.Baber, D.Levens, and G.M.Clore (2002).
Molecular basis of sequence-specific single-stranded DNA recognition by KH domains: solution structure of a complex between hnRNP K KH3 and single-stranded DNA.
  EMBO J, 21, 3476-3485.
PDB code: 1j5k
12358751 M.Rehbein, K.Wege, F.Buck, M.Schweizer, D.Richter, and S.Kindler (2002).
Molecular characterization of MARTA1, a protein interacting with the dendritic targeting element of MAP2 mRNAs.
  J Neurochem, 82, 1039-1046.  
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.