PDBsum entry: 1j4w

Transcription/DNA

PDB-id: 1j4w

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PROCHECK

Protein chain

145 a.a. *

DNA/RNA

* Residue conservation analysis

Tools

Clefts Calculation

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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

UniProt:

Q96AE4 (FUBP1_HUMAN)

Seq:

Struc:

Seq:

Struc:

Seq:

644 a.a.

Struc:

145 a.a.*

Key:	PfamA domain	PfamB domain
Secondary structure	CATH domain

* PDB and UniProt seqs differ at 4 residue positions (black crosses)

Resolution:

not givenÅ

NMR structure:

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

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Key reference

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.