1J4W | pdb_00001j4w

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

• PDB DOI: https://doi.org/10.2210/pdb1J4W/pdb
• NAKB: 1J4W

• Classification: TRANSCRIPTION/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2001-11-30 Released: 2002-03-06 
• Deposition Author(s): Clore, G.M., Braddock, D.T.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 80 
• Conformers Submitted: 1 
• Selection Criteria: REGULARIZED MEAN STRUCTURE 

Literature

Structure and dynamics of KH domains from FBP bound to single-stranded DNA.

Braddock, D.T., Louis, J.M., Baber, J.L., Levens, D., Clore, G.M.

(2002) Nature 415: 1051-1056

• PubMed: 11875576 
• DOI: https://doi.org/10.1038/4151051a
• Primary Citation Related Structures: 
  1J4W


• PubMed 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.

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Organizational Affiliation: 
• Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 27.52 kDa 
• Atom Count: 1,413 
• Modeled Residue Count: 160 
• Deposited Residue Count: 203 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
FUSE binding protein	B [auth A]	174	Homo sapiens	Mutation(s): 1
UniProt & NIH Common Fund Data Resources
Find proteins for Q96AE4 (Homo sapiens) Explore Q96AE4  Go to UniProtKB:  Q96AE4
PHAROS:  Q96AE4 GTEx:  ENSG00000162613

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*TP*A*TP*AP*TP*TP*CP*CP*CP*TP*CP*GP*GP*G*AP*TP*TP*TP*TP*TP*TP*AP*TP*TP*TP*TP*GP*T)-3')	A [auth B]	29	N/A

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 80 
• Conformers Submitted: 1 
• Selection Criteria: REGULARIZED MEAN STRUCTURE 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-03-06 
Deposition Author(s): Clore, G.M., Braddock, D.T.

Revision History  

• Version 1.0: 2002-03-06
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-10-27
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2023-12-27
  Changes: Data collection