2H8R

Hepatocyte Nuclear Factor 1b bound to DNA: MODY5 Gene Product

• PDB DOI: https://doi.org/10.2210/pdb2H8R/pdb
• NAKB: 2H8R

• Classification: TRANSCRIPTION ACTIVATOR/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-06-07 Released: 2007-06-19 
• Deposition Author(s): Lu, P., Rha, G.B., Chi, Y.I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.290 
• R-Value Work: 0.223 
• R-Value Observed: 0.226 

Literature

Structural basis of disease-causing mutations in hepatocyte nuclear factor 1beta.

Lu, P., Rha, G.B., Chi, Y.I.

(2007) Biochemistry 46: 12071-12080

• PubMed: 17924661 
• DOI: https://doi.org/10.1021/bi7010527
• Primary Citation of Related Structures:  
  2H8R


• PubMed Abstract: 
  

  HNF1beta is an atypical POU transcription factor that participates in a hierarchical network of transcription factors controlling the development and proper function of vital organs such as liver, pancreas, and kidney. Many inheritable mutations on HNF1beta are the monogenic causes of diabetes and several kidney diseases. To elucidate the molecular mechanism of its function and the structural basis of mutations, we have determined the crystal structure of human HNF1beta DNA binding domain in complex with a high-affinity promoter. Disease-causing mutations have been mapped to our structure, and their predicted effects have been tested by a set of biochemical/ functional studies. These findings together with earlier findings with a homologous protein HNF1alpha, help us to understand the structural basis of promoter recognition by these atypical POU transcription factors and the site-specific functional disruption by disease-causing mutations.

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Organizational Affiliation: 

Department of Molecular and Cellular Biochemistry, Center for Structural Biology, University of Kentucky, Lexington, Kentucky 40536, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 63.69 kDa 
• Atom Count: 3,736 
• Modelled Residue Count: 392 
• Deposited Residue Count: 482 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Hepatocyte nuclear factor 1-beta	C [auth A], D [auth B]	221	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P35680 (Homo sapiens) Explore P35680  Go to UniProtKB:  P35680
PHAROS:  P35680 GTEx:  ENSG00000275410

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*CP*TP*TP*GP*GP*TP*TP*AP*AP*TP*AP*AP*TP*TP*CP*AP*CP*CP*AP*G)-3'	A [auth E]	20	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*GP*CP*TP*GP*GP*TP*GP*AP*AP*TP*TP*AP*TP*TP*AP*AP*CP*CP*AP*A)-3'	B [auth F]	20	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.290 
• R-Value Work: 0.223 
• R-Value Observed: 0.226 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 174.689	α = 90
b = 174.689	β = 90
c = 72.434	γ = 120

Software Package:

Software Name	Purpose
SERGUI	data collection
HKL-2000	data reduction
MOLREP	phasing
REFMAC	refinement
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-06-19 
Deposition Author(s): Lu, P., Rha, G.B., Chi, Y.I.

Revision History  

• Version 1.0: 2007-06-19
  Type: Initial release
  
• Version 1.1: 2008-02-04
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Refinement description