2H8R

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

> Summary

Summary for 2H8R

DescriptorHepatocyte nuclear factor 1-beta/DNA Complex
Functional Keywordstrasncription factor, pou, homeo, protein-dna, human disease, transcription activator-dna complex, transcription activator/dna
Biological sourceHomo sapiens (human)
Cellular locationNucleus P35680
Total number of polymer chains4
Total molecular weight63689.22
Authors
Lu, P.,Rha, G.B.,Chi, Y.I. (deposition date: 2006-06-07, release date: 2007-06-19, modification date: 2009-02-24)
Primary citation
Lu, P.,Rha, G.B.,Chi, Y.I.
Structural basis of disease-causing mutations in hepatocyte nuclear factor 1beta.
Biochemistry, 46:12071-12080, 2007
PubMed: 17924661
DOI: 10.1021/bi7010527
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (3.2 Å)
NMR Information
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.2667510.8%21.8%0MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 2h8r
no rotation
Molmil generated image of 2h8r
rotated about x axis by 90°
Molmil generated image of 2h8r
rotated about y axis by 90°

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
E5'-D(*CP*TP*TP*GP*GP*TP*TP*AP*AP*TP*AP*AP*TP*TP*CP*AP*CP*CP*AP*G)-3'polymer206108.01
F5'-D(*GP*CP*TP*GP*GP*TP*GP*AP*AP*TP*TP*AP*TP*TP*AP*AP*CP*CP*AP*A)-3'polymer206157.11
A, BHepatocyte nuclear factor 1-betapolymer22125712.12
UniProt (P35680)
Pfam (PF00046)
Pfam (PF04814)
Homo sapiens (human)@PDBjHNF-1beta, HNF-1B, Variant hepatic nuclear factor 1, VHNF1, Homeoprotein LFB3, Transcription factor 2, TCF-2
waterwater18.07

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains4
Total molecular weight63689.2
Non-Polymers*Number of molecules0
Total molecular weight0.0
All*Total molecular weight63689.2
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (3.2 Å)

Cell axes174.689174.68972.434
Cell angles90.0090.00120.00
SpacegroupH 3
Resolution limits20.00 - 3.20
the highest resolution shell value3.282 - 3.201
R-factor0.22614
R-work0.22292
the highest resolution shell value0.230
R-free0.28990
the highest resolution shell value0.415
RMSD bond length0.079
RMSD bond angle5.450

Data Collection Statistics

Resolution limits27.90 - 3.20
the highest resolution shell value -
Number of reflections12582
Rmerge_l_obs0.088
the highest resolution shell value0.313
Completeness93.9
Redundancy6.3
the highest resolution shell value3.8
I/sigma(I)0

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, HANGING DROP8295

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
111PEG300
211PEG8000
311glycerol
411Tris
511H2O
612PEG300
712PEG8000
812Tris
912H2O
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
A0005654cellular_componentnucleoplasm
A0005634cellular_componentnucleus
A0005667cellular_componenttranscription factor complex
A0001159molecular_functioncore promoter proximal region DNA binding
A0003677molecular_functionDNA binding
A0042803molecular_functionprotein homodimerization activity
A0000977molecular_functionRNA polymerase II regulatory region sequence-specific DNA binding
A0003705molecular_functiontranscription factor activity, RNA polymerase II distal enhancer sequence-specific binding
A0003700molecular_functiontranscription factor activity, sequence-specific DNA binding
A0009952biological_processanterior/posterior pattern specification
A0048754biological_processbranching morphogenesis of an epithelial tube
A0032922biological_processcircadian regulation of gene expression
A0048557biological_processembryonic digestive tract morphogenesis
A0031018biological_processendocrine pancreas development
A0001714biological_processendodermal cell fate specification
A0050673biological_processepithelial cell proliferation
A0048806biological_processgenitalia development
A0061017biological_processhepatoblast differentiation
A0070365biological_processhepatocyte differentiation
A0030902biological_processhindbrain development
A0001826biological_processinner cell mass cell differentiation
A0030073biological_processinsulin secretion
A0001822biological_processkidney development
A0072181biological_processmesonephric duct formation
A0061296biological_processnegative regulation of mesenchymal cell apoptotic process involved in mesonephric nephron morphogenesis
A1900212biological_processnegative regulation of mesenchymal cell apoptotic process involved in metanephros development
A0000122biological_processnegative regulation of transcription from RNA polymerase II promoter
A0007219biological_processNotch signaling pathway
A0060261biological_processpositive regulation of transcription initiation from RNA polymerase II promoter
A0045893biological_processpositive regulation of transcription, DNA-templated
A0039020biological_processpronephric nephron tubule development
A0048793biological_processpronephros development
A0065004biological_processprotein-DNA complex assembly
A0072095biological_processregulation of branch elongation involved in ureteric bud branching
A0042663biological_processregulation of endodermal cell fate specification
A0035565biological_processregulation of pronephros size
A0030111biological_processregulation of Wnt signaling pathway
A0042493biological_processresponse to drug
A0009749biological_processresponse to glucose
A0014070biological_processresponse to organic cyclic compound
A0006351biological_processtranscription, DNA-templated
A0060677biological_processureteric bud elongation
B0005654cellular_componentnucleoplasm
B0005634cellular_componentnucleus
B0005667cellular_componenttranscription factor complex
B0001159molecular_functioncore promoter proximal region DNA binding
B0003677molecular_functionDNA binding
B0042803molecular_functionprotein homodimerization activity
B0000977molecular_functionRNA polymerase II regulatory region sequence-specific DNA binding
B0003705molecular_functiontranscription factor activity, RNA polymerase II distal enhancer sequence-specific binding
B0003700molecular_functiontranscription factor activity, sequence-specific DNA binding
B0009952biological_processanterior/posterior pattern specification
B0048754biological_processbranching morphogenesis of an epithelial tube
B0032922biological_processcircadian regulation of gene expression
B0048557biological_processembryonic digestive tract morphogenesis
B0031018biological_processendocrine pancreas development
B0001714biological_processendodermal cell fate specification
B0050673biological_processepithelial cell proliferation
B0048806biological_processgenitalia development
B0061017biological_processhepatoblast differentiation
B0070365biological_processhepatocyte differentiation
B0030902biological_processhindbrain development
B0001826biological_processinner cell mass cell differentiation
B0030073biological_processinsulin secretion
B0001822biological_processkidney development
B0072181biological_processmesonephric duct formation
B0061296biological_processnegative regulation of mesenchymal cell apoptotic process involved in mesonephric nephron morphogenesis
B1900212biological_processnegative regulation of mesenchymal cell apoptotic process involved in metanephros development
B0000122biological_processnegative regulation of transcription from RNA polymerase II promoter
B0007219biological_processNotch signaling pathway
B0060261biological_processpositive regulation of transcription initiation from RNA polymerase II promoter
B0045893biological_processpositive regulation of transcription, DNA-templated
B0039020biological_processpronephric nephron tubule development
B0048793biological_processpronephros development
B0065004biological_processprotein-DNA complex assembly
B0072095biological_processregulation of branch elongation involved in ureteric bud branching
B0042663biological_processregulation of endodermal cell fate specification
B0035565biological_processregulation of pronephros size
B0030111biological_processregulation of Wnt signaling pathway
B0042493biological_processresponse to drug
B0009749biological_processresponse to glucose
B0014070biological_processresponse to organic cyclic compound
B0006351biological_processtranscription, DNA-templated
B0060677biological_processureteric bud elongation
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
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Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
PS000272'Homeobox' domain signature. [LIVMFYG]-[ASLVR]-x(2)-[LIVMSTACN]-x-[LIVM]-{Y}-x(2)-{L}-[LIV]
ChainResidueDetails
ANA*
BNA*

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Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
SWS_FT_FI11Homeobox; HNF1-type.
ChainResidueDetails
ANA*

SWS_FT_FI21Homeobox; HNF1-type.
ChainResidueDetails
BNA*

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Catalytic Information from CSA

site_idNumber of ResiduesDetails
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Catalytic Information from CATRES

site_idNumber of ResiduesDetails

> Sequence Neighbor

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