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- PDB-8pi9: DNA binding domain of HNF-1A bound to P2-HNF4A promoter DNA varia... -

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Basic information

Entry
Database: PDB / ID: 8pi9
TitleDNA binding domain of HNF-1A bound to P2-HNF4A promoter DNA variant (P2 -181G>A)
Components
  • Chains: E
  • Chains: F
  • Hepatocyte nuclear factor 1-alpha
KeywordsDNA BINDING PROTEIN / Transcription factor / gene transcription / HNF-1A / HNF4A / MODY
Function / homology
Function and homology information


renal D-glucose absorption / pancreas development / insulin secretion / D-glucose import / Regulation of gene expression in beta cells / positive regulation of transcription initiation by RNA polymerase II / liver development / glucose homeostasis / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific ...renal D-glucose absorption / pancreas development / insulin secretion / D-glucose import / Regulation of gene expression in beta cells / positive regulation of transcription initiation by RNA polymerase II / liver development / glucose homeostasis / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / protein dimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein heterodimerization activity / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleus / cytoplasm
Similarity search - Function
Hepatocyte nuclear factor 1, alpha isoform C-terminal / Hepatocyte nuclear factor 1 (HNF-1), alpha isoform C terminus / Hepatocyte nuclear factor 1, beta isoform, C-terminal / Hepatocyte nuclear factor 1, N-terminal domain superfamily / Hepatocyte nuclear factor 1 / Hepatocyte nuclear factor 1 (HNF-1), beta isoform C terminus / Hepatocyte nuclear factor 1, N-terminal / HNF-1, dimerization domain / HNF-1, POU-specific (POUs) atypical domain / Hepatocyte nuclear factor 1 (HNF-1), N terminus ...Hepatocyte nuclear factor 1, alpha isoform C-terminal / Hepatocyte nuclear factor 1 (HNF-1), alpha isoform C terminus / Hepatocyte nuclear factor 1, beta isoform, C-terminal / Hepatocyte nuclear factor 1, N-terminal domain superfamily / Hepatocyte nuclear factor 1 / Hepatocyte nuclear factor 1 (HNF-1), beta isoform C terminus / Hepatocyte nuclear factor 1, N-terminal / HNF-1, dimerization domain / HNF-1, POU-specific (POUs) atypical domain / Hepatocyte nuclear factor 1 (HNF-1), N terminus / POU-specific (POUs) atypical domain profile. / HNF-1 dimerization (HNF-p1) domain profile. / 'Homeobox' domain signature. / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Lambda repressor-like, DNA-binding domain superfamily / Homeobox-like domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Hepatocyte nuclear factor 1-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKind, L. / Myllykoski, M. / Raasakka, A. / Kursula, P.
Funding support Norway, Denmark, 4items
OrganizationGrant numberCountry
Research Council of Norway245828 Norway
Research Council of Norway245922 Norway
Research Council of Norway240413 Norway
Novo Nordisk Foundation54741 Denmark
CitationJournal: JCI Insight / Year: 2024
Title: Molecular mechanism of HNF-1A-mediated HNF4A gene regulation and promoter-driven HNF4A-MODY diabetes.
Authors: Kind, L. / Molnes, J. / Tjora, E. / Raasakka, A. / Myllykoski, M. / Colclough, K. / Saint-Martin, C. / Adelfalk, C. / Dusatkova, P. / Pruhova, S. / Valtonen-Andre, C. / Bellanne-Chantelot, C. ...Authors: Kind, L. / Molnes, J. / Tjora, E. / Raasakka, A. / Myllykoski, M. / Colclough, K. / Saint-Martin, C. / Adelfalk, C. / Dusatkova, P. / Pruhova, S. / Valtonen-Andre, C. / Bellanne-Chantelot, C. / Arnesen, T. / Kursula, P. / Njolstad, P.R.
History
DepositionJun 21, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Chains: E
F: Chains: F
A: Hepatocyte nuclear factor 1-alpha
B: Hepatocyte nuclear factor 1-alpha


Theoretical massNumber of molelcules
Total (without water)58,6354
Polymers58,6354
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7350 Å2
ΔGint-42 kcal/mol
Surface area23990 Å2
Unit cell
Length a, b, c (Å)49.008, 53.065, 202.671
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: DNA chain Chains: E


Mass: 6387.158 Da / Num. of mol.: 1 / Mutation: NM_175914.5 c.-181G>A (g.42984264) / Source method: obtained synthetically / Details: NM_175914.5 c.-181G>A (g.42984264) / Source: (synth.) Homo sapiens (human)
#2: DNA chain Chains: F


Mass: 6494.247 Da / Num. of mol.: 1 / Mutation: NM_175914.5 c.-181G>A (g.42984264) / Source method: obtained synthetically / Details: NM_175914.5 c.-181G>A (g.42984264) / Source: (synth.) Homo sapiens (human)
#3: Protein Hepatocyte nuclear factor 1-alpha / HNF-1-alpha / HNF-1A / Liver-specific transcription factor LF-B1 / LFB1 / Transcription factor 1 / TCF-1


Mass: 22876.746 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HNF1A, TCF1 / Plasmid: pTH27 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: P20823

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.27 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ca acetate, 0.1 M Na cacodylate, pH 6.5, 40% v/v PEG300

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.8→47.64 Å / Num. obs: 13600 / % possible obs: 99.1 % / Redundancy: 7.4 % / Biso Wilson estimate: 101.02 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.116 / Net I/σ(I): 9.77
Reflection shellResolution: 2.8→2.92 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 0.43 / Num. unique obs: 994 / CC1/2: 0.307 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEJan 10, 2022data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→47.64 Å / SU ML: 0.5221 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 39.2287
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2934 1217 4.98 %
Rwork0.2339 23213 -
obs0.2368 13481 97.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 120.12 Å2
Refinement stepCycle: LAST / Resolution: 2.8→47.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2802 855 0 0 3657
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00423815
X-RAY DIFFRACTIONf_angle_d0.69825327
X-RAY DIFFRACTIONf_chiral_restr0.0391569
X-RAY DIFFRACTIONf_plane_restr0.0092553
X-RAY DIFFRACTIONf_dihedral_angle_d23.4628789
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.920.44751300.43972199X-RAY DIFFRACTION83.09
2.92-3.050.44071270.39832619X-RAY DIFFRACTION99.1
3.05-3.210.38031390.40432612X-RAY DIFFRACTION99.75
3.21-3.410.3221370.2742655X-RAY DIFFRACTION99.39
3.41-3.670.37361350.27242592X-RAY DIFFRACTION98.84
3.67-4.040.31821440.26272645X-RAY DIFFRACTION98.94
4.04-4.630.29611340.22222613X-RAY DIFFRACTION99.71
4.63-5.830.27271380.22632642X-RAY DIFFRACTION99.57
5.83-47.640.23211330.17122636X-RAY DIFFRACTION99.46
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.69617018513-2.757039176813.782653307052.71028301224-2.943513531874.382521690040.4158317896251.97299215644-0.196656448861-0.789841030170.4726868101160.803855386225-1.606073524410.119921303771-0.4971384750561.42778951215-0.017579251917-0.01753710628061.268856532930.3416266068521.090570611651.42625315623-17.77350908245.0018934303
24.737219440510.561609773041-1.402642852945.05001186747-3.187354008585.75091876329-0.5219503018850.1201414506210.6222317235050.7762900067770.1767851406210.341174562459-1.600483318290.5351522768040.2776202018681.020118890370.1159539687420.03846365204630.584115150439-0.0602622334760.742503943238-3.9171441047-0.93509098986626.9038376592
33.709244844021.19522905304-0.8577839397232.67216764071-2.586938813096.085710689130.2859271677940.634257081060.431715015299-0.0328506241170.000533108777010.972279230502-1.484700648631.64082639407-0.001669623458711.854471387360.1343210954410.07459463685261.436522491950.3286513658491.1176921724-10.914673096318.63803604028.61439177769
43.323450739822.79259941508-2.787990299044.98645242271.305896923067.1322087806-0.3005733160080.7381489800740.430106788479-1.06710275659-0.4526132594150.24251368468-0.4996802793870.06729421813920.5886838645211.3814372190.207351646889-0.09819399432781.197296248540.1050030528851.06664640147-10.809335965411.658135818712.3206586216
55.45192428144-3.70036961382-2.459667901945.264499657412.293277982974.926071270270.283604654873-0.259605721715-0.8419384198940.373764044792-0.2835159140760.522309845755-0.08564644681051.091119509120.07697063121.338503876760.0475371450490.007380332572780.839143818510.06892909254820.97530689791.14468876257-9.5177118758637.4718758722
66.660247174183.16672462065-0.9792375395576.483451648490.8328465460187.56027203496-1.021019863561.468988689820.175722233881-1.326913477860.762119362672-0.459997748520.7143686642050.2675319227450.2380668019951.243681790880.05513591835810.1645637416570.978934401516-0.07189931469060.8465239457035.15251905306-5.88355888224.42212169135
77.80779250463-0.419710845969-0.4038974327362.984796282080.51687916626.22659887866-0.08493800195840.9775958271550.00494968986787-0.2017304882890.271577661157-0.4616344343220.2128442028270.3086435324130.03634658806681.07807472704-0.1189767854430.05172907602520.77913390654-0.0526000050180.8277231753755.1962243266-3.30170963868.08171995321
82.780203987321.22731976297-1.328266164433.86378151209-0.1953461937896.446408750020.237056007676-0.150178556422-0.85682561385-0.449003496695-0.294819640665-0.004322706458560.4323629654620.2415158455510.1654042338741.294447040950.304425421005-0.06100447629230.8422065116050.1294461681751.205957374374.67293477989-22.350097848326.430400357
96.18108261027-4.688547380434.276456946253.57872472848-3.556571852715.765561409680.4524575799880.601584504386-0.01007851820610.987882006262-0.8184732201811.073662049080.1959862372481.424765999320.8576777159830.9959703034470.2266741378380.2829922911330.871961206701-0.1171135210341.30088259313-20.664476681524.683055828852.8208143165
103.60042638845-0.006988690783650.4283181873092.56130098667-2.60602818057.12486564330.135388254101-0.145397960724-0.1740420118060.197281858765-0.2062371982750.1604272131860.06933909406060.4686047648620.05939574031030.7939243514850.01779237656950.05546224958310.664839009275-0.07515251686480.792757066572-15.75393442134.6825243127844.5374304536
115.21876007026-0.03723768701930.6091502116542.891754101172.423541793457.21973684938-0.09370315010020.66176581849-0.0576194885787-0.982987926927-0.0006412768785150.54743796269-0.884575760218-0.3556034947880.255011116171.126521758140.199715939204-0.0525531330330.7160000932960.115070306670.923227804481-26.234631246711.818001882921.1103848084
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'E' and (resid 301 through 305 )EA301 - 305
22chain 'E' and (resid 306 through 315 )EA306 - 315
33chain 'E' and (resid 316 through 321 )EA316 - 321
44chain 'F' and (resid 401 through 410 )FB401 - 410
55chain 'F' and (resid 411 through 421 )FB411 - 421
66chain 'A' and (resid 93 through 137 )AC93 - 1371 - 45
77chain 'A' and (resid 138 through 180 )AC138 - 18046 - 88
88chain 'A' and (resid 200 through 276 )AC200 - 27689 - 165
99chain 'B' and (resid 84 through 93 )BD84 - 931 - 10
1010chain 'B' and (resid 94 through 184 )BD94 - 18411 - 101
1111chain 'B' and (resid 201 through 276 )BD201 - 276102 - 177

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