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

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Basic information

Entry
Database: PDB / ID: 8pia
TitleDNA binding domain of HNF-1A bound to P2-HNF4A promoter DNA variant (P2 -181G>T)
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 glucose absorption / pancreas development / insulin secretion / 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 / protein dimerization activity ...renal glucose absorption / pancreas development / insulin secretion / 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 / protein dimerization activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin / regulation of transcription by RNA polymerase II / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7275
Polymers58,6354
Non-polymers921
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.695, 48.752, 215.811
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: 6378.144 Da / Num. of mol.: 1 / Mutation: NM_175914.5 c.-181G>T (g.42984264) / Source method: obtained synthetically / Details: NM_175914.5 c.-181G>T (g.42984264) / Source: (synth.) Homo sapiens (human)
#2: DNA chain Chains: F


Mass: 6503.261 Da / Num. of mol.: 1 / Mutation: NM_175914.5 c.-181G>T (g.42984264) / Source method: obtained synthetically / Details: NM_175914.5 c.-181G>T (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
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
Has ligand of interestN

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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: 2.18 Å3/Da / Density % sol: 43.69 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Citrate, pH 5.0, 20% w/v PEG 6000

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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→47.55 Å / Num. obs: 12346 / % possible obs: 92.4 % / Redundancy: 8.9 % / Biso Wilson estimate: 81.36 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.199 / Net I/σ(I): 7.15
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 9.2 % / Mean I/σ(I) obs: 0.63 / Num. unique obs: 986 / CC1/2: 0.289 / % possible all: 98.3

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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→47.55 Å / SU ML: 0.5795 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 44.0215
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3 1112 4.99 %
Rwork0.2451 21184 -
obs0.2481 12303 91.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 99.18 Å2
Refinement stepCycle: LAST / Resolution: 2.8→47.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2684 855 6 0 3545
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00373701
X-RAY DIFFRACTIONf_angle_d0.63095172
X-RAY DIFFRACTIONf_chiral_restr0.0326552
X-RAY DIFFRACTIONf_plane_restr0.0046530
X-RAY DIFFRACTIONf_dihedral_angle_d25.894774
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.930.39431450.41242634X-RAY DIFFRACTION91.38
2.93-3.080.39341540.36892902X-RAY DIFFRACTION99.03
3.08-3.280.32551570.31362919X-RAY DIFFRACTION99.87
3.28-3.530.3331140.25922111X-RAY DIFFRACTION73.68
3.53-3.870.33091100.30082228X-RAY DIFFRACTION80.01
3.93-4.450.29261300.23292621X-RAY DIFFRACTION99.82
4.45-5.60.31441480.24072856X-RAY DIFFRACTION99.4
5.6-47.550.25721540.18982913X-RAY DIFFRACTION99.8
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)
12.00800022122-7.29591886929-0.1842275871936.48501408498-2.673679732554.99245833974-0.01602320063321.52630061522-0.1333299188091.16659703257-0.295085222588-1.46507212214-1.06781177898-0.4887731750720.4372575820081.237843709780.02140591719310.2905367725451.37732538959-0.2306483085371.06269193999-4.36046769707-14.10501593034.86229205312
28.097612611120.711131463448-0.9646120750016.819968719814.885182108976.081883860890.319725376339-0.268071950151.040944368340.0383064757839-1.005905584110.719033510780.844518367965-2.201968187910.5308022380221.02205319875-0.00324109754980.0057924597931.09874593784-0.159901356190.704167974028-16.0868509058-5.9036058447325.6449944242
32.598228262643.627895841932.142789968375.437939470664.665044628989.782080477220.4061874153060.5353605503170.4929648237071.700553440620.2671122982820.8402162686181.99353222888-2.64294779805-1.008723280751.466989543080.2846118867790.3393222345951.618301878820.1865969818360.768397178804-30.9771344512.1020896810644.6278293256
41.092325790550.553604953026-0.2771056797782.064769757630.4569539651481.000499146240.278720127148-0.900058069399-0.2819446934520.790332240375-0.843152448242-0.1696411372190.08275137510440.599375407229-0.03615919129042.628743107950.2433845701720.4235918695032.151450948850.3435742389960.29091083082-31.92927096895.3443797634456.4380912691
57.36073181277-2.691129449654.738251702395.97907268377-2.528164097415.02399174350.1221941133262.54473319744-0.04731455222681.43232910042-0.3596371755730.936739451542-1.1191603122.301521052830.1606141286541.632853129140.1376995002240.2893581601211.47397735783-0.3073682518510.907168307942-26.52853035017.8532619554748.957101823
64.600389604140.499827819321-0.2441269171346.94383021903-2.882673134337.59875595493-1.025792268830.40250405704-0.7883010968760.418159905110.286059437411-0.8167763731420.895152861541-1.312479831190.7251937266651.03308362857-0.01315671684320.1587636089590.926596833335-0.1654209930840.807372262418-17.9975204748-3.870650500928.2613212121
71.817364861592.12783926606-3.041491199112.566691414-3.197300553246.807929104070.04148577238642.50742590048-1.78680087224-1.796872482981.36195999747-1.452329413580.0327772697512-1.01291814048-1.041529630741.986913276240.406469244644-0.08434251376591.8234924628-0.2837606573490.662283215893-10.0621227334-18.82576035799.31141573868
80.9992036705910.6369112159861.716369491660.8631670222151.295102336363.03755070907-0.3207304932590.1805105350960.0124332125065-0.3615920964850.2082588102760.0482020614934-0.332140875633-0.0299901113658-0.09406118020341.89710266370.771687265425-0.3712468021892.9912484466-0.3473580283580.13498245394-7.0764487048-19.5184403121-2.6393726392
96.125659880410.704267843467-0.4404175981045.03212111349-0.9319930552535.54568405052-0.0940759063814-1.64530802588-0.4810524701670.07750386003920.180363946754-0.01732180794730.2178236045150.410312176825-0.06907059909360.594608281872-0.02275674945880.007056336686420.9082406401840.05901530438990.448517481574-7.60778161892-13.074226409545.2321930048
102.39123652957-0.2548073954340.554013238832.54364830185-1.655189332225.22271906215-0.1035749340310.7569556088950.170747648981-0.721078961182-0.143454630172-0.2117709861730.4265483140070.6026778221180.2395331663820.7585363601920.008645110928120.03501230606250.822851814135-0.06098970800160.5213664071085.36426035488-13.771482521521.2777393178
111.203784527170.2468094661711.165809050825.860540186820.7439216542263.90692744591-0.04696916182890.729380000239-0.388223509799-1.199454725480.0573991640140.297785698647-0.0461603187211-0.0659292721084-0.2807946327510.9211501295180.0416602943393-0.03679352706150.8493689990560.02731258765660.450315010359-25.23709858334.64533809758.63104137305
123.835646755020.1364224106553.070878586282.02311395176-0.2883572697517.23729284773-0.118569645966-0.188636098272-0.05276242898590.134582185771-0.03400666195210.00623870384292-0.02115080233630.06736735744860.2663825424870.7626410216980.0646592101810.1065530864140.618758892508-0.08710329060410.424568962009-25.874412169917.545345311532.6744693753
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 320 )EA316 - 320
44chain 'E' and (resid 321 through 321 )EA321
55chain 'F' and (resid 401 through 405 )FB401 - 405
66chain 'F' and (resid 406 through 415 )FB406 - 415
77chain 'F' and (resid 416 through 420 )FB416 - 420
88chain 'F' and (resid 421 through 421 )FB421
99chain 'A' and (resid 94 through 180 )AC94 - 1801 - 87
1010chain 'A' and (resid 201 through 276 )AC201 - 27688 - 163
1111chain 'B' and (resid 94 through 180 )BD94 - 1801 - 87
1212chain 'B' and (resid 201 through 276 )BD201 - 27688 - 163

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