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- PDB-8pi7: DNA binding domain of HNF-1A bound to P2-HNF4A promoter DNA varia... -

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Basic information

Entry
Database: PDB / ID: 8pi7
TitleDNA binding domain of HNF-1A bound to P2-HNF4A promoter DNA variant (P2 -169C>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 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: 3.2 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)58,7066
Polymers58,6354
Non-polymers712
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)49.456, 52.506, 210.278
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: 6418.167 Da / Num. of mol.: 1 / Mutation: NM_175914.5 c.-169C>T (g.42984276) / Source method: obtained synthetically / Details: NM_175914.5 c.-169C>T (g.42984276) / Source: (synth.) Homo sapiens (human)
#2: DNA chain Chains: F


Mass: 6463.237 Da / Num. of mol.: 1 / Mutation: NM_175914.5 c.-169C>T (g.42984276) / Source method: obtained synthetically / Details: NM_175914.5 c.-169C>T (g.42984276) / 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
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: 2.33 Å3/Da / Density % sol: 47.17 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / Details: 10% w/v PEG 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 3.2→48.14 Å / Num. obs: 9655 / % possible obs: 99.6 % / Redundancy: 7.2 % / Biso Wilson estimate: 112.2 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.16 / Net I/σ(I): 10.86
Reflection shellResolution: 3.2→3.29 Å / Redundancy: 7.6 % / Mean I/σ(I) obs: 1.34 / Num. unique obs: 729 / CC1/2: 0.572 / % possible all: 99.7

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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: 3.2→48.14 Å / SU ML: 0.5664 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.09
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2804 1756 10.08 %
Rwork0.2206 15665 -
obs0.2267 9605 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 132.58 Å2
Refinement stepCycle: LAST / Resolution: 3.2→48.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2750 855 2 0 3607
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00233763
X-RAY DIFFRACTIONf_angle_d0.42475260
X-RAY DIFFRACTIONf_chiral_restr0.0284562
X-RAY DIFFRACTIONf_plane_restr0.0032545
X-RAY DIFFRACTIONf_dihedral_angle_d23.7265780
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.290.38811400.3631245X-RAY DIFFRACTION99.21
3.29-3.380.35261290.30471159X-RAY DIFFRACTION99.84
3.38-3.490.36011280.31431251X-RAY DIFFRACTION99.93
3.49-3.620.3281430.28771195X-RAY DIFFRACTION99.78
3.62-3.760.38251280.30231200X-RAY DIFFRACTION99.85
3.76-3.930.36441270.24051190X-RAY DIFFRACTION100
3.93-4.140.26411360.22741249X-RAY DIFFRACTION100
4.14-4.40.31311350.20931174X-RAY DIFFRACTION99.85
4.4-4.740.30651360.21571195X-RAY DIFFRACTION99.4
4.74-5.210.2791310.21521225X-RAY DIFFRACTION100
5.21-5.970.28031430.22131201X-RAY DIFFRACTION99.78
5.97-7.50.26411300.21131213X-RAY DIFFRACTION99.7
7.53-48.140.20811500.15991168X-RAY DIFFRACTION98.51
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)
13.62242278867-4.436610456-1.646122979995.398792870412.129269185040.804686923009-1.2613783667-1.6923538433.055623817860.977263457760.904795650872-1.49676093969-1.383910005580.7512725109750.1153317861892.00821531164-0.01580636937190.1549284569931.19992293347-0.0651480796591.5325935244-5.36977349062-14.69189788695.13950713254
23.519440160051.397374339871.538902636912.908219691533.297041613713.662918361141.03939490469-1.02410224801-0.917945030917-1.15744455003-0.306215082761-0.115998991303-0.384202984731-1.01242068381-0.3771084564421.554044374220.0140072252352-0.2885066964621.12861586399-0.06380422326371.14608676257-16.5424079354-11.972499489318.9249986111
36.97424418831-0.887728105824-0.6660245433534.055476316451.619754963272.610078374440.714936023194-0.1291979408950.636948543809-0.81279266253-0.8587428311381.80414903479-0.169580914078-1.50978013588-0.1437420484070.9368193757670.09970382658830.01536291953061.17727088444-0.1027855163951.46357995332-17.67634898762.1183881915131.4182976567
44.36712828225-0.320630683735-0.2441293359613.663462396833.267990538252.918946543441.38102562954-0.472056666669-0.2760597227951.180401884781.709316575460.445550566438-0.215254066877-3.89258460153-3.037635169541.17584618310.151639482287-0.02077172882052.011269301140.1662573562541.2378833474-31.10711916395.6238506469944.3024355241
51.218696787651.105159415320.1917142502411.63648512793-0.4353822773240.609585168867-1.655278791930.563973977262-1.31009822985-0.82247267101-1.243489035130.6497379243981.566211353830.03303811001971.833985773361.95591088791-0.06065673922570.0829728900341.46012322288-0.1982282651382.38700099904-29.801458288710.224499218357.2730299962
61.32953946568-2.13121739553-0.1944480147883.84479088388-2.175172235554.65441658492-0.00700332815163-2.27922467260.8229480179020.08261515073191.0217747886-0.918564018637-0.871054389705-0.632166726299-1.099128468981.109233815880.0791143011580.1233219805052.1882609886-0.2665597496931.30987560628-25.4292475024.8073416199341.2310056154
73.58537882486-0.917042792228-0.1421625482662.520850430282.759958458073.735762988070.4719878930350.5324329722390.03172021876460.458727955965-0.201253965131-1.329979668291.46887827266-0.96240310854-0.4656693431521.616665598420.242135145228-0.006627232792071.00352370927-0.07257877756561.20587716984-11.5743146135-12.369654755414.0207350951
84.23656161334-0.1953301161-0.9422144210790.541198355327-0.05993429728531.20221177478-0.379078994226-1.3603411928-1.177991506230.6457443441920.1821248129051.230127990090.6683736986-1.301591386390.3606849105020.969877055737-0.128173530419-0.01970203998172.277979167780.377034532831.47655597422-6.54938634817-16.670261586356.7269893789
97.94468273297-0.2817634476221.065953343684.67003061442-0.6615178747675.598373903210.259066116243-2.04268178514-0.9807319556530.04402034391720.02762785355380.163297965105-0.182198166534-0.808338345311-0.1423646899580.6983361518610.07984701453970.04514411110031.411282888410.318237748950.763294277569-9.23890186435-8.7758287108843.3028430104
106.77092259950.299001017907-0.1014957546534.124766355521.166556655675.056187994670.5300351839280.0969585529655-0.0898009584827-2.916455190650.3107700937610.8603799358190.3138105100850.775936724119-0.9880080508911.432809468440.37357100826-0.09244590513921.125908848860.003592369294721.25631272958-2.32035111272-17.718717585729.8803173683
113.973184277692.73502941255-2.788560414922.28201099121-0.197587542944.28050678802-0.189152217566-0.237773004434-0.355476059415-0.4460521588820.206629893857-0.9455579955230.9103193080421.5722467541-0.1038900081671.014506950680.3265317710350.0344365286230.993521673451-0.1601764999431.141778915785.26758983244-13.572475645920.82454044
120.9888781698292.41881779425-0.8508641453047.383085129670.4769402540944.2718628990.5396616183641.49121514236-0.387129738401-2.96280441255-0.2150466906220.402460954596-0.970696519659-0.546891309366-0.3352342901311.89840074820.0809990025063-0.4660892882051.002308696180.1086682244661.34686983572-34.05586825436.24988287768-2.64245089907
139.49746604788-0.5703115831891.542252445541.961960666543.182732477155.79111347682-0.4494948282640.9605440768612.269334924330.780385068283-0.010805640347-0.370206555173-0.7127177168761.211917727340.2463309425891.351778699970.0421021949298-0.0786778598480.637417790740.1605362496940.91321001756-19.90796890298.898884049237.65343496491
143.554199878130.2799364940220.5521934842413.72726877331-0.1757673825613.98206780461-0.235889364058-0.153923166255-0.368928270401-0.5073034300480.1286998920610.861527588521-0.0437687910793-0.061741262377-0.05749274645691.12249664840.131689361949-0.1969625605680.9117006826180.02355757742610.814047833723-26.28244981941.7822894596910.4188662586
154.96920310318-2.33489999073-0.7835155495314.91926628791-1.944508072424.449026068880.1336684254930.536790108840.957016871002-0.279542141154-0.0131735989556-0.43204165520.01892139701240.4709413854350.07951215838990.964688968795-0.0760681155217-0.2238562025161.238715471170.002945389591721.14034130147-31.61882909910.052588161823.7700666902
164.469254179850.4567790196681.506917853853.924190795560.9866551293953.77782737574-0.497581810996-1.168045176820.892352431434-0.338433422159-0.217737551335-0.110317475113-1.05417196024-0.1615202103990.6336643100251.108821484270.26407643430.04975956353181.05303969244-0.1808836481581.20455333586-26.836185890220.312876675931.0683159844
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 310 )EA306 - 310
33chain 'E' and (resid 311 through 315 )EA311 - 315
44chain 'E' and (resid 316 through 320 )EA316 - 320
55chain 'E' and (resid 321 through 321 )EA321
66chain 'F' and (resid 401 through 410 )FB401 - 410
77chain 'F' and (resid 411 through 421 )FB411 - 421
88chain 'A' and (resid 90 through 109 )AC90 - 1091 - 20
99chain 'A' and (resid 110 through 178 )AC110 - 17821 - 89
1010chain 'A' and (resid 179 through 207 )AC179 - 20790 - 98
1111chain 'A' and (resid 208 through 277 )AC208 - 27799 - 168
1212chain 'B' and (resid 90 through 109 )BD90 - 1091 - 20
1313chain 'B' and (resid 110 through 126 )BD110 - 12621 - 37
1414chain 'B' and (resid 127 through 178 )BD127 - 17838 - 89
1515chain 'B' and (resid 179 through 207 )BD179 - 20790 - 98
1616chain 'B' and (resid 208 through 276 )BD208 - 27699 - 167

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