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- PDB-8pi8: DNA binding domain of HNF-1A bound to P2-HNF4A promoter DNA -

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Basic information

Entry
Database: PDB / ID: 8pi8
TitleDNA binding domain of HNF-1A bound to P2-HNF4A promoter DNA
Components
  • Chains: E
  • Chains: F
  • Hepatocyte nuclear factor 1-alpha
KeywordsDNA BINDING PROTEIN / Transcription factor / gene transcription / HNF-1A / HNF4A
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: 2.3 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)58,8206
Polymers58,6364
Non-polymers1842
Water543
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)46.703, 55.038, 202.071
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: 6403.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: NM_175914.5 / Source: (synth.) Homo sapiens (human)
#2: DNA chain Chains: F


Mass: 6479.236 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: NM_175914.5 / 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.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
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: 2.21 Å3/Da / Density % sol: 44.46 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MMT, pH 4.0, 25% w/v PEG 1500

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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: 2.3→48.33 Å / Num. obs: 24010 / % possible obs: 99.5 % / Redundancy: 7.4 % / Biso Wilson estimate: 58.67 Å2 / CC1/2: 0.994 / Rrim(I) all: 0.203 / Net I/σ(I): 6.41
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 7.8 % / Mean I/σ(I) obs: 0.6 / Num. unique obs: 1724 / CC1/2: 0.206 / % possible all: 98.9

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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: 2.3→48.33 Å / SU ML: 0.4857 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.6896
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2607 2187 4.99 %
Rwork0.2138 41622 -
obs0.2161 23743 98.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.5 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2781 855 12 3 3651
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00323803
X-RAY DIFFRACTIONf_angle_d0.53695308
X-RAY DIFFRACTIONf_chiral_restr0.0335568
X-RAY DIFFRACTIONf_plane_restr0.004548
X-RAY DIFFRACTIONf_dihedral_angle_d23.436789
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.350.4114990.39882116X-RAY DIFFRACTION78.94
2.35-2.410.39421400.39072586X-RAY DIFFRACTION97.81
2.41-2.470.41411380.36722657X-RAY DIFFRACTION99.43
2.47-2.530.38621340.35722588X-RAY DIFFRACTION99.56
2.53-2.610.39011430.33992669X-RAY DIFFRACTION99.89
2.61-2.690.35411330.31052643X-RAY DIFFRACTION100
2.69-2.790.36111450.33232673X-RAY DIFFRACTION100
2.79-2.90.35411410.29812678X-RAY DIFFRACTION100
2.9-3.030.34391390.28852607X-RAY DIFFRACTION99.78
3.03-3.190.3521380.26072645X-RAY DIFFRACTION99.78
3.19-3.390.21631430.20742620X-RAY DIFFRACTION98.96
3.39-3.650.24441360.19822552X-RAY DIFFRACTION96.07
3.65-4.020.24371390.1782663X-RAY DIFFRACTION99.54
4.02-4.60.19741380.1582650X-RAY DIFFRACTION99.86
4.6-5.790.24331390.17952620X-RAY DIFFRACTION99.93
5.79-48.330.20051420.15662655X-RAY DIFFRACTION99.68
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)
11.76940301112-0.5879988459440.5759350394030.2461953765320.1579373369954.14661517483-0.0598150333396-0.2484629041180.2375489495070.150020841156-0.01251162631410.05093093952820.359493151344-0.6447716051910.02992578401510.604323922899-0.07221443482220.01423605198080.6289106933780.06906117821390.586790374563-28.558813478-12.4032648919-18.428960616
23.17595428455-0.5342032525080.739137121721.771525145410.007243866143242.82423670213-0.239186582680.06442826999710.007734044453030.1938362140670.1888939701150.23306324640.0836943137524-0.1307052613150.07513625402390.466430733749-0.0930321085253-0.006144804032720.3946899055950.0791762780340.529343705232-21.6849874147-13.9019979-21.3731936917
33.38272728837-0.880865068351.228071467822.19454053680.6397860347162.90836632646-0.0504715242491-1.293559266590.1089632041690.952528731422-0.300365839428-0.3415138335750.2057662175451.154584117980.08996774189150.7718806313420.00864558989623-0.09765713286430.942339378073-0.01423911292190.60100384709913.61386556274.117338734594.9424379428
41.638049816440.7392158340690.8594206825442.99388558882-0.6369084725732.16027646412-0.0967975921857-0.267360712124-0.1035393678090.2061116463560.230115324910.120530587653-0.159468628465-0.141989657326-0.09059601073230.4101898106260.0437828372205-0.008034399862680.5038364672990.02266937122870.5008962635611.040061596793.13491430493-9.54905203567
52.543340498941.10623838987-0.2210710249545.70837631933-0.876861297911.74708577586-0.121272877155-0.0339972132561-0.1080789415630.387904441950.124852421569-0.605960799073-0.08317310036550.2248582766-0.03384690977180.5002879402160.0217643585909-0.05423881182090.593166598207-0.005233955844740.4966433749111.42909776115.76733247255-5.76621629834
61.979697252241.618984913630.3623174437992.59008806927-0.6905332677552.40261814741-0.1562973953050.5043443637520.433146626475-0.006602295133490.05075194285880.370776882049-0.186536413927-0.211552812553-0.01029921486970.629248154536-0.119161443618-0.001610609204440.6148093770390.03351055845470.5637724398511.6502818240222.2894744368-25.9679268049
72.231374354170.0115247955771-0.3066743895921.70544432395-1.478249123686.71608742708-0.07051310181650.1594474440770.4078970376580.2093420986420.136738948452-0.0544075146362-0.4272846277290.1295035118310.0341647459390.72813320447-0.0612780002666-0.008426534724530.575427612836-0.006854878709240.7242189932857.6840900513427.9368557977-23.4609903378
80.4475614246-0.0143092024240.1534732831411.429635829151.8702025413.73634732386-0.09038555980380.135658792069-0.0766828618675-0.383733349360.0575853388434-0.2709934932810.005125015143510.4026691566590.079617066120.562798793464-0.1149404555460.003358371854830.528485691383-0.004526984858760.49063255598512.850047862621.2269105361-16.8126013583
90.6105515121510.6397097663741.171870937232.65072824837-0.2304190806023.294811204030.2791793532430.2497603968160.484888071243-0.415721538345-0.182795370160.5180761082320.390630107098-0.1297937469380.02640122995010.685900565477-0.142536672950.03101049190610.5692500780790.05889059101350.6739474436890.51215704757320.2912311643-33.7569763069
106.06735577903-0.0843110285575-3.546127661043.05857843314-2.002293361033.942854393460.3586533077030.4436140247391.37223415248-0.2207714640670.4324475384590.599136691705-0.563166401345-1.04926802566-0.7301725058730.937499554694-0.1042501140610.1680153645360.7666283703180.08747456523250.70702771679-12.8089856626-14.9122585497-4.8046487097
110.735736897740.555679637545-1.001985372081.5283132157-0.2481536790031.803312096640.267933349807-0.06586367329430.0751642625309-0.197606556813-0.2284872597060.1279078433730.1717734435090.477913885989-0.01509277404410.5200078354-0.06021089395180.006960162997290.5134930592510.05535544993850.509032970903-0.3048925369382.98247895302-30.3022648235
125.138702546321.799541288730.2756497654942.1196767155-0.6838964608980.8226582192180.7140222645440.3230199178310.0736109930034-0.7397616145550.1976973752480.462582299232-0.21495969283-0.30577887711-0.592396074130.875254391514-0.191854275154-0.1704673175480.6372320949430.09125894195060.9586103806941.879251534517.8064790754-53.7055189947
131.05813445033-0.0624371749154-0.78729915073.20642688866-1.55606554941.398149552240.230738739719-0.0762994549690.234681569170.639524860284-0.1408679770.317139753757-0.3381006264720.403164150603-0.04646468512360.697601895222-0.070229963608-0.00123324390810.7173628688380.07103449227720.6828410645020.60890786378818.598010505-44.9351684289
140.5721846493890.482120975545-0.630000881681.09457856788-0.2658588097531.097357508130.0525449904552-0.0718429072952-0.398268045339-0.145033327189-0.1757324791960.04957361043910.1945029103390.1989813160760.05817367851110.56681589274-0.04348816469-0.0002037395547130.4402214001510.111172351950.529354640881-2.498977282990.74896726487-26.6862584042
150.9174099946640.0799534763789-0.9391636909772.29760614785-2.793321702694.290426835921.13314893426-0.774240156592-0.849336241920.387170093512-0.02749991244061.437684137570.767033779880.759814396168-0.06817397864620.876293897187-0.071703105133-0.0113171437890.7543108660660.1671838123970.628835829817-8.29180674964-19.5781153199-8.47856735937
161.344860244570.6171496761890.1451640585251.653839023430.8463661124080.455904660763-0.0680775060992-0.927695714821-0.150802088017-0.08143437026020.494484926217-1.40139899388-0.2058976086640.755040304387-0.1166766430530.770623255436-0.0274503123690.01437499801170.807529392115-0.01547413671320.949183047511-19.7707155547-25.513356929-52.7258871495
172.84729615239-0.6409630702960.01782692364586.262405297921.505801644413.15871148946-0.4458569893210.835114323104-0.249445383819-0.294374723370.7259037281660.5458650405520.425081358892-0.270297233032-0.1348256509480.744629048579-0.09727983101760.04000647690840.7572506954620.03106250465520.568705930487-16.8310656059-5.85103514966-56.8286611447
181.710174614240.947096961592-0.5238304513161.59589331861-0.3334452321071.676884753660.0859793401367-0.3349305782980.00108810372414-0.230866764826-0.06590360480610.1037548059040.17956160094-0.09052948121480.008700661220220.3998550576650.00310104097249-0.01875616036370.4651332923710.02203073123670.339632988281-14.3855263914-2.44327690129-39.8015106146
192.53686981745-0.242017730701-0.4077431230392.144778844090.3416124568492.254869833780.282580183851-0.339016151436-0.07084564114640.405180634227-0.0380638916264-0.492797989014-0.7482069675550.512155952573-0.1728116194490.572257473729-0.06813715067130.05237013303650.4234572654590.007495786399850.583314784435-7.817351586184.79317048687-39.1451956101
203.982532181254.12033656288-1.576605400875.17249010881-1.375348115351.91924918203-0.01812007403560.728678184848-0.257485275-0.1490873976650.372061520833-0.0947111670986-0.131608945253-0.462110111371-0.2123019021880.4984679725870.0179088225202-0.03486958019280.59668403636-0.0143205863640.478146725168-15.0433111378-8.93405094595-46.0656093049
211.902859346511.130701151730.6332046262312.432205864211.89495403853.893006012260.19321668332-0.0671309306675-0.6518540120630.1299741238060.02697999679780.03133747307980.156421177255-0.305185086145-0.1619928182120.6525181420590.0458817671202-0.0465982643640.5310986858940.03886388578290.64625246463-15.9640115954-15.5861834648-30.5640428221
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 208 through 243 )AC208 - 243106 - 141
22chain 'A' and (resid 244 through 276 )AC244 - 276142 - 174
33chain 'B' and (resid 92 through 109 )BE92 - 1091 - 18
44chain 'B' and (resid 110 through 155 )BE110 - 15519 - 64
55chain 'B' and (resid 156 through 178 )BE156 - 17865 - 87
66chain 'B' and (resid 179 through 225 )BE179 - 22588 - 113
77chain 'B' and (resid 226 through 243 )BE226 - 243114 - 131
88chain 'B' and (resid 244 through 260 )BE244 - 260132 - 148
99chain 'B' and (resid 261 through 276 )BE261 - 276149 - 164
1010chain 'E' and (resid 301 through 305 )EA301 - 305
1111chain 'E' and (resid 306 through 320 )EA306 - 320
1212chain 'E' and (resid 321 through 321 )EA321
1313chain 'F' and (resid 401 through 405 )FB401 - 405
1414chain 'F' and (resid 406 through 415 )FB406 - 415
1515chain 'F' and (resid 416 through 421 )FB416 - 421
1616chain 'A' and (resid 85 through 93 )AC85 - 931 - 9
1717chain 'A' and (resid 94 through 109 )AC94 - 10910 - 25
1818chain 'A' and (resid 110 through 140 )AC110 - 14026 - 56
1919chain 'A' and (resid 141 through 155 )AC141 - 15557 - 71
2020chain 'A' and (resid 156 through 178 )AC156 - 17872 - 94
2121chain 'A' and (resid 179 through 207 )AC179 - 20795 - 105

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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