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- PDB-7yze: Crystal structure of the human FoxA2 bound to the TGTTTACT site (... -

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Basic information

Entry
Database: PDB / ID: 7yze
TitleCrystal structure of the human FoxA2 bound to the TGTTTACT site (forkhead motif GTAAACA)
Components
  • DNA (5'-D(*AP*GP*AP*TP*TP*GP*TP*TP*TP*AP*CP*TP*GP*AP*GP*A)-3')
  • DNA (5'-D(*TP*CP*TP*CP*AP*GP*TP*AP*AP*AP*CP*AP*AP*TP*CP*T)-3')
  • Hepatocyte nuclear factor 3-beta
KeywordsDNA BINDING PROTEIN / transcription factor
Function / homology
Function and homology information


positive regulation of cell-cell adhesion mediated by cadherin / primitive streak formation / positive regulation of embryonic development / response to interleukin-6 / endocrine pancreas development / regulation of insulin secretion involved in cellular response to glucose stimulus / Formation of definitive endoderm / Formation of axial mesoderm / dopaminergic neuron differentiation / Developmental Lineage of Pancreatic Acinar Cells ...positive regulation of cell-cell adhesion mediated by cadherin / primitive streak formation / positive regulation of embryonic development / response to interleukin-6 / endocrine pancreas development / regulation of insulin secretion involved in cellular response to glucose stimulus / Formation of definitive endoderm / Formation of axial mesoderm / dopaminergic neuron differentiation / Developmental Lineage of Pancreatic Acinar Cells / positive regulation of gastrulation / cell fate specification / negative regulation of epithelial to mesenchymal transition / regulation of blood coagulation / Regulation of gene expression in beta cells / anatomical structure morphogenesis / adult locomotory behavior / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding / cell junction / transcription corepressor activity / chromatin organization / DNA-binding transcription activator activity, RNA polymerase II-specific / nucleic acid binding / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Forkhead box protein, C-terminal / HNF3 C-terminal domain / Fork-head N-terminal / Forkhead N-terminal region / : / Fork head domain conserved site1 / Fork head domain signature 1. / Fork head domain / Forkhead domain / Fork head domain profile. ...Forkhead box protein, C-terminal / HNF3 C-terminal domain / Fork-head N-terminal / Forkhead N-terminal region / : / Fork head domain conserved site1 / Fork head domain signature 1. / Fork head domain / Forkhead domain / Fork head domain profile. / FORKHEAD / Fork head domain conserved site 2 / Fork head domain signature 2. / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / DNA / DNA (> 10) / Hepatocyte nuclear factor 3-beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsPluta, R. / Macias, M.J.
Funding support Spain, European Union, 2items
OrganizationGrant numberCountry
Ministry of Economy and Competitiveness (MINECO)BFU2017-82675-P Spain
H2020 Marie Curie Actions of the European Commission754510European Union
CitationJournal: Nat Commun / Year: 2022
Title: Molecular basis for DNA recognition by the maternal pioneer transcription factor FoxH1.
Authors: Pluta, R. / Aragon, E. / Prescott, N.A. / Ruiz, L. / Mees, R.A. / Baginski, B. / Flood, J.R. / Martin-Malpartida, P. / Massague, J. / David, Y. / Macias, M.J.
History
DepositionFeb 19, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hepatocyte nuclear factor 3-beta
B: DNA (5'-D(*AP*GP*AP*TP*TP*GP*TP*TP*TP*AP*CP*TP*GP*AP*GP*A)-3')
C: DNA (5'-D(*TP*CP*TP*CP*AP*GP*TP*AP*AP*AP*CP*AP*AP*TP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5815
Polymers24,4463
Non-polymers1352
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-31 kcal/mol
Surface area10600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.035, 92.369, 118.795
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Hepatocyte nuclear factor 3-beta / HNF-3-beta / HNF-3B / Forkhead box protein A2 / Transcription factor 3B / TCF-3B


Mass: 14652.791 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FOXA2, HNF3B, TCF3B / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y261

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DNA chain , 2 types, 2 molecules BC

#2: DNA chain DNA (5'-D(*AP*GP*AP*TP*TP*GP*TP*TP*TP*AP*CP*TP*GP*AP*GP*A)-3')


Mass: 4952.239 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*TP*CP*TP*CP*AP*GP*TP*AP*AP*AP*CP*AP*AP*TP*CP*T)-3')


Mass: 4841.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 3 types, 30 molecules

#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.58 Å3/Da / Density % sol: 52.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% PEG 3350, 0.2 M ammonium sulfate, 0.1 M Bis-Tris pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.985→46.185 Å / Num. obs: 15071 / % possible obs: 93.9 % / Redundancy: 13.1 % / CC1/2: 0.999 / Rpim(I) all: 0.012 / Net I/σ(I): 26.3
Reflection shellResolution: 1.985→2.126 Å / Num. unique obs: 756 / CC1/2: 0.573 / Rpim(I) all: 0.584 / % possible all: 53.5

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Processing

Software
NameVersionClassification
PHENIX1.19_4080refinement
PDB_EXTRACT3.27data extraction
autoPROCdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5x07

5x07


Resolution: 1.99→46.18 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 35.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2151 730 4.85 %
Rwork0.2084 14328 -
obs0.2087 15058 84.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 135.32 Å2 / Biso mean: 67.4917 Å2 / Biso min: 43.43 Å2
Refinement stepCycle: final / Resolution: 1.99→46.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms737 650 6 28 1421
Biso mean--66.05 56.53 -
Num. residues----119
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.99-2.140.3434420.310187391526
2.14-2.350.3331550.33123148330393
2.35-2.690.32481720.294133783550100
2.69-3.390.2631950.24853365356099
3.39-46.180.16921660.170735643730100
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)
13.1814-2.30711.11951.662-0.6660.4111-0.17430.7412-0.31990.0835-0.06720.58320.16830.50630.23350.5382-0.04730.09450.7667-0.02930.584-4.2063-6.2601-32.4339
23.80440.31510.16818.18330.83185.57640.022-0.11870.2186-0.1548-0.14950.2442-0.24750.02630.14080.3740.09990.02810.49080.05660.3761-10.7496-0.8713-14.2911
32.54182.0178-1.18913.23552.71077.76640.07290.48060.349-0.78420.05582.1429-0.1561-0.6731-0.22550.46240.1351-0.12320.60610.05470.9433-25.9707-2.6448-15.8515
42.2151-1.3125-1.85084.34770.44944.3321-1.00971.5325-2.9531-0.2227-0.2492-0.41740.56380.5190.99611.03540.31040.05210.80.07831.1644-13.138-24.8765-20.1697
54.69463.2865-0.02887.3002-2.68137.67261.0507-0.3496-2.07281.3664-0.81461.31250.6880.2078-0.26361.04250.313-0.00230.85420.1571.4119-12.5405-25.9856-13.1228
68.16564.7319-2.11854.58671.0254.6623-0.52950.9771-0.7517-0.39060.16940.40320.0528-0.49690.40090.78110.1434-0.14780.6598-0.05480.7247-21.9098-12.7879-20.8234
78.88825.40562.5364.30434.33338.14810.6776-0.62330.96771.0878-1.92512.7408-0.5036-0.81210.99810.63520.09510.02520.7257-0.06731.1285-29.06323.0674-13.0126
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 152 through 163 )A152 - 163
2X-RAY DIFFRACTION2chain 'A' and (resid 164 through 238 )A164 - 238
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 10 )B1 - 10
4X-RAY DIFFRACTION4chain 'B' and (resid 11 through 16 )B11 - 16
5X-RAY DIFFRACTION5chain 'C' and (resid 1 through 5 )C1 - 5
6X-RAY DIFFRACTION6chain 'C' and (resid 6 through 10 )C6 - 10
7X-RAY DIFFRACTION7chain 'C' and (resid 11 through 16 )C11 - 16

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