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- PDB-7vox: The crystal structure of human forkhead box protein A in complex ... -

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Basic information

Entry
Database: PDB / ID: 7vox
TitleThe crystal structure of human forkhead box protein A in complex with DNA 2
Components
  • DNA (5'-D(P*AP*AP*AP*TP*AP*TP*TP*TP*AP*TP*TP*AP*TP*CP*GP*A)-3')
  • DNA (5'-D(P*TP*CP*GP*AP*TP*AP*AP*TP*AP*AP*AP*TP*AP*TP*TP*T)-3')
  • Hepatocyte nuclear factor 3-alpha
KeywordsTRANSCRIPTION/DNA / DNA-protein complex / transcription factor / TRANSCRIPTION / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


alveolar secondary septum development / respiratory basal cell differentiation / prostate gland stromal morphogenesis / positive regulation of dopaminergic neuron differentiation / mesenchymal-epithelial cell signaling involved in prostate gland development / anatomical structure formation involved in morphogenesis / positive regulation of cell-cell adhesion mediated by cadherin / epithelial cell maturation involved in prostate gland development / neuron fate specification / secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development ...alveolar secondary septum development / respiratory basal cell differentiation / prostate gland stromal morphogenesis / positive regulation of dopaminergic neuron differentiation / mesenchymal-epithelial cell signaling involved in prostate gland development / anatomical structure formation involved in morphogenesis / positive regulation of cell-cell adhesion mediated by cadherin / epithelial cell maturation involved in prostate gland development / neuron fate specification / secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development / lung epithelial cell differentiation / dorsal/ventral neural tube patterning / prostate gland epithelium morphogenesis / dopaminergic neuron differentiation / Formation of axial mesoderm / positive regulation of smoothened signaling pathway / hormone metabolic process / positive regulation of intracellular estrogen receptor signaling pathway / negative regulation of epithelial to mesenchymal transition / smoothened signaling pathway / epithelial tube branching involved in lung morphogenesis / microvillus / anatomical structure morphogenesis / Notch signaling pathway / positive regulation of mitotic cell cycle / positive regulation of DNA-binding transcription factor activity / fibrillar center / positive regulation of miRNA transcription / sequence-specific double-stranded DNA binding / response to estradiol / glucose homeostasis / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / cell differentiation / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin remodeling / positive regulation of apoptotic process / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus
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 DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Hepatocyte nuclear factor 3-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsChoi, Y. / Yoon, H.J. / Lee, H.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2018R1A2B2008142 Korea, Republic Of
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: FOXL2 and FOXA1 cooperatively assemble on the TP53 promoter in alternative dimer configurations.
Authors: Choi, Y. / Luo, Y. / Lee, S. / Jin, H. / Yoon, H.J. / Hahn, Y. / Bae, J. / Lee, H.H.
History
DepositionOct 15, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 17, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 7, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: DNA (5'-D(P*TP*CP*GP*AP*TP*AP*AP*TP*AP*AP*AP*TP*AP*TP*TP*T)-3')
E: DNA (5'-D(P*AP*AP*AP*TP*AP*TP*TP*TP*AP*TP*TP*AP*TP*CP*GP*A)-3')
F: DNA (5'-D(P*TP*CP*GP*AP*TP*AP*AP*TP*AP*AP*AP*TP*AP*TP*TP*T)-3')
G: DNA (5'-D(P*AP*AP*AP*TP*AP*TP*TP*TP*AP*TP*TP*AP*TP*CP*GP*A)-3')
A: Hepatocyte nuclear factor 3-alpha
B: Hepatocyte nuclear factor 3-alpha
C: Hepatocyte nuclear factor 3-alpha
H: Hepatocyte nuclear factor 3-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,32810
Polymers67,2798
Non-polymers492
Water8,035446
1
D: DNA (5'-D(P*TP*CP*GP*AP*TP*AP*AP*TP*AP*AP*AP*TP*AP*TP*TP*T)-3')
E: DNA (5'-D(P*AP*AP*AP*TP*AP*TP*TP*TP*AP*TP*TP*AP*TP*CP*GP*A)-3')
A: Hepatocyte nuclear factor 3-alpha
C: Hepatocyte nuclear factor 3-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6645
Polymers33,6404
Non-polymers241
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-45 kcal/mol
Surface area14270 Å2
MethodPISA
2
F: DNA (5'-D(P*TP*CP*GP*AP*TP*AP*AP*TP*AP*AP*AP*TP*AP*TP*TP*T)-3')
G: DNA (5'-D(P*AP*AP*AP*TP*AP*TP*TP*TP*AP*TP*TP*AP*TP*CP*GP*A)-3')
B: Hepatocyte nuclear factor 3-alpha
H: Hepatocyte nuclear factor 3-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6645
Polymers33,6404
Non-polymers241
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-41 kcal/mol
Surface area14230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.547, 144.291, 75.034
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11B-448-

HOH

21C-331-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 169 through 188 or resid 191...
21(chain B and (resid 169 through 188 or resid 191...
31(chain C and (resid 169 through 188 or resid 191...
41(chain H and (resid 169 through 188 or resid 191...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALASERSER(chain A and (resid 169 through 188 or resid 191...AE169 - 1887 - 26
12LEULEUGLNGLN(chain A and (resid 169 through 188 or resid 191...AE191 - 21229 - 50
13TRPTRPPROPRO(chain A and (resid 169 through 188 or resid 191...AE214 - 23552 - 73
14LYSLYSGLYGLY(chain A and (resid 169 through 188 or resid 191...AE237 - 23975 - 77
15GLYGLYASPASP(chain A and (resid 169 through 188 or resid 191...AE241 - 24979 - 87
21ALAALASERSER(chain B and (resid 169 through 188 or resid 191...BF169 - 1887 - 26
22LEULEUGLNGLN(chain B and (resid 169 through 188 or resid 191...BF191 - 21229 - 50
23TRPTRPPROPRO(chain B and (resid 169 through 188 or resid 191...BF214 - 23552 - 73
24LYSLYSGLYGLY(chain B and (resid 169 through 188 or resid 191...BF237 - 23975 - 77
25GLYGLYASPASP(chain B and (resid 169 through 188 or resid 191...BF241 - 24979 - 87
31ALAALASERSER(chain C and (resid 169 through 188 or resid 191...CG169 - 1887 - 26
32LEULEUGLNGLN(chain C and (resid 169 through 188 or resid 191...CG191 - 21229 - 50
33TRPTRPPROPRO(chain C and (resid 169 through 188 or resid 191...CG214 - 23552 - 73
34LYSLYSGLYGLY(chain C and (resid 169 through 188 or resid 191...CG237 - 23975 - 77
35GLYGLYASPASP(chain C and (resid 169 through 188 or resid 191...CG241 - 24979 - 87
41ALAALASERSER(chain H and (resid 169 through 188 or resid 191...HH169 - 1887 - 26
42LEULEUGLNGLN(chain H and (resid 169 through 188 or resid 191...HH191 - 21229 - 50
43TRPTRPPROPRO(chain H and (resid 169 through 188 or resid 191...HH214 - 23552 - 73
44LYSLYSGLYGLY(chain H and (resid 169 through 188 or resid 191...HH237 - 23975 - 77
45GLYGLYASPASP(chain H and (resid 169 through 188 or resid 191...HH241 - 24979 - 87

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Components

#1: DNA chain DNA (5'-D(P*TP*CP*GP*AP*TP*AP*AP*TP*AP*AP*AP*TP*AP*TP*TP*T)-3')


Mass: 4895.227 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: DNA chain DNA (5'-D(P*AP*AP*AP*TP*AP*TP*TP*TP*AP*TP*TP*AP*TP*CP*GP*A)-3')


Mass: 4895.227 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Protein
Hepatocyte nuclear factor 3-alpha / HNF-3-alpha / HNF-3A / Forkhead box protein A1 / Transcription factor 3A / TCF-3A


Mass: 11924.612 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FOXA1, HNF3A, TCF3A / Production host: Escherichia coli (E. coli) / References: UniProt: P55317
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 446 / Source method: isolated from a natural source / Formula: H2O
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: 2.79 Å3/Da / Density % sol: 55.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES pH 6.0, 6% Tacsimate pH 6.0, and 20% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 44236 / % possible obs: 100 % / Redundancy: 9.2 % / Biso Wilson estimate: 25.26 Å2 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.037 / Rrim(I) all: 0.113 / Χ2: 1.001 / Net I/σ(I): 6.3 / Num. measured all: 406203
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.149.10.61621790.9220.2140.6530.599100
2.14-2.189.30.54321970.9270.1870.5750.582100
2.18-2.229.40.45821690.9470.1570.4840.588100
2.22-2.268.90.68621880.9330.2430.7291.622100
2.26-2.319.40.3821910.9560.130.4020.622100
2.31-2.379.40.3521910.9510.120.370.61100
2.37-2.429.30.27321820.9760.0940.2890.635100
2.42-2.499.20.2422030.9790.0840.2550.625100
2.49-2.568.90.20121890.9810.0710.2130.642100
2.56-2.658.20.17721720.9820.0650.1890.641100
2.65-2.748.60.21422080.9840.0760.2280.96100
2.74-2.859.20.13722160.9820.0480.1450.78100
2.85-2.989.80.12321960.9920.0410.130.823100
2.98-3.149.70.10122210.9940.0350.1070.979100
3.14-3.339.80.08622060.9950.0310.0921.16100
3.33-3.599.50.08822230.9950.0310.0931.506100
3.59-3.959.30.0922340.9970.0310.0951.824100
3.95-4.5290.06822410.9970.0240.0721.53100
4.52-5.78.10.0722580.9950.0260.0751.59100
5.7-509.50.06223720.9970.0210.0661.63999.7

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CBY

7cby


Resolution: 2.1→43.984 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 21.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2118 1914 4.65 %
Rwork0.1858 39234 -
obs0.1871 41148 93.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 154.17 Å2 / Biso mean: 34.462 Å2 / Biso min: 7.41 Å2
Refinement stepCycle: final / Resolution: 2.1→43.984 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2804 1312 2 446 4564
Biso mean--9.4 37.86 -
Num. residues----402
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A864X-RAY DIFFRACTION8.801TORSIONAL
12B864X-RAY DIFFRACTION8.801TORSIONAL
13C864X-RAY DIFFRACTION8.801TORSIONAL
14H864X-RAY DIFFRACTION8.801TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1003-2.15280.2894890.2324208770
2.1528-2.2110.25611100.2163223875
2.211-2.27610.24061370.2139239480
2.2761-2.34950.26561320.2186256587
2.3495-2.43350.24091330.209274292
2.4335-2.53090.27011090.2164295398
2.5309-2.64610.23341270.2152297899
2.6461-2.78560.27441460.21673016100
2.7856-2.96010.2541320.21753007100
2.9601-3.18850.23151370.1963008100
3.1885-3.50930.20681760.16672986100
3.5093-4.01680.1811420.15743051100
4.0168-5.05960.15951880.1483026100
5.0596-43.9840.18151560.17563183100
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)
10.10330.010.01720.01420.03550.07120.0464-0.09370.2165-0.0684-0.0088-0.0188-0.033-0.1094-0.00320.1521-0.19220.08520.2101-0.04390.2879-28.526212.214619.6267
20.02-0.0184-0.00860.02220.00410.01420.0238-0.08330.1820.0503-0.03230.0233-0.0148-0.0248-0.07980.0972-0.1840.06220.1821-0.03220.2192-27.41210.102620.283
30.01070.0205-0.00580.05470.02260.02250.0038-0.02880.0508-0.0527-0.0005-0.08610.0752-0.0089-0.04960.1191-0.16740.05570.0843-0.05570.184712.511742.135918.0645
40.02830.0333-0.00650.09660.04340.0319-0.01960.0053-0.069-0.15450.0369-0.02410.0397-0.0031-0.00770.203-0.13280.02960.1241-0.06990.171410.357243.127117.4567
50.07020.00310.0130.0697-0.01960.0086-0.0308-0.0312-0.046-0.06440.0397-0.00180.0662-0.070.03120.1443-0.070.02490.16240.00470.0894-18.68471.032514.1575
60.41890.11240.04350.19330.18020.3242-0.13740.03080.4074-0.04660.00660.1551-0.08040.0453-0.17870.078-0.0505-0.02190.1626-0.00560.19918.544771.493921.427
70.0724-0.0003-0.00260.142-0.05720.08560.0503-0.0264-0.02870.0591-0.055-0.11360.00310.0135-0.01850.1471-0.0512-0.01350.0670.00820.08910.309119.262616.1763
80.04540.02220.02960.4308-0.04710.03210.087-0.15640.0861-0.0476-0.05350.22920.0098-0.13160.19090.1448-0.05320.02520.1389-0.06570.11050.990351.61623.4745
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'D' and resid 1 through 16)D1 - 16
2X-RAY DIFFRACTION2(chain 'E' and resid 1 through 16)E1 - 16
3X-RAY DIFFRACTION3(chain 'F' and resid 1 through 16)F1 - 16
4X-RAY DIFFRACTION4(chain 'G' and resid 1 through 16)G1 - 16
5X-RAY DIFFRACTION5(chain 'A' and resid 168 through 252)A168 - 252
6X-RAY DIFFRACTION6(chain 'B' and resid 168 through 250)B168 - 250
7X-RAY DIFFRACTION7(chain 'C' and resid 168 through 252)C168 - 252
8X-RAY DIFFRACTION8(chain 'H' and resid 168 through 252)H168 - 252

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